Starting phenix.real_space_refine on Sun Aug 24 19:17:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gq6_34199/08_2025/8gq6_34199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gq6_34199/08_2025/8gq6_34199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gq6_34199/08_2025/8gq6_34199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gq6_34199/08_2025/8gq6_34199.map" model { file = "/net/cci-nas-00/data/ceres_data/8gq6_34199/08_2025/8gq6_34199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gq6_34199/08_2025/8gq6_34199.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 172 5.16 5 C 14114 2.51 5 N 3850 2.21 5 O 4151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22293 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4535 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 538} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 737 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "C" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5866 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 4546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4546 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 22, 'TRANS': 540} Chain breaks: 2 Chain: "F" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5866 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 737 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4732 SG CYS E 42 97.824 132.212 203.054 1.00135.97 S ATOM 4751 SG CYS E 45 97.332 135.997 203.064 1.00137.74 S ATOM 5046 SG CYS E 83 95.455 133.950 200.438 1.00118.07 S ATOM 4975 SG CYS E 75 99.032 119.450 200.491 1.00115.91 S ATOM 5142 SG CYS E 94 100.927 123.010 199.342 1.00129.19 S ATOM 4818 SG CYS E 53 91.949 137.158 200.696 1.00143.05 S ATOM 4841 SG CYS E 56 88.516 138.753 200.124 1.00146.03 S ATOM 4925 SG CYS E 68 88.779 135.715 202.407 1.00133.77 S ATOM 21747 SG CYS D 42 132.130 62.809 51.273 1.00135.97 S ATOM 21766 SG CYS D 45 135.799 61.647 52.145 1.00137.74 S ATOM 22061 SG CYS D 83 133.073 61.294 54.944 1.00118.07 S ATOM 21990 SG CYS D 75 123.469 71.768 55.932 1.00115.91 S ATOM 22157 SG CYS D 94 126.259 71.634 56.989 1.00129.19 S ATOM 21833 SG CYS D 53 134.193 56.390 55.193 1.00143.05 S ATOM 21856 SG CYS D 56 133.279 52.693 55.048 1.00146.03 S ATOM 21940 SG CYS D 68 130.649 55.324 54.136 1.00133.77 S Time building chain proxies: 5.89, per 1000 atoms: 0.26 Number of scatterers: 22293 At special positions: 0 Unit cell: (149.184, 154.512, 258.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 172 16.00 O 4151 8.00 N 3850 7.00 C 14114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D4001 " pdb="ZN ZN D4001 " - pdb=" ND1 HIS D 80 " pdb="ZN ZN D4001 " - pdb=" SG CYS D 45 " pdb="ZN ZN D4001 " - pdb=" SG CYS D 83 " pdb="ZN ZN D4001 " - pdb=" SG CYS D 42 " pdb=" ZN D4002 " pdb="ZN ZN D4002 " - pdb=" SG CYS D 94 " pdb="ZN ZN D4002 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D4002 " - pdb=" SG CYS D 75 " pdb=" ZN D4003 " pdb="ZN ZN D4003 " - pdb=" ND1 HIS D 82 " pdb="ZN ZN D4003 " - pdb=" SG CYS D 56 " pdb="ZN ZN D4003 " - pdb=" SG CYS D 68 " pdb="ZN ZN D4003 " - pdb=" SG CYS D 53 " pdb=" ZN E4001 " pdb="ZN ZN E4001 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E4001 " - pdb=" SG CYS E 45 " pdb="ZN ZN E4001 " - pdb=" SG CYS E 83 " pdb="ZN ZN E4001 " - pdb=" SG CYS E 42 " pdb=" ZN E4002 " pdb="ZN ZN E4002 " - pdb=" SG CYS E 75 " pdb="ZN ZN E4002 " - pdb=" ND1 HIS E 77 " pdb="ZN ZN E4002 " - pdb=" SG CYS E 94 " pdb=" ZN E4003 " pdb="ZN ZN E4003 " - pdb=" ND1 HIS E 82 " pdb="ZN ZN E4003 " - pdb=" SG CYS E 56 " pdb="ZN ZN E4003 " - pdb=" SG CYS E 68 " pdb="ZN ZN E4003 " - pdb=" SG CYS E 53 " Number of angles added : 12 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5270 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 24 sheets defined 49.3% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.570A pdb=" N LEU A 49 " --> pdb=" O HIS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 131 through 143 removed outlier: 4.662A pdb=" N ARG A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 removed outlier: 4.535A pdb=" N THR A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA A 162 " --> pdb=" O HIS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.870A pdb=" N MET A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 171' Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.866A pdb=" N ARG A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.540A pdb=" N ARG A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'E' and resid 81 through 88 Processing helix chain 'C' and resid 26 through 46 removed outlier: 3.551A pdb=" N VAL C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 67 removed outlier: 3.950A pdb=" N HIS C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 96 removed outlier: 4.078A pdb=" N ARG C 90 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 134 removed outlier: 4.358A pdb=" N MET C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL C 129 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'C' and resid 156 through 175 removed outlier: 3.677A pdb=" N GLY C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 195 removed outlier: 3.892A pdb=" N LEU C 195 " --> pdb=" O MET C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 228 removed outlier: 3.777A pdb=" N GLU C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) Proline residue: C 208 - end of helix removed outlier: 3.753A pdb=" N ALA C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 Processing helix chain 'C' and resid 257 through 273 removed outlier: 3.997A pdb=" N SER C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 292 through 304 Processing helix chain 'C' and resid 308 through 329 removed outlier: 3.879A pdb=" N THR C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 360 Processing helix chain 'C' and resid 363 through 379 removed outlier: 4.042A pdb=" N ASN C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 398 removed outlier: 4.276A pdb=" N LYS C 398 " --> pdb=" O ASP C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 421 removed outlier: 4.141A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 441 removed outlier: 3.739A pdb=" N PHE C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.986A pdb=" N ASN C 453 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 495 removed outlier: 3.600A pdb=" N ALA C 493 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 494 " --> pdb=" O HIS C 490 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 542 Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'C' and resid 612 through 619 Processing helix chain 'C' and resid 624 through 635 removed outlier: 3.654A pdb=" N VAL C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 711 Processing helix chain 'C' and resid 712 through 714 No H-bonds generated for 'chain 'C' and resid 712 through 714' Processing helix chain 'C' and resid 721 through 730 removed outlier: 3.918A pdb=" N GLU C 725 " --> pdb=" O VAL C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 746 removed outlier: 3.849A pdb=" N GLU C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 751 removed outlier: 3.865A pdb=" N GLU C 750 " --> pdb=" O GLY C 747 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 751 " --> pdb=" O LEU C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 747 through 751' Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.860A pdb=" N LEU B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 113 through 128 Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 145 through 164 Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 191 through 203 removed outlier: 3.897A pdb=" N ARG B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.980A pdb=" N SER B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 236 Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'F' and resid 26 through 46 removed outlier: 3.586A pdb=" N VAL F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 67 removed outlier: 4.010A pdb=" N HIS F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 96 removed outlier: 4.095A pdb=" N ARG F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 134 removed outlier: 4.250A pdb=" N MET F 118 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL F 129 " --> pdb=" O TYR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 151 Processing helix chain 'F' and resid 156 through 175 removed outlier: 3.697A pdb=" N GLY F 175 " --> pdb=" O ARG F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 195 removed outlier: 3.902A pdb=" N LEU F 195 " --> pdb=" O MET F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 removed outlier: 3.590A pdb=" N GLU F 203 " --> pdb=" O SER F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 228 removed outlier: 4.084A pdb=" N GLN F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA F 226 " --> pdb=" O GLN F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 252 Processing helix chain 'F' and resid 257 through 273 removed outlier: 3.997A pdb=" N SER F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 292 through 304 Processing helix chain 'F' and resid 308 through 329 removed outlier: 3.904A pdb=" N THR F 312 " --> pdb=" O ASN F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 360 Processing helix chain 'F' and resid 363 through 379 removed outlier: 4.104A pdb=" N ASN F 379 " --> pdb=" O GLU F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 398 removed outlier: 4.293A pdb=" N LYS F 398 " --> pdb=" O ASP F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 421 removed outlier: 4.069A pdb=" N VAL F 408 " --> pdb=" O THR F 404 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE F 421 " --> pdb=" O VAL F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 441 removed outlier: 3.713A pdb=" N PHE F 428 " --> pdb=" O GLU F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 462 removed outlier: 3.949A pdb=" N ASN F 453 " --> pdb=" O ASP F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 495 Processing helix chain 'F' and resid 525 through 542 Processing helix chain 'F' and resid 598 through 608 Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.726A pdb=" N GLU F 619 " --> pdb=" O GLU F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 624 through 635 Processing helix chain 'F' and resid 684 through 711 removed outlier: 3.663A pdb=" N GLU F 704 " --> pdb=" O LYS F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 714 No H-bonds generated for 'chain 'F' and resid 712 through 714' Processing helix chain 'F' and resid 721 through 730 removed outlier: 3.912A pdb=" N GLU F 725 " --> pdb=" O VAL F 721 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 746 removed outlier: 3.918A pdb=" N GLU F 746 " --> pdb=" O LYS F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 751 removed outlier: 4.051A pdb=" N GLU F 750 " --> pdb=" O GLY F 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 86 removed outlier: 3.502A pdb=" N ARG D 86 " --> pdb=" O HIS D 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 44 removed outlier: 3.576A pdb=" N ILE A 33 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 72 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 586 removed outlier: 3.543A pdb=" N ARG A 580 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 272 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 266 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE A 270 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR A 288 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE A 272 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 286 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER A 285 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU A 592 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 312 removed outlier: 3.591A pdb=" N GLY A 309 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 321 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 311 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 319 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE A 318 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=AA5, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.573A pdb=" N SER A 374 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 408 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 423 through 427 removed outlier: 3.586A pdb=" N TYR A 440 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 448 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 463 through 467 removed outlier: 4.106A pdb=" N SER A 463 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 474 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 503 " --> pdb=" O GLU A 508 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 508 " --> pdb=" O ASP A 503 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.611A pdb=" N CYS A 535 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU A 534 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 538 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 550 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 540 " --> pdb=" O LYS A 548 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 548 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N TYR A 549 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N HIS A 566 " --> pdb=" O TYR A 549 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR A 551 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 564 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 560 " --> pdb=" O ASP A 555 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 502 through 503 removed outlier: 6.766A pdb=" N ASP C 558 " --> pdb=" O LYS E 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 506 through 509 removed outlier: 4.245A pdb=" N LEU E 32 " --> pdb=" O THR C 549 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 78 through 80 Processing sheet with id=AB3, first strand: chain 'C' and resid 645 through 646 Processing sheet with id=AB4, first strand: chain 'B' and resid 40 through 44 removed outlier: 3.652A pdb=" N ILE B 33 " --> pdb=" O CYS B 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 72 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.628A pdb=" N SER B 285 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 286 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE B 272 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR B 288 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE B 270 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 266 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 586 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 580 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 309 through 312 removed outlier: 3.632A pdb=" N GLY B 309 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 321 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 311 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE B 318 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AB8, first strand: chain 'B' and resid 374 through 378 removed outlier: 3.765A pdb=" N SER B 374 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 400 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 423 through 427 removed outlier: 3.546A pdb=" N VAL B 433 " --> pdb=" O TYR B 440 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 440 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 448 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 463 through 467 removed outlier: 3.892A pdb=" N SER B 463 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 465 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 472 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL B 499 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 512 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 508 " --> pdb=" O ASP B 503 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 527 through 530 removed outlier: 4.825A pdb=" N LEU B 534 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 550 " --> pdb=" O MET B 538 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR B 549 " --> pdb=" O HIS B 566 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS B 566 " --> pdb=" O TYR B 549 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR B 551 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 564 " --> pdb=" O THR B 551 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 502 through 503 removed outlier: 7.071A pdb=" N ASP F 502 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP F 558 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 506 through 509 removed outlier: 6.287A pdb=" N ARG F 506 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TRP D 33 " --> pdb=" O ARG F 506 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU F 508 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU D 32 " --> pdb=" O THR F 549 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA D 34 " --> pdb=" O GLN F 547 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN F 547 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 645 through 646 Processing sheet with id=AC6, first strand: chain 'D' and resid 78 through 80 1102 hydrogen bonds defined for protein. 3228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6166 1.33 - 1.45: 3885 1.45 - 1.57: 12410 1.57 - 1.69: 0 1.69 - 1.82: 270 Bond restraints: 22731 Sorted by residual: bond pdb=" N ALA F 207 " pdb=" CA ALA F 207 " ideal model delta sigma weight residual 1.462 1.484 -0.022 7.70e-03 1.69e+04 8.33e+00 bond pdb=" N VAL B 399 " pdb=" CA VAL B 399 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.32e-02 5.74e+03 7.74e+00 bond pdb=" N GLU F 202 " pdb=" CA GLU F 202 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N GLU F 206 " pdb=" CA GLU F 206 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 6.01e+00 bond pdb=" N ARG B 396 " pdb=" CA ARG B 396 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.40e-02 5.10e+03 5.75e+00 ... (remaining 22726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 30012 1.54 - 3.09: 550 3.09 - 4.63: 78 4.63 - 6.17: 38 6.17 - 7.71: 6 Bond angle restraints: 30684 Sorted by residual: angle pdb=" C SER E 65 " pdb=" CA SER E 65 " pdb=" CB SER E 65 " ideal model delta sigma weight residual 117.23 110.37 6.86 1.36e+00 5.41e-01 2.54e+01 angle pdb=" N ARG B 396 " pdb=" CA ARG B 396 " pdb=" C ARG B 396 " ideal model delta sigma weight residual 113.15 107.81 5.34 1.19e+00 7.06e-01 2.01e+01 angle pdb=" CA VAL B 399 " pdb=" C VAL B 399 " pdb=" O VAL B 399 " ideal model delta sigma weight residual 121.92 117.16 4.76 1.17e+00 7.31e-01 1.66e+01 angle pdb=" CA SER E 65 " pdb=" C SER E 65 " pdb=" N GLU E 66 " ideal model delta sigma weight residual 119.98 116.76 3.22 8.50e-01 1.38e+00 1.44e+01 angle pdb=" CA GLU F 206 " pdb=" C GLU F 206 " pdb=" O GLU F 206 " ideal model delta sigma weight residual 120.82 117.16 3.66 1.05e+00 9.07e-01 1.21e+01 ... (remaining 30679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12597 17.96 - 35.93: 986 35.93 - 53.89: 184 53.89 - 71.85: 43 71.85 - 89.82: 22 Dihedral angle restraints: 13832 sinusoidal: 5726 harmonic: 8106 Sorted by residual: dihedral pdb=" CA SER C 255 " pdb=" C SER C 255 " pdb=" N THR C 256 " pdb=" CA THR C 256 " ideal model delta harmonic sigma weight residual 180.00 152.64 27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LYS A 255 " pdb=" C LYS A 255 " pdb=" N PHE A 256 " pdb=" CA PHE A 256 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA SER F 255 " pdb=" C SER F 255 " pdb=" N THR F 256 " pdb=" CA THR F 256 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 13829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2895 0.054 - 0.107: 428 0.107 - 0.161: 56 0.161 - 0.214: 3 0.214 - 0.268: 3 Chirality restraints: 3385 Sorted by residual: chirality pdb=" CB VAL B 399 " pdb=" CA VAL B 399 " pdb=" CG1 VAL B 399 " pdb=" CG2 VAL B 399 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ARG B 397 " pdb=" N ARG B 397 " pdb=" C ARG B 397 " pdb=" CB ARG B 397 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ARG B 396 " pdb=" N ARG B 396 " pdb=" C ARG B 396 " pdb=" CB ARG B 396 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3382 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 519 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO F 520 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 520 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 520 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 622 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO C 623 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 623 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 623 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 524 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO C 525 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 525 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 525 " 0.024 5.00e-02 4.00e+02 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 361 2.67 - 3.23: 21453 3.23 - 3.78: 35917 3.78 - 4.34: 45492 4.34 - 4.90: 74179 Nonbonded interactions: 177402 Sorted by model distance: nonbonded pdb=" OD2 ASP E 97 " pdb="ZN ZN E4002 " model vdw 2.109 2.230 nonbonded pdb=" OD2 ASP D 97 " pdb="ZN ZN D4002 " model vdw 2.122 2.230 nonbonded pdb=" O GLU C 206 " pdb=" N LEU C 210 " model vdw 2.199 3.120 nonbonded pdb=" OG SER A 374 " pdb=" O ILE A 385 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O ASP B 574 " model vdw 2.235 3.040 ... (remaining 177397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 328 or resid 330 through 598)) selection = (chain 'B' and (resid 8 through 328 or resid 342 or resid 344 through 477 or res \ id 496 through 598)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.040 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22753 Z= 0.131 Angle : 0.539 10.746 30696 Z= 0.313 Chirality : 0.040 0.268 3385 Planarity : 0.003 0.065 3934 Dihedral : 13.629 89.815 8562 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.92 % Favored : 93.01 % Rotamer: Outliers : 0.32 % Allowed : 14.49 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.16), residues: 2718 helix: 1.10 (0.15), residues: 1260 sheet: -0.95 (0.31), residues: 269 loop : -2.31 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.015 0.001 TYR F 753 PHE 0.011 0.001 PHE F 205 TRP 0.015 0.001 TRP D 35 HIS 0.014 0.001 HIS C 701 Details of bonding type rmsd covalent geometry : bond 0.00210 (22731) covalent geometry : angle 0.53432 (30684) hydrogen bonds : bond 0.16614 ( 1102) hydrogen bonds : angle 6.08964 ( 3228) metal coordination : bond 0.00887 ( 22) metal coordination : angle 3.79914 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 867 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 PHE cc_start: 0.8261 (m-10) cc_final: 0.8009 (m-80) REVERT: A 26 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7104 (mt-10) REVERT: A 29 LEU cc_start: 0.8823 (mp) cc_final: 0.8401 (mm) REVERT: A 42 PHE cc_start: 0.8764 (m-80) cc_final: 0.8344 (m-10) REVERT: A 47 MET cc_start: 0.7389 (ttt) cc_final: 0.6915 (ttt) REVERT: A 49 LEU cc_start: 0.8206 (mt) cc_final: 0.7832 (mp) REVERT: A 59 MET cc_start: 0.7402 (ttt) cc_final: 0.7027 (ttt) REVERT: A 60 PHE cc_start: 0.8229 (m-80) cc_final: 0.7604 (m-10) REVERT: A 68 LYS cc_start: 0.8583 (tptp) cc_final: 0.8304 (tptp) REVERT: A 73 HIS cc_start: 0.7355 (m-70) cc_final: 0.6968 (m-70) REVERT: A 84 ILE cc_start: 0.8494 (tp) cc_final: 0.8196 (tt) REVERT: A 87 THR cc_start: 0.8320 (t) cc_final: 0.7948 (p) REVERT: A 103 GLN cc_start: 0.7660 (tp40) cc_final: 0.7397 (tp40) REVERT: A 109 CYS cc_start: 0.8122 (t) cc_final: 0.7791 (t) REVERT: A 110 PHE cc_start: 0.8370 (t80) cc_final: 0.7917 (t80) REVERT: A 112 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7826 (tp40) REVERT: A 121 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8222 (ttp80) REVERT: A 122 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 123 TYR cc_start: 0.8191 (t80) cc_final: 0.7869 (t80) REVERT: A 124 LEU cc_start: 0.8480 (mp) cc_final: 0.8235 (mt) REVERT: A 127 LYS cc_start: 0.8383 (tppt) cc_final: 0.8045 (mmmt) REVERT: A 147 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 150 GLN cc_start: 0.7996 (mm110) cc_final: 0.7729 (mm-40) REVERT: A 159 LYS cc_start: 0.7038 (mtmt) cc_final: 0.5753 (mtpp) REVERT: A 180 ILE cc_start: 0.8385 (mt) cc_final: 0.8176 (tp) REVERT: A 183 SER cc_start: 0.8181 (t) cc_final: 0.7628 (p) REVERT: A 184 ASP cc_start: 0.7872 (p0) cc_final: 0.7365 (p0) REVERT: A 191 GLU cc_start: 0.7188 (pp20) cc_final: 0.6789 (tm-30) REVERT: A 195 ARG cc_start: 0.8327 (tmm160) cc_final: 0.8087 (ttm-80) REVERT: A 196 GLU cc_start: 0.7311 (pp20) cc_final: 0.6880 (pp20) REVERT: A 225 LEU cc_start: 0.5278 (mt) cc_final: 0.4834 (mt) REVERT: A 271 PHE cc_start: 0.7787 (m-80) cc_final: 0.7540 (m-10) REVERT: A 293 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7970 (mt-10) REVERT: A 296 TYR cc_start: 0.7668 (m-80) cc_final: 0.7241 (m-80) REVERT: A 311 VAL cc_start: 0.8227 (p) cc_final: 0.7865 (t) REVERT: A 352 TRP cc_start: 0.8050 (t60) cc_final: 0.7606 (t60) REVERT: A 361 PHE cc_start: 0.7182 (m-80) cc_final: 0.6659 (m-80) REVERT: A 379 GLU cc_start: 0.7183 (tp30) cc_final: 0.6633 (tp30) REVERT: A 381 TYR cc_start: 0.7577 (m-80) cc_final: 0.7163 (m-80) REVERT: A 383 TYR cc_start: 0.6574 (m-80) cc_final: 0.6199 (m-80) REVERT: A 403 ASP cc_start: 0.7686 (t0) cc_final: 0.6969 (t0) REVERT: A 443 PHE cc_start: 0.8714 (t80) cc_final: 0.8325 (t80) REVERT: A 502 TYR cc_start: 0.6125 (t80) cc_final: 0.5852 (t80) REVERT: A 503 ASP cc_start: 0.7912 (t0) cc_final: 0.5086 (p0) REVERT: A 587 TYR cc_start: 0.6845 (m-80) cc_final: 0.6605 (m-10) REVERT: E 23 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6342 (mp0) REVERT: E 28 ASN cc_start: 0.6374 (t0) cc_final: 0.5766 (t0) REVERT: E 48 HIS cc_start: 0.5195 (t70) cc_final: 0.4701 (t70) REVERT: E 93 VAL cc_start: 0.7122 (m) cc_final: 0.6722 (p) REVERT: C 28 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7398 (mmmm) REVERT: C 33 ILE cc_start: 0.8950 (mm) cc_final: 0.8666 (tt) REVERT: C 42 GLN cc_start: 0.8090 (mt0) cc_final: 0.7679 (mt0) REVERT: C 58 TYR cc_start: 0.8074 (t80) cc_final: 0.7829 (t80) REVERT: C 71 GLU cc_start: 0.7322 (tm-30) cc_final: 0.7008 (tm-30) REVERT: C 72 LYS cc_start: 0.8082 (tttt) cc_final: 0.7832 (tptm) REVERT: C 83 GLU cc_start: 0.7417 (tp30) cc_final: 0.6951 (tp30) REVERT: C 91 GLU cc_start: 0.7452 (tp30) cc_final: 0.7131 (mm-30) REVERT: C 118 MET cc_start: 0.7030 (mtm) cc_final: 0.6332 (mtm) REVERT: C 145 ILE cc_start: 0.8198 (mt) cc_final: 0.7909 (tt) REVERT: C 153 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7435 (mmt90) REVERT: C 163 GLN cc_start: 0.8226 (mm110) cc_final: 0.7617 (mm110) REVERT: C 168 MET cc_start: 0.7564 (ptp) cc_final: 0.6954 (ptp) REVERT: C 188 GLN cc_start: 0.7456 (tp40) cc_final: 0.7109 (tp40) REVERT: C 192 ILE cc_start: 0.8341 (mm) cc_final: 0.8113 (mt) REVERT: C 215 GLU cc_start: 0.7721 (mp0) cc_final: 0.7494 (mp0) REVERT: C 217 PHE cc_start: 0.7881 (m-80) cc_final: 0.7389 (m-10) REVERT: C 222 GLN cc_start: 0.7625 (tp40) cc_final: 0.7220 (tm-30) REVERT: C 235 LYS cc_start: 0.8342 (mmmt) cc_final: 0.8074 (mtmt) REVERT: C 238 GLU cc_start: 0.7179 (tp30) cc_final: 0.6517 (tm-30) REVERT: C 250 HIS cc_start: 0.7772 (t-90) cc_final: 0.7193 (t-90) REVERT: C 253 ASP cc_start: 0.6386 (p0) cc_final: 0.5912 (t70) REVERT: C 258 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7047 (mm-30) REVERT: C 262 LYS cc_start: 0.8008 (tmtm) cc_final: 0.7400 (ttpp) REVERT: C 265 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7199 (mm-30) REVERT: C 270 SER cc_start: 0.8342 (m) cc_final: 0.8070 (t) REVERT: C 287 MET cc_start: 0.7788 (ptt) cc_final: 0.5941 (ptt) REVERT: C 292 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8224 (mmtm) REVERT: C 301 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7975 (ptpp) REVERT: C 302 LEU cc_start: 0.8464 (tp) cc_final: 0.8211 (tp) REVERT: C 306 VAL cc_start: 0.8536 (t) cc_final: 0.8155 (p) REVERT: C 346 LEU cc_start: 0.7997 (tp) cc_final: 0.7658 (tp) REVERT: C 353 ASP cc_start: 0.7789 (t0) cc_final: 0.7563 (t0) REVERT: C 354 ARG cc_start: 0.8005 (ttp-110) cc_final: 0.7642 (ttp-110) REVERT: C 360 PHE cc_start: 0.7644 (m-10) cc_final: 0.7290 (m-10) REVERT: C 368 GLN cc_start: 0.6922 (tm-30) cc_final: 0.6445 (tm-30) REVERT: C 369 THR cc_start: 0.7974 (p) cc_final: 0.7266 (t) REVERT: C 386 GLU cc_start: 0.8226 (mp0) cc_final: 0.7219 (mp0) REVERT: C 394 ASP cc_start: 0.7839 (t0) cc_final: 0.7405 (t0) REVERT: C 395 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8390 (mmtm) REVERT: C 412 LEU cc_start: 0.8724 (mt) cc_final: 0.8055 (pp) REVERT: C 413 ASP cc_start: 0.8438 (m-30) cc_final: 0.7292 (m-30) REVERT: C 418 LEU cc_start: 0.8687 (tt) cc_final: 0.8068 (tp) REVERT: C 424 GLU cc_start: 0.7511 (mp0) cc_final: 0.6755 (mp0) REVERT: C 431 TYR cc_start: 0.7810 (m-80) cc_final: 0.6904 (m-80) REVERT: C 441 LEU cc_start: 0.8306 (mt) cc_final: 0.7565 (mp) REVERT: C 457 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8556 (mmtp) REVERT: C 479 ILE cc_start: 0.7650 (mm) cc_final: 0.7423 (mm) REVERT: C 554 MET cc_start: 0.6774 (tpp) cc_final: 0.6320 (tpp) REVERT: C 603 MET cc_start: 0.7399 (tmm) cc_final: 0.7073 (tmm) REVERT: C 687 GLU cc_start: 0.6194 (pp20) cc_final: 0.4324 (tt0) REVERT: C 688 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7650 (mmm-85) REVERT: C 692 ARG cc_start: 0.8454 (tpp-160) cc_final: 0.7969 (tpp80) REVERT: B 19 GLU cc_start: 0.7375 (pp20) cc_final: 0.6989 (pp20) REVERT: B 24 PHE cc_start: 0.8399 (m-10) cc_final: 0.8071 (m-80) REVERT: B 36 ILE cc_start: 0.8542 (mm) cc_final: 0.8275 (mt) REVERT: B 44 CYS cc_start: 0.8398 (p) cc_final: 0.8065 (p) REVERT: B 46 LYS cc_start: 0.8893 (mttt) cc_final: 0.8531 (mtpp) REVERT: B 60 PHE cc_start: 0.8344 (m-10) cc_final: 0.7777 (m-10) REVERT: B 61 MET cc_start: 0.6835 (tmm) cc_final: 0.6357 (tmm) REVERT: B 66 GLU cc_start: 0.8034 (mp0) cc_final: 0.7725 (mp0) REVERT: B 72 VAL cc_start: 0.8752 (m) cc_final: 0.8286 (p) REVERT: B 85 ILE cc_start: 0.8644 (mt) cc_final: 0.8353 (tp) REVERT: B 90 TYR cc_start: 0.7964 (m-80) cc_final: 0.7475 (m-80) REVERT: B 106 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7392 (mt-10) REVERT: B 112 GLN cc_start: 0.7824 (mm-40) cc_final: 0.6570 (mm-40) REVERT: B 114 GLU cc_start: 0.6430 (tm-30) cc_final: 0.6075 (mm-30) REVERT: B 115 ASP cc_start: 0.7595 (p0) cc_final: 0.6968 (p0) REVERT: B 123 TYR cc_start: 0.7301 (t80) cc_final: 0.6708 (t80) REVERT: B 127 LYS cc_start: 0.7876 (tptt) cc_final: 0.7606 (tptt) REVERT: B 136 LEU cc_start: 0.8276 (mt) cc_final: 0.7858 (mm) REVERT: B 149 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7786 (tptp) REVERT: B 153 LYS cc_start: 0.8284 (tptm) cc_final: 0.8064 (tppt) REVERT: B 155 MET cc_start: 0.8009 (tpt) cc_final: 0.7272 (tpp) REVERT: B 167 ASP cc_start: 0.7176 (p0) cc_final: 0.6957 (p0) REVERT: B 184 ASP cc_start: 0.7690 (t70) cc_final: 0.7235 (t0) REVERT: B 199 MET cc_start: 0.7310 (mmp) cc_final: 0.7093 (mmp) REVERT: B 212 TYR cc_start: 0.7963 (m-10) cc_final: 0.7420 (m-80) REVERT: B 229 THR cc_start: 0.5601 (p) cc_final: 0.4609 (p) REVERT: B 263 MET cc_start: 0.6709 (mpp) cc_final: 0.6400 (mtm) REVERT: B 353 PHE cc_start: 0.8300 (t80) cc_final: 0.7448 (t80) REVERT: B 363 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8146 (mmtt) REVERT: B 381 TYR cc_start: 0.7630 (m-80) cc_final: 0.6984 (m-80) REVERT: B 383 TYR cc_start: 0.5681 (m-80) cc_final: 0.5477 (m-80) REVERT: B 403 ASP cc_start: 0.8368 (t0) cc_final: 0.8106 (t70) REVERT: B 429 ASP cc_start: 0.7710 (m-30) cc_final: 0.7085 (m-30) REVERT: B 430 CYS cc_start: 0.6040 (m) cc_final: 0.5152 (t) REVERT: B 434 MET cc_start: 0.1668 (tpt) cc_final: 0.1270 (tpt) REVERT: B 469 ASP cc_start: 0.7146 (t70) cc_final: 0.6427 (t0) REVERT: B 470 LYS cc_start: 0.7126 (mttm) cc_final: 0.6825 (mtpp) REVERT: B 529 VAL cc_start: 0.5922 (t) cc_final: 0.5098 (m) REVERT: F 28 LYS cc_start: 0.7796 (mmmm) cc_final: 0.7466 (mmmm) REVERT: F 35 ASP cc_start: 0.7551 (t0) cc_final: 0.7242 (t70) REVERT: F 60 ASN cc_start: 0.7940 (m-40) cc_final: 0.7734 (m-40) REVERT: F 64 MET cc_start: 0.6875 (tpt) cc_final: 0.6646 (tpt) REVERT: F 68 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8261 (mttm) REVERT: F 78 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7620 (ttm-80) REVERT: F 124 MET cc_start: 0.3809 (tmm) cc_final: 0.3359 (tmm) REVERT: F 126 MET cc_start: 0.8240 (tmt) cc_final: 0.7826 (tmm) REVERT: F 139 VAL cc_start: 0.7208 (m) cc_final: 0.6470 (t) REVERT: F 140 TYR cc_start: 0.7893 (t80) cc_final: 0.7393 (t80) REVERT: F 145 ILE cc_start: 0.8766 (mt) cc_final: 0.8451 (mm) REVERT: F 153 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7387 (mtt180) REVERT: F 167 ASP cc_start: 0.6934 (t0) cc_final: 0.6472 (t0) REVERT: F 168 MET cc_start: 0.7116 (ptp) cc_final: 0.6579 (ptp) REVERT: F 188 GLN cc_start: 0.7547 (tp40) cc_final: 0.7334 (mm-40) REVERT: F 193 LEU cc_start: 0.8873 (tp) cc_final: 0.8642 (tt) REVERT: F 200 VAL cc_start: 0.7432 (t) cc_final: 0.7143 (t) REVERT: F 204 ASP cc_start: 0.7763 (m-30) cc_final: 0.7472 (p0) REVERT: F 215 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7240 (mm-30) REVERT: F 219 MET cc_start: 0.7274 (mmt) cc_final: 0.7065 (mmt) REVERT: F 223 LYS cc_start: 0.7744 (tmtp) cc_final: 0.7046 (tmtt) REVERT: F 235 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8245 (mmmt) REVERT: F 240 ARG cc_start: 0.7905 (mmt180) cc_final: 0.7536 (tpp80) REVERT: F 243 GLU cc_start: 0.7471 (pp20) cc_final: 0.6946 (pp20) REVERT: F 246 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7159 (tp30) REVERT: F 249 MET cc_start: 0.7602 (ppp) cc_final: 0.7227 (ppp) REVERT: F 251 CYS cc_start: 0.8065 (t) cc_final: 0.7857 (t) REVERT: F 258 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7806 (mm-30) REVERT: F 265 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7034 (mm-30) REVERT: F 270 SER cc_start: 0.8662 (m) cc_final: 0.8085 (t) REVERT: F 295 ASP cc_start: 0.7265 (m-30) cc_final: 0.6868 (m-30) REVERT: F 302 LEU cc_start: 0.8673 (tp) cc_final: 0.8370 (tp) REVERT: F 303 PHE cc_start: 0.7607 (m-80) cc_final: 0.6851 (m-80) REVERT: F 311 LYS cc_start: 0.7672 (tmmt) cc_final: 0.7208 (ttmm) REVERT: F 316 CYS cc_start: 0.7705 (t) cc_final: 0.7493 (p) REVERT: F 319 SER cc_start: 0.8625 (t) cc_final: 0.8079 (p) REVERT: F 322 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7744 (mmt-90) REVERT: F 346 LEU cc_start: 0.7621 (tp) cc_final: 0.7347 (pp) REVERT: F 411 ILE cc_start: 0.8643 (tt) cc_final: 0.8380 (pt) REVERT: F 423 GLN cc_start: 0.7870 (tt0) cc_final: 0.7436 (tt0) REVERT: F 431 TYR cc_start: 0.6687 (m-80) cc_final: 0.6324 (m-80) REVERT: F 457 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7962 (mmtt) REVERT: F 473 MET cc_start: 0.6879 (ptm) cc_final: 0.6662 (ttm) REVERT: F 489 GLN cc_start: 0.8049 (mt0) cc_final: 0.7826 (tp-100) outliers start: 8 outliers final: 2 residues processed: 873 average time/residue: 0.1953 time to fit residues: 249.1888 Evaluate side-chains 725 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 723 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain F residue 748 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.0040 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.0270 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 187 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN E 48 HIS C 60 ASN C 106 ASN C 163 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 657 HIS C 718 GLN B 71 HIS B 316 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 163 GLN F 434 GLN F 606 ASN F 618 GLN F 718 GLN F 719 HIS D 47 ASN D 48 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.171813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.145353 restraints weight = 50340.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.149864 restraints weight = 26914.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.152719 restraints weight = 16309.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.154619 restraints weight = 10910.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.155899 restraints weight = 7871.144| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22753 Z= 0.168 Angle : 0.660 11.185 30696 Z= 0.344 Chirality : 0.043 0.227 3385 Planarity : 0.005 0.120 3934 Dihedral : 4.462 45.771 3012 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.84 % Favored : 92.09 % Rotamer: Outliers : 3.44 % Allowed : 19.14 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.16), residues: 2718 helix: 1.02 (0.15), residues: 1265 sheet: -0.94 (0.30), residues: 274 loop : -2.35 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 455 TYR 0.025 0.002 TYR C 130 PHE 0.021 0.002 PHE C 605 TRP 0.027 0.002 TRP E 101 HIS 0.011 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00347 (22731) covalent geometry : angle 0.65174 (30684) hydrogen bonds : bond 0.04869 ( 1102) hydrogen bonds : angle 5.06987 ( 3228) metal coordination : bond 0.01171 ( 22) metal coordination : angle 5.37672 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 765 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7522 (pp20) REVERT: A 20 GLN cc_start: 0.8749 (mm-40) cc_final: 0.7649 (mm110) REVERT: A 24 PHE cc_start: 0.8521 (m-10) cc_final: 0.8247 (m-80) REVERT: A 26 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 34 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8600 (m) REVERT: A 42 PHE cc_start: 0.8878 (m-80) cc_final: 0.8640 (m-80) REVERT: A 47 MET cc_start: 0.7521 (ttt) cc_final: 0.7144 (ttt) REVERT: A 59 MET cc_start: 0.7601 (ttt) cc_final: 0.7351 (ttt) REVERT: A 60 PHE cc_start: 0.8469 (m-80) cc_final: 0.7781 (m-10) REVERT: A 64 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7641 (mp) REVERT: A 66 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7044 (pt0) REVERT: A 75 ARG cc_start: 0.7912 (ptp-170) cc_final: 0.7561 (ptp-170) REVERT: A 83 GLN cc_start: 0.8439 (tp40) cc_final: 0.8127 (tp40) REVERT: A 84 ILE cc_start: 0.8598 (tp) cc_final: 0.8333 (tt) REVERT: A 87 THR cc_start: 0.8500 (t) cc_final: 0.8039 (p) REVERT: A 90 TYR cc_start: 0.7794 (m-80) cc_final: 0.7591 (m-80) REVERT: A 102 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 112 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7759 (mm-40) REVERT: A 117 LEU cc_start: 0.8215 (mt) cc_final: 0.7914 (tt) REVERT: A 121 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8217 (ttp80) REVERT: A 122 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 127 LYS cc_start: 0.8401 (tppt) cc_final: 0.7907 (mmmt) REVERT: A 157 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7075 (mm-30) REVERT: A 159 LYS cc_start: 0.7228 (mtmt) cc_final: 0.6403 (mtmm) REVERT: A 165 HIS cc_start: 0.6383 (m90) cc_final: 0.6062 (m90) REVERT: A 170 MET cc_start: 0.6883 (mmp) cc_final: 0.6458 (mmp) REVERT: A 184 ASP cc_start: 0.7766 (p0) cc_final: 0.7445 (p0) REVERT: A 191 GLU cc_start: 0.7397 (pp20) cc_final: 0.7041 (tm-30) REVERT: A 196 GLU cc_start: 0.7538 (pp20) cc_final: 0.7050 (pp20) REVERT: A 225 LEU cc_start: 0.5276 (mt) cc_final: 0.4999 (mt) REVERT: A 267 GLU cc_start: 0.7567 (tp30) cc_final: 0.7191 (tp30) REVERT: A 269 MET cc_start: 0.6814 (mmp) cc_final: 0.6430 (mmp) REVERT: A 271 PHE cc_start: 0.7628 (m-80) cc_final: 0.7312 (m-10) REVERT: A 288 TYR cc_start: 0.7252 (t80) cc_final: 0.6872 (t80) REVERT: A 294 LYS cc_start: 0.8300 (mmmm) cc_final: 0.7800 (mmtm) REVERT: A 296 TYR cc_start: 0.7023 (m-80) cc_final: 0.6512 (m-80) REVERT: A 297 LYS cc_start: 0.8190 (ptpt) cc_final: 0.7961 (ptpt) REVERT: A 301 PRO cc_start: 0.7407 (Cg_exo) cc_final: 0.7160 (Cg_endo) REVERT: A 311 VAL cc_start: 0.8207 (p) cc_final: 0.7797 (t) REVERT: A 352 TRP cc_start: 0.7819 (t60) cc_final: 0.7422 (t60) REVERT: A 353 PHE cc_start: 0.8027 (t80) cc_final: 0.7690 (t80) REVERT: A 354 ASP cc_start: 0.6526 (t0) cc_final: 0.5823 (t70) REVERT: A 361 PHE cc_start: 0.7266 (m-80) cc_final: 0.6439 (m-80) REVERT: A 408 GLU cc_start: 0.7434 (pm20) cc_final: 0.6739 (pm20) REVERT: A 443 PHE cc_start: 0.8461 (t80) cc_final: 0.8177 (t80) REVERT: A 555 ASP cc_start: 0.5481 (m-30) cc_final: 0.5263 (m-30) REVERT: A 587 TYR cc_start: 0.6864 (m-80) cc_final: 0.6659 (m-10) REVERT: E 23 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6586 (mp0) REVERT: E 25 LYS cc_start: 0.5196 (mmpt) cc_final: 0.4828 (mmpt) REVERT: E 48 HIS cc_start: 0.5027 (t-90) cc_final: 0.4288 (t-90) REVERT: C 28 LYS cc_start: 0.8005 (mmmm) cc_final: 0.7480 (mmmm) REVERT: C 33 ILE cc_start: 0.8948 (mm) cc_final: 0.8652 (tt) REVERT: C 62 TYR cc_start: 0.7934 (t80) cc_final: 0.7492 (t80) REVERT: C 68 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8259 (mttt) REVERT: C 71 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7414 (tm-30) REVERT: C 72 LYS cc_start: 0.8376 (tttt) cc_final: 0.8000 (tptm) REVERT: C 83 GLU cc_start: 0.7637 (tp30) cc_final: 0.7063 (tp30) REVERT: C 91 GLU cc_start: 0.7293 (tp30) cc_final: 0.6992 (mm-30) REVERT: C 113 GLN cc_start: 0.8028 (tp40) cc_final: 0.7815 (tp40) REVERT: C 118 MET cc_start: 0.7297 (mtm) cc_final: 0.7052 (mtm) REVERT: C 125 TYR cc_start: 0.4890 (t80) cc_final: 0.4667 (t80) REVERT: C 153 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7575 (mmm160) REVERT: C 163 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7658 (mm110) REVERT: C 188 GLN cc_start: 0.7734 (tp40) cc_final: 0.7529 (tp40) REVERT: C 204 ASP cc_start: 0.7131 (t0) cc_final: 0.6719 (t0) REVERT: C 206 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6524 (mp0) REVERT: C 215 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: C 217 PHE cc_start: 0.7879 (m-80) cc_final: 0.7504 (m-10) REVERT: C 222 GLN cc_start: 0.7734 (tp40) cc_final: 0.7319 (tm-30) REVERT: C 235 LYS cc_start: 0.8393 (mmmt) cc_final: 0.7925 (mtmm) REVERT: C 236 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8468 (ptpp) REVERT: C 238 GLU cc_start: 0.7413 (tp30) cc_final: 0.6686 (tm-30) REVERT: C 246 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7554 (tm-30) REVERT: C 247 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7949 (ttm170) REVERT: C 250 HIS cc_start: 0.7845 (t-90) cc_final: 0.7226 (t-90) REVERT: C 258 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6957 (mm-30) REVERT: C 262 LYS cc_start: 0.7880 (tmtm) cc_final: 0.7333 (ttpp) REVERT: C 282 SER cc_start: 0.7410 (m) cc_final: 0.6813 (p) REVERT: C 292 LYS cc_start: 0.8583 (mmmm) cc_final: 0.7960 (mmtm) REVERT: C 301 LYS cc_start: 0.8361 (ptpt) cc_final: 0.8087 (ptpt) REVERT: C 306 VAL cc_start: 0.8557 (t) cc_final: 0.8168 (p) REVERT: C 317 MET cc_start: 0.7987 (tpp) cc_final: 0.7733 (tpp) REVERT: C 321 LEU cc_start: 0.8565 (mt) cc_final: 0.8318 (mt) REVERT: C 346 LEU cc_start: 0.8036 (tp) cc_final: 0.7748 (tp) REVERT: C 353 ASP cc_start: 0.7836 (t0) cc_final: 0.7574 (t0) REVERT: C 354 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7834 (ttp-110) REVERT: C 360 PHE cc_start: 0.8131 (m-10) cc_final: 0.7618 (m-10) REVERT: C 368 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6618 (tm-30) REVERT: C 369 THR cc_start: 0.8120 (p) cc_final: 0.7708 (t) REVERT: C 394 ASP cc_start: 0.7977 (t0) cc_final: 0.7624 (t0) REVERT: C 395 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8540 (mmmm) REVERT: C 409 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7083 (mt-10) REVERT: C 412 LEU cc_start: 0.8696 (mt) cc_final: 0.8153 (pp) REVERT: C 413 ASP cc_start: 0.8267 (m-30) cc_final: 0.7566 (m-30) REVERT: C 418 LEU cc_start: 0.8742 (tt) cc_final: 0.8444 (tp) REVERT: C 424 GLU cc_start: 0.7300 (mp0) cc_final: 0.6944 (mp0) REVERT: C 429 GLU cc_start: 0.8001 (tp30) cc_final: 0.7781 (tp30) REVERT: C 431 TYR cc_start: 0.7924 (m-80) cc_final: 0.7126 (m-10) REVERT: C 436 LEU cc_start: 0.8876 (mt) cc_final: 0.8670 (mt) REVERT: C 438 ARG cc_start: 0.7763 (tpm170) cc_final: 0.7024 (tpm170) REVERT: C 441 LEU cc_start: 0.8195 (mt) cc_final: 0.7931 (mt) REVERT: C 457 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8658 (mmmt) REVERT: C 554 MET cc_start: 0.6564 (tpp) cc_final: 0.6140 (tpp) REVERT: C 603 MET cc_start: 0.7217 (tmm) cc_final: 0.6804 (tmm) REVERT: C 687 GLU cc_start: 0.6560 (pp20) cc_final: 0.4474 (tt0) REVERT: C 692 ARG cc_start: 0.8476 (tpp-160) cc_final: 0.8177 (mmp80) REVERT: B 19 GLU cc_start: 0.7593 (pp20) cc_final: 0.6996 (pp20) REVERT: B 20 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8349 (mm-40) REVERT: B 24 PHE cc_start: 0.8522 (m-10) cc_final: 0.7973 (m-80) REVERT: B 29 LEU cc_start: 0.8237 (mp) cc_final: 0.7990 (mp) REVERT: B 32 ASP cc_start: 0.8044 (p0) cc_final: 0.7719 (p0) REVERT: B 44 CYS cc_start: 0.8160 (p) cc_final: 0.7950 (p) REVERT: B 46 LYS cc_start: 0.8691 (mttt) cc_final: 0.8371 (mtpp) REVERT: B 61 MET cc_start: 0.7042 (tmm) cc_final: 0.6627 (tmm) REVERT: B 72 VAL cc_start: 0.8722 (m) cc_final: 0.8354 (p) REVERT: B 75 ARG cc_start: 0.7737 (ttm110) cc_final: 0.7422 (ptp-110) REVERT: B 76 ASN cc_start: 0.8940 (m-40) cc_final: 0.8665 (m-40) REVERT: B 85 ILE cc_start: 0.8676 (mt) cc_final: 0.8455 (tp) REVERT: B 88 TYR cc_start: 0.8775 (t80) cc_final: 0.8242 (t80) REVERT: B 103 GLN cc_start: 0.7564 (pm20) cc_final: 0.7002 (pm20) REVERT: B 105 TYR cc_start: 0.8048 (t80) cc_final: 0.7637 (t80) REVERT: B 106 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 112 GLN cc_start: 0.7626 (mm-40) cc_final: 0.6984 (mm110) REVERT: B 114 GLU cc_start: 0.6448 (tm-30) cc_final: 0.6223 (mm-30) REVERT: B 115 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.6958 (p0) REVERT: B 123 TYR cc_start: 0.7525 (t80) cc_final: 0.6812 (t80) REVERT: B 132 ASN cc_start: 0.7780 (p0) cc_final: 0.7413 (p0) REVERT: B 136 LEU cc_start: 0.8200 (mt) cc_final: 0.7860 (mm) REVERT: B 149 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7750 (tptp) REVERT: B 155 MET cc_start: 0.7887 (tpt) cc_final: 0.7175 (tpp) REVERT: B 166 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7162 (mp10) REVERT: B 167 ASP cc_start: 0.7459 (p0) cc_final: 0.7127 (p0) REVERT: B 170 MET cc_start: 0.7839 (mmm) cc_final: 0.7586 (mmm) REVERT: B 184 ASP cc_start: 0.8002 (t70) cc_final: 0.7485 (t0) REVERT: B 195 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.7366 (ttt180) REVERT: B 199 MET cc_start: 0.7505 (mmp) cc_final: 0.7270 (mmp) REVERT: B 203 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7145 (mm-30) REVERT: B 242 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7925 (mmtt) REVERT: B 269 MET cc_start: 0.5445 (mmp) cc_final: 0.5101 (mmp) REVERT: B 307 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8297 (mmtm) REVERT: B 363 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8132 (mmtm) REVERT: B 381 TYR cc_start: 0.7730 (m-80) cc_final: 0.6913 (m-80) REVERT: B 383 TYR cc_start: 0.5586 (m-80) cc_final: 0.5014 (m-80) REVERT: B 429 ASP cc_start: 0.7886 (m-30) cc_final: 0.7303 (m-30) REVERT: B 430 CYS cc_start: 0.5636 (m) cc_final: 0.5267 (t) REVERT: B 436 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.5897 (tt) REVERT: B 437 ASN cc_start: 0.7165 (m-40) cc_final: 0.6964 (m-40) REVERT: B 469 ASP cc_start: 0.7421 (t70) cc_final: 0.6745 (t0) REVERT: B 470 LYS cc_start: 0.7035 (mttm) cc_final: 0.6615 (mtpp) REVERT: B 502 TYR cc_start: 0.6733 (t80) cc_final: 0.6216 (t80) REVERT: B 507 ASN cc_start: 0.8172 (t0) cc_final: 0.7773 (t0) REVERT: B 529 VAL cc_start: 0.6058 (t) cc_final: 0.5362 (m) REVERT: F 28 LYS cc_start: 0.7752 (mmmm) cc_final: 0.7432 (mmmm) REVERT: F 35 ASP cc_start: 0.7636 (t0) cc_final: 0.7322 (t70) REVERT: F 60 ASN cc_start: 0.8043 (m-40) cc_final: 0.7824 (m-40) REVERT: F 64 MET cc_start: 0.7462 (tpt) cc_final: 0.6972 (tpt) REVERT: F 66 LEU cc_start: 0.7392 (tp) cc_final: 0.7106 (tp) REVERT: F 68 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8344 (mttm) REVERT: F 74 TYR cc_start: 0.8067 (t80) cc_final: 0.7623 (t80) REVERT: F 78 ARG cc_start: 0.8292 (ttm170) cc_final: 0.8030 (ttm-80) REVERT: F 79 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6854 (tp30) REVERT: F 126 MET cc_start: 0.8204 (tmt) cc_final: 0.7758 (tmm) REVERT: F 130 TYR cc_start: 0.4838 (t80) cc_final: 0.4510 (t80) REVERT: F 139 VAL cc_start: 0.7264 (m) cc_final: 0.6554 (t) REVERT: F 140 TYR cc_start: 0.7900 (t80) cc_final: 0.7650 (t80) REVERT: F 145 ILE cc_start: 0.8738 (mt) cc_final: 0.8486 (mm) REVERT: F 153 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7412 (mtt180) REVERT: F 160 HIS cc_start: 0.8063 (t-90) cc_final: 0.7813 (t-90) REVERT: F 167 ASP cc_start: 0.6961 (t0) cc_final: 0.6601 (t0) REVERT: F 168 MET cc_start: 0.7264 (ptp) cc_final: 0.6679 (ptp) REVERT: F 188 GLN cc_start: 0.7789 (tp40) cc_final: 0.7565 (mm-40) REVERT: F 208 PRO cc_start: 0.8474 (Cg_exo) cc_final: 0.8239 (Cg_endo) REVERT: F 216 PHE cc_start: 0.7488 (t80) cc_final: 0.7097 (t80) REVERT: F 220 GLU cc_start: 0.7048 (tp30) cc_final: 0.6733 (tp30) REVERT: F 223 LYS cc_start: 0.7676 (tmtp) cc_final: 0.7350 (ttpt) REVERT: F 224 PHE cc_start: 0.6528 (m-10) cc_final: 0.6234 (m-10) REVERT: F 233 TYR cc_start: 0.7431 (t80) cc_final: 0.7119 (t80) REVERT: F 235 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8390 (mmmt) REVERT: F 240 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7643 (tpp80) REVERT: F 241 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8516 (tp) REVERT: F 243 GLU cc_start: 0.7575 (pp20) cc_final: 0.7055 (pp20) REVERT: F 246 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7266 (tp30) REVERT: F 249 MET cc_start: 0.7792 (ppp) cc_final: 0.7409 (ppp) REVERT: F 257 GLU cc_start: 0.7433 (pp20) cc_final: 0.7023 (pp20) REVERT: F 258 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7596 (mp0) REVERT: F 262 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7957 (tmtt) REVERT: F 265 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7177 (mm-30) REVERT: F 266 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7836 (ttp80) REVERT: F 270 SER cc_start: 0.8478 (m) cc_final: 0.8016 (t) REVERT: F 274 LYS cc_start: 0.8045 (tppt) cc_final: 0.7100 (tmmt) REVERT: F 287 MET cc_start: 0.7762 (ptm) cc_final: 0.7208 (ppp) REVERT: F 295 ASP cc_start: 0.7399 (m-30) cc_final: 0.6805 (m-30) REVERT: F 303 PHE cc_start: 0.7867 (m-80) cc_final: 0.7258 (m-80) REVERT: F 319 SER cc_start: 0.8621 (t) cc_final: 0.8109 (p) REVERT: F 322 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7760 (mmt-90) REVERT: F 323 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7577 (tm-30) REVERT: F 423 GLN cc_start: 0.7996 (tt0) cc_final: 0.7637 (tt0) REVERT: F 457 LYS cc_start: 0.8519 (mmmt) cc_final: 0.7970 (mmtt) REVERT: F 461 GLU cc_start: 0.6661 (tp30) cc_final: 0.6111 (tp30) REVERT: F 473 MET cc_start: 0.6761 (ptm) cc_final: 0.6336 (ptm) REVERT: F 484 MET cc_start: 0.3040 (mtp) cc_final: 0.2545 (mtp) REVERT: F 489 GLN cc_start: 0.7995 (mt0) cc_final: 0.7721 (tp-100) REVERT: F 490 HIS cc_start: 0.6865 (m90) cc_final: 0.6645 (m-70) REVERT: F 506 ARG cc_start: 0.5584 (mtm-85) cc_final: 0.5262 (mtm-85) REVERT: F 539 TYR cc_start: 0.6508 (OUTLIER) cc_final: 0.6162 (m-80) outliers start: 85 outliers final: 37 residues processed: 817 average time/residue: 0.1730 time to fit residues: 208.9221 Evaluate side-chains 744 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 699 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 158 HIS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 539 TYR Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 245 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 178 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 182 optimal weight: 0.4980 chunk 252 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN C 60 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 HIS B 69 GLN B 187 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.168599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.142405 restraints weight = 50366.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.146705 restraints weight = 27369.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.149451 restraints weight = 16814.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.151327 restraints weight = 11336.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.152524 restraints weight = 8206.993| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22753 Z= 0.184 Angle : 0.682 10.269 30696 Z= 0.354 Chirality : 0.044 0.248 3385 Planarity : 0.005 0.064 3934 Dihedral : 4.506 30.917 3008 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.09 % Favored : 91.83 % Rotamer: Outliers : 3.93 % Allowed : 20.23 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.16), residues: 2718 helix: 0.85 (0.15), residues: 1280 sheet: -1.01 (0.30), residues: 263 loop : -2.41 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 455 TYR 0.026 0.002 TYR C 432 PHE 0.031 0.002 PHE B 537 TRP 0.025 0.002 TRP B 233 HIS 0.011 0.002 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00375 (22731) covalent geometry : angle 0.67674 (30684) hydrogen bonds : bond 0.04696 ( 1102) hydrogen bonds : angle 4.93027 ( 3228) metal coordination : bond 0.01151 ( 22) metal coordination : angle 4.47666 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 744 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7743 (pt) REVERT: A 19 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7599 (pp20) REVERT: A 20 GLN cc_start: 0.8783 (mm-40) cc_final: 0.7725 (mm110) REVERT: A 22 LYS cc_start: 0.8666 (ttmt) cc_final: 0.7848 (ttmt) REVERT: A 24 PHE cc_start: 0.8556 (m-10) cc_final: 0.8248 (m-80) REVERT: A 26 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 34 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8575 (m) REVERT: A 42 PHE cc_start: 0.8904 (m-80) cc_final: 0.8617 (m-80) REVERT: A 47 MET cc_start: 0.7465 (ttt) cc_final: 0.6963 (ttt) REVERT: A 57 ARG cc_start: 0.8339 (ptm160) cc_final: 0.8020 (ttm-80) REVERT: A 59 MET cc_start: 0.7622 (ttt) cc_final: 0.7330 (ttt) REVERT: A 60 PHE cc_start: 0.8525 (m-80) cc_final: 0.7792 (m-10) REVERT: A 66 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6988 (pt0) REVERT: A 84 ILE cc_start: 0.8681 (tp) cc_final: 0.8337 (tt) REVERT: A 87 THR cc_start: 0.8554 (t) cc_final: 0.8080 (p) REVERT: A 88 TYR cc_start: 0.8434 (t80) cc_final: 0.7436 (t80) REVERT: A 90 TYR cc_start: 0.7964 (m-80) cc_final: 0.7277 (m-80) REVERT: A 106 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 109 CYS cc_start: 0.8203 (t) cc_final: 0.6797 (t) REVERT: A 112 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7800 (mm-40) REVERT: A 115 ASP cc_start: 0.8023 (p0) cc_final: 0.7212 (p0) REVERT: A 117 LEU cc_start: 0.8265 (mt) cc_final: 0.7942 (tt) REVERT: A 121 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8309 (ttp80) REVERT: A 122 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 127 LYS cc_start: 0.8349 (tppt) cc_final: 0.7970 (mmmt) REVERT: A 157 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7085 (mm-30) REVERT: A 159 LYS cc_start: 0.7344 (mtmt) cc_final: 0.6908 (mtmm) REVERT: A 165 HIS cc_start: 0.6672 (m90) cc_final: 0.6300 (m90) REVERT: A 170 MET cc_start: 0.6912 (mmp) cc_final: 0.6492 (mmp) REVERT: A 191 GLU cc_start: 0.7430 (pp20) cc_final: 0.7078 (tm-30) REVERT: A 196 GLU cc_start: 0.7663 (pp20) cc_final: 0.7170 (pp20) REVERT: A 199 MET cc_start: 0.7783 (mmm) cc_final: 0.7431 (mmp) REVERT: A 209 ARG cc_start: 0.7522 (mtm180) cc_final: 0.7124 (mtm180) REVERT: A 225 LEU cc_start: 0.5376 (mt) cc_final: 0.5074 (mt) REVERT: A 267 GLU cc_start: 0.7459 (tp30) cc_final: 0.7205 (tp30) REVERT: A 294 LYS cc_start: 0.8443 (mmmm) cc_final: 0.8039 (mmmm) REVERT: A 297 LYS cc_start: 0.8224 (ptpt) cc_final: 0.8020 (ptpt) REVERT: A 301 PRO cc_start: 0.7392 (Cg_exo) cc_final: 0.7146 (Cg_endo) REVERT: A 311 VAL cc_start: 0.8262 (p) cc_final: 0.7843 (t) REVERT: A 352 TRP cc_start: 0.7874 (t60) cc_final: 0.7450 (t60) REVERT: A 358 ASN cc_start: 0.8107 (t0) cc_final: 0.7898 (t0) REVERT: A 361 PHE cc_start: 0.7177 (m-80) cc_final: 0.6192 (m-80) REVERT: A 382 ILE cc_start: 0.7252 (mm) cc_final: 0.6892 (pt) REVERT: A 383 TYR cc_start: 0.5814 (m-80) cc_final: 0.5472 (m-80) REVERT: A 439 MET cc_start: 0.5135 (ptt) cc_final: 0.4740 (ptt) REVERT: A 443 PHE cc_start: 0.8437 (t80) cc_final: 0.8154 (t80) REVERT: A 454 MET cc_start: 0.7349 (tpp) cc_final: 0.6974 (tpp) REVERT: A 502 TYR cc_start: 0.5861 (t80) cc_final: 0.3969 (t80) REVERT: E 22 PHE cc_start: 0.6792 (m-80) cc_final: 0.6541 (m-80) REVERT: E 23 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6782 (mp0) REVERT: E 48 HIS cc_start: 0.5125 (t-90) cc_final: 0.4330 (t-90) REVERT: C 28 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7654 (tptp) REVERT: C 33 ILE cc_start: 0.9000 (mm) cc_final: 0.8717 (mm) REVERT: C 43 GLU cc_start: 0.7354 (tp30) cc_final: 0.6429 (tp30) REVERT: C 48 ASN cc_start: 0.8238 (t0) cc_final: 0.6779 (t0) REVERT: C 62 TYR cc_start: 0.7995 (t80) cc_final: 0.7552 (t80) REVERT: C 68 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8192 (mptt) REVERT: C 71 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7528 (tm-30) REVERT: C 72 LYS cc_start: 0.8453 (tttt) cc_final: 0.8010 (tptm) REVERT: C 83 GLU cc_start: 0.7659 (tp30) cc_final: 0.7142 (tp30) REVERT: C 91 GLU cc_start: 0.7267 (tp30) cc_final: 0.6986 (mm-30) REVERT: C 124 MET cc_start: 0.2430 (tmm) cc_final: 0.2078 (tmm) REVERT: C 125 TYR cc_start: 0.4773 (t80) cc_final: 0.4397 (t80) REVERT: C 126 MET cc_start: 0.8053 (tmm) cc_final: 0.7835 (tmm) REVERT: C 127 ASP cc_start: 0.6617 (p0) cc_final: 0.6258 (p0) REVERT: C 153 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7370 (mmm-85) REVERT: C 163 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7687 (mm110) REVERT: C 167 ASP cc_start: 0.7393 (t0) cc_final: 0.6926 (t70) REVERT: C 188 GLN cc_start: 0.8104 (tp40) cc_final: 0.7656 (tp40) REVERT: C 204 ASP cc_start: 0.7204 (t0) cc_final: 0.6935 (t0) REVERT: C 206 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6567 (mp0) REVERT: C 215 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: C 222 GLN cc_start: 0.7711 (tp40) cc_final: 0.7293 (tm-30) REVERT: C 224 PHE cc_start: 0.6845 (m-80) cc_final: 0.5808 (m-80) REVERT: C 235 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7937 (mtmm) REVERT: C 238 GLU cc_start: 0.7404 (tp30) cc_final: 0.6781 (tm-30) REVERT: C 243 GLU cc_start: 0.8280 (pt0) cc_final: 0.7529 (pp20) REVERT: C 244 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7373 (tp30) REVERT: C 246 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7483 (tm-30) REVERT: C 248 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8175 (p) REVERT: C 250 HIS cc_start: 0.7813 (t-90) cc_final: 0.7261 (t-90) REVERT: C 258 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7041 (mm-30) REVERT: C 262 LYS cc_start: 0.8057 (tmtm) cc_final: 0.7396 (ttpp) REVERT: C 274 LYS cc_start: 0.8307 (tppt) cc_final: 0.8082 (tppt) REVERT: C 282 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7396 (t) REVERT: C 288 LEU cc_start: 0.9024 (tp) cc_final: 0.8494 (tp) REVERT: C 292 LYS cc_start: 0.8420 (mmmm) cc_final: 0.7952 (mmtm) REVERT: C 299 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7452 (ttm) REVERT: C 301 LYS cc_start: 0.8351 (ptpt) cc_final: 0.8078 (ptpp) REVERT: C 306 VAL cc_start: 0.8592 (t) cc_final: 0.8253 (p) REVERT: C 315 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7098 (mm-30) REVERT: C 346 LEU cc_start: 0.8204 (tp) cc_final: 0.7968 (tp) REVERT: C 353 ASP cc_start: 0.7899 (t0) cc_final: 0.7525 (t70) REVERT: C 360 PHE cc_start: 0.8198 (m-10) cc_final: 0.7935 (m-10) REVERT: C 368 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6662 (tm-30) REVERT: C 369 THR cc_start: 0.8199 (p) cc_final: 0.7721 (t) REVERT: C 373 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.6004 (t0) REVERT: C 394 ASP cc_start: 0.7958 (t0) cc_final: 0.7613 (t0) REVERT: C 395 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8415 (mmmt) REVERT: C 409 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7138 (pt0) REVERT: C 412 LEU cc_start: 0.8720 (mt) cc_final: 0.8258 (pp) REVERT: C 413 ASP cc_start: 0.8364 (m-30) cc_final: 0.8004 (m-30) REVERT: C 418 LEU cc_start: 0.8744 (tt) cc_final: 0.8437 (tp) REVERT: C 424 GLU cc_start: 0.7299 (mp0) cc_final: 0.7005 (mp0) REVERT: C 431 TYR cc_start: 0.8091 (m-80) cc_final: 0.7294 (m-80) REVERT: C 438 ARG cc_start: 0.7856 (tpm170) cc_final: 0.7241 (tpm170) REVERT: C 441 LEU cc_start: 0.8300 (mt) cc_final: 0.7884 (mt) REVERT: C 454 MET cc_start: 0.8124 (tmm) cc_final: 0.7902 (tmm) REVERT: C 457 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8621 (mmmt) REVERT: C 473 MET cc_start: 0.7804 (mmt) cc_final: 0.7002 (mmt) REVERT: C 484 MET cc_start: 0.3071 (OUTLIER) cc_final: 0.2541 (tpt) REVERT: C 554 MET cc_start: 0.6517 (tpp) cc_final: 0.6115 (tpp) REVERT: C 684 SER cc_start: 0.7367 (p) cc_final: 0.6845 (p) REVERT: C 685 ASP cc_start: 0.7918 (t0) cc_final: 0.7650 (t0) REVERT: C 687 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5916 (pt0) REVERT: C 688 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7594 (mmm-85) REVERT: C 692 ARG cc_start: 0.8495 (tpp-160) cc_final: 0.8213 (mmp80) REVERT: B 19 GLU cc_start: 0.7635 (pp20) cc_final: 0.7075 (pp20) REVERT: B 24 PHE cc_start: 0.8529 (m-10) cc_final: 0.8317 (m-80) REVERT: B 29 LEU cc_start: 0.8330 (mp) cc_final: 0.8044 (mp) REVERT: B 32 ASP cc_start: 0.8033 (p0) cc_final: 0.7410 (p0) REVERT: B 46 LYS cc_start: 0.8817 (mttt) cc_final: 0.8490 (mttm) REVERT: B 55 TYR cc_start: 0.8548 (t80) cc_final: 0.7361 (t80) REVERT: B 57 ARG cc_start: 0.8551 (ptm160) cc_final: 0.8205 (ttm110) REVERT: B 61 MET cc_start: 0.7111 (tmm) cc_final: 0.6627 (tmm) REVERT: B 69 GLN cc_start: 0.7868 (tt0) cc_final: 0.7450 (tt0) REVERT: B 72 VAL cc_start: 0.8887 (m) cc_final: 0.8419 (p) REVERT: B 85 ILE cc_start: 0.8767 (mt) cc_final: 0.8454 (tp) REVERT: B 105 TYR cc_start: 0.7895 (t80) cc_final: 0.7501 (t80) REVERT: B 106 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 112 GLN cc_start: 0.7894 (mm-40) cc_final: 0.6311 (mm-40) REVERT: B 114 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6339 (mm-30) REVERT: B 123 TYR cc_start: 0.7704 (t80) cc_final: 0.7018 (t80) REVERT: B 132 ASN cc_start: 0.8074 (p0) cc_final: 0.7754 (p0) REVERT: B 136 LEU cc_start: 0.8156 (mt) cc_final: 0.7854 (mm) REVERT: B 149 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7659 (tptp) REVERT: B 153 LYS cc_start: 0.8501 (tptm) cc_final: 0.8058 (tptm) REVERT: B 154 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7477 (mtp85) REVERT: B 155 MET cc_start: 0.7903 (tpt) cc_final: 0.7387 (tpp) REVERT: B 170 MET cc_start: 0.7860 (mmm) cc_final: 0.7606 (mmm) REVERT: B 184 ASP cc_start: 0.8045 (t70) cc_final: 0.7537 (t0) REVERT: B 199 MET cc_start: 0.7607 (mmp) cc_final: 0.7327 (mmp) REVERT: B 202 LEU cc_start: 0.7953 (mt) cc_final: 0.7708 (mt) REVERT: B 203 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 209 ARG cc_start: 0.8199 (mmt90) cc_final: 0.7513 (mmt90) REVERT: B 212 TYR cc_start: 0.7936 (m-10) cc_final: 0.7625 (m-80) REVERT: B 242 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8008 (mmtt) REVERT: B 245 VAL cc_start: 0.6965 (t) cc_final: 0.6622 (p) REVERT: B 267 GLU cc_start: 0.7097 (tp30) cc_final: 0.6685 (tp30) REVERT: B 269 MET cc_start: 0.5405 (mmp) cc_final: 0.5041 (mmp) REVERT: B 307 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8097 (mmtm) REVERT: B 363 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8227 (mmtp) REVERT: B 381 TYR cc_start: 0.7617 (m-80) cc_final: 0.6886 (m-80) REVERT: B 383 TYR cc_start: 0.5645 (m-80) cc_final: 0.5113 (m-80) REVERT: B 429 ASP cc_start: 0.8031 (m-30) cc_final: 0.7123 (m-30) REVERT: B 430 CYS cc_start: 0.5798 (m) cc_final: 0.5322 (t) REVERT: B 436 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6216 (tt) REVERT: B 469 ASP cc_start: 0.7572 (t70) cc_final: 0.6959 (t0) REVERT: B 470 LYS cc_start: 0.7063 (mttm) cc_final: 0.6670 (mtpp) REVERT: B 472 PHE cc_start: 0.6082 (m-80) cc_final: 0.5334 (m-80) REVERT: B 502 TYR cc_start: 0.6754 (t80) cc_final: 0.6073 (t80) REVERT: B 534 LEU cc_start: 0.6216 (tp) cc_final: 0.5877 (tt) REVERT: F 35 ASP cc_start: 0.7412 (t0) cc_final: 0.7150 (t70) REVERT: F 58 TYR cc_start: 0.8192 (t80) cc_final: 0.7822 (t80) REVERT: F 60 ASN cc_start: 0.8140 (m-40) cc_final: 0.7893 (m-40) REVERT: F 62 TYR cc_start: 0.7998 (t80) cc_final: 0.7369 (t80) REVERT: F 63 THR cc_start: 0.7431 (t) cc_final: 0.7113 (p) REVERT: F 64 MET cc_start: 0.7379 (tpt) cc_final: 0.6978 (tpt) REVERT: F 68 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8364 (mttm) REVERT: F 78 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7954 (ttm-80) REVERT: F 79 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6748 (tp30) REVERT: F 113 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7753 (tp40) REVERT: F 116 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8211 (tpp) REVERT: F 125 TYR cc_start: 0.5667 (t80) cc_final: 0.5453 (t80) REVERT: F 126 MET cc_start: 0.8303 (tmt) cc_final: 0.7914 (tmm) REVERT: F 128 ARG cc_start: 0.6601 (mtm-85) cc_final: 0.5184 (mtm-85) REVERT: F 139 VAL cc_start: 0.7514 (m) cc_final: 0.6900 (t) REVERT: F 140 TYR cc_start: 0.8031 (t80) cc_final: 0.7545 (t80) REVERT: F 145 ILE cc_start: 0.8842 (mt) cc_final: 0.8550 (tt) REVERT: F 153 ARG cc_start: 0.7807 (mtt180) cc_final: 0.7454 (mtt180) REVERT: F 154 TYR cc_start: 0.7205 (t80) cc_final: 0.5602 (t80) REVERT: F 160 HIS cc_start: 0.8116 (t-90) cc_final: 0.7916 (t-90) REVERT: F 167 ASP cc_start: 0.7084 (t0) cc_final: 0.6719 (t0) REVERT: F 168 MET cc_start: 0.7206 (ptp) cc_final: 0.6728 (ptp) REVERT: F 188 GLN cc_start: 0.7929 (tp40) cc_final: 0.7612 (tp40) REVERT: F 223 LYS cc_start: 0.7760 (tmtp) cc_final: 0.7408 (ttpt) REVERT: F 224 PHE cc_start: 0.6518 (m-10) cc_final: 0.6166 (m-10) REVERT: F 233 TYR cc_start: 0.7621 (t80) cc_final: 0.7137 (t80) REVERT: F 234 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8130 (tt) REVERT: F 235 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8265 (mmmm) REVERT: F 240 ARG cc_start: 0.7963 (mmt180) cc_final: 0.7635 (tpp80) REVERT: F 243 GLU cc_start: 0.7567 (pp20) cc_final: 0.7166 (pp20) REVERT: F 246 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7214 (tp30) REVERT: F 249 MET cc_start: 0.7743 (ppp) cc_final: 0.7340 (ppp) REVERT: F 257 GLU cc_start: 0.7407 (pp20) cc_final: 0.7060 (pp20) REVERT: F 258 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7623 (mp0) REVERT: F 262 LYS cc_start: 0.8232 (tmtt) cc_final: 0.8019 (tmtt) REVERT: F 265 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7165 (mm-30) REVERT: F 266 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7858 (ttp80) REVERT: F 270 SER cc_start: 0.8555 (m) cc_final: 0.8058 (t) REVERT: F 272 HIS cc_start: 0.6055 (m-70) cc_final: 0.5776 (m170) REVERT: F 274 LYS cc_start: 0.8172 (tppt) cc_final: 0.7649 (tmmt) REVERT: F 287 MET cc_start: 0.7669 (ptm) cc_final: 0.7098 (ppp) REVERT: F 295 ASP cc_start: 0.7335 (m-30) cc_final: 0.6814 (m-30) REVERT: F 303 PHE cc_start: 0.7918 (m-80) cc_final: 0.7425 (m-80) REVERT: F 322 ARG cc_start: 0.8092 (mmt90) cc_final: 0.7780 (mmt-90) REVERT: F 332 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6176 (pm20) REVERT: F 353 ASP cc_start: 0.7365 (t0) cc_final: 0.7090 (t0) REVERT: F 423 GLN cc_start: 0.8182 (tt0) cc_final: 0.7626 (tt0) REVERT: F 457 LYS cc_start: 0.8493 (mmmt) cc_final: 0.7826 (mmtt) REVERT: F 490 HIS cc_start: 0.6827 (m90) cc_final: 0.6614 (m-70) REVERT: F 539 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.6212 (m-80) REVERT: F 671 ARG cc_start: 0.6460 (tpt-90) cc_final: 0.5846 (tpt90) REVERT: F 689 LYS cc_start: 0.8024 (pttm) cc_final: 0.7817 (pttm) REVERT: F 734 PHE cc_start: 0.6903 (p90) cc_final: 0.6690 (p90) REVERT: D 42 CYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5700 (m) outliers start: 97 outliers final: 47 residues processed: 792 average time/residue: 0.1808 time to fit residues: 213.4071 Evaluate side-chains 774 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 711 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 539 TYR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 42 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 38 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 215 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 ASN E 77 HIS C 45 GLN C 84 HIS C 100 ASN C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.168046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.141634 restraints weight = 50356.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.145934 restraints weight = 27364.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.148735 restraints weight = 16853.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.150617 restraints weight = 11348.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.151844 restraints weight = 8243.738| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.627 22753 Z= 0.394 Angle : 0.685 13.833 30696 Z= 0.351 Chirality : 0.044 0.266 3385 Planarity : 0.005 0.058 3934 Dihedral : 4.519 29.471 3006 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.72 % Favored : 91.21 % Rotamer: Outliers : 4.49 % Allowed : 21.85 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.16), residues: 2718 helix: 0.83 (0.15), residues: 1262 sheet: -0.95 (0.30), residues: 265 loop : -2.40 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 266 TYR 0.022 0.002 TYR F 130 PHE 0.039 0.002 PHE B 56 TRP 0.022 0.002 TRP A 509 HIS 0.015 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00339 (22731) covalent geometry : angle 0.68030 (30684) hydrogen bonds : bond 0.04504 ( 1102) hydrogen bonds : angle 4.86263 ( 3228) metal coordination : bond 0.34715 ( 22) metal coordination : angle 4.15030 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 728 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7798 (pt) REVERT: A 13 TYR cc_start: 0.7062 (t80) cc_final: 0.6681 (t80) REVERT: A 19 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7552 (pp20) REVERT: A 20 GLN cc_start: 0.8790 (mm-40) cc_final: 0.7710 (mm110) REVERT: A 24 PHE cc_start: 0.8569 (m-10) cc_final: 0.8294 (m-80) REVERT: A 26 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7369 (mt-10) REVERT: A 29 LEU cc_start: 0.8657 (mp) cc_final: 0.8322 (mm) REVERT: A 34 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8659 (m) REVERT: A 37 VAL cc_start: 0.8679 (t) cc_final: 0.8321 (m) REVERT: A 47 MET cc_start: 0.7485 (ttt) cc_final: 0.6878 (ttt) REVERT: A 57 ARG cc_start: 0.8345 (ptm160) cc_final: 0.7994 (ttm-80) REVERT: A 60 PHE cc_start: 0.8537 (m-80) cc_final: 0.8224 (m-10) REVERT: A 84 ILE cc_start: 0.8662 (tp) cc_final: 0.8304 (tt) REVERT: A 87 THR cc_start: 0.8573 (t) cc_final: 0.8157 (p) REVERT: A 88 TYR cc_start: 0.8429 (t80) cc_final: 0.7384 (t80) REVERT: A 90 TYR cc_start: 0.7953 (m-80) cc_final: 0.7585 (m-80) REVERT: A 106 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 112 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7778 (mm-40) REVERT: A 115 ASP cc_start: 0.7998 (p0) cc_final: 0.7105 (p0) REVERT: A 118 GLN cc_start: 0.8259 (tt0) cc_final: 0.7682 (tt0) REVERT: A 121 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8334 (ttp80) REVERT: A 122 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 127 LYS cc_start: 0.8485 (tppt) cc_final: 0.8057 (mmmt) REVERT: A 147 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7395 (mt-10) REVERT: A 149 LYS cc_start: 0.8153 (tttt) cc_final: 0.7749 (ttmt) REVERT: A 157 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6964 (mm-30) REVERT: A 159 LYS cc_start: 0.7260 (mtmt) cc_final: 0.7023 (mtmm) REVERT: A 165 HIS cc_start: 0.6760 (m90) cc_final: 0.6556 (m90) REVERT: A 170 MET cc_start: 0.6777 (mmp) cc_final: 0.6413 (mmp) REVERT: A 191 GLU cc_start: 0.7416 (pp20) cc_final: 0.7072 (tm-30) REVERT: A 196 GLU cc_start: 0.7792 (pp20) cc_final: 0.7334 (pp20) REVERT: A 199 MET cc_start: 0.7842 (mmm) cc_final: 0.7453 (mmp) REVERT: A 209 ARG cc_start: 0.7515 (mtm180) cc_final: 0.7162 (mtm180) REVERT: A 267 GLU cc_start: 0.7490 (tp30) cc_final: 0.7001 (tp30) REVERT: A 294 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8104 (mmmm) REVERT: A 297 LYS cc_start: 0.8127 (ptpt) cc_final: 0.7891 (ptpt) REVERT: A 357 GLN cc_start: 0.7571 (mm-40) cc_final: 0.6605 (mm-40) REVERT: A 358 ASN cc_start: 0.8197 (t0) cc_final: 0.7914 (t0) REVERT: A 361 PHE cc_start: 0.7190 (m-80) cc_final: 0.6259 (m-80) REVERT: A 382 ILE cc_start: 0.7264 (mm) cc_final: 0.7045 (mm) REVERT: A 383 TYR cc_start: 0.5688 (m-80) cc_final: 0.5303 (m-80) REVERT: A 443 PHE cc_start: 0.8397 (t80) cc_final: 0.8142 (t80) REVERT: A 454 MET cc_start: 0.7498 (tpp) cc_final: 0.7128 (tpp) REVERT: A 502 TYR cc_start: 0.5685 (t80) cc_final: 0.4631 (t80) REVERT: A 583 VAL cc_start: 0.6510 (OUTLIER) cc_final: 0.6184 (m) REVERT: E 23 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7094 (mp0) REVERT: E 48 HIS cc_start: 0.5189 (t-90) cc_final: 0.4517 (t-90) REVERT: C 28 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7687 (tptp) REVERT: C 33 ILE cc_start: 0.8990 (mm) cc_final: 0.8724 (mm) REVERT: C 62 TYR cc_start: 0.8031 (t80) cc_final: 0.7687 (t80) REVERT: C 68 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8183 (mptt) REVERT: C 71 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7511 (tm-30) REVERT: C 72 LYS cc_start: 0.8462 (tttt) cc_final: 0.8019 (tptm) REVERT: C 83 GLU cc_start: 0.7686 (tp30) cc_final: 0.7022 (tp30) REVERT: C 118 MET cc_start: 0.7312 (mtm) cc_final: 0.7096 (mtm) REVERT: C 124 MET cc_start: 0.2797 (tmm) cc_final: 0.2302 (tmm) REVERT: C 125 TYR cc_start: 0.4874 (t80) cc_final: 0.4423 (t80) REVERT: C 126 MET cc_start: 0.8038 (tmm) cc_final: 0.7763 (tmm) REVERT: C 127 ASP cc_start: 0.6680 (p0) cc_final: 0.6150 (p0) REVERT: C 153 ARG cc_start: 0.7851 (mtt180) cc_final: 0.7388 (mmm-85) REVERT: C 163 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7745 (mm110) REVERT: C 188 GLN cc_start: 0.8023 (tp40) cc_final: 0.7609 (tp40) REVERT: C 193 LEU cc_start: 0.8907 (tp) cc_final: 0.8688 (tp) REVERT: C 204 ASP cc_start: 0.7237 (t0) cc_final: 0.6959 (t0) REVERT: C 215 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: C 222 GLN cc_start: 0.7826 (tp40) cc_final: 0.7328 (tm-30) REVERT: C 224 PHE cc_start: 0.6673 (m-80) cc_final: 0.5835 (m-10) REVERT: C 235 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7895 (mtmm) REVERT: C 238 GLU cc_start: 0.7437 (tp30) cc_final: 0.6775 (tm-30) REVERT: C 243 GLU cc_start: 0.8286 (pt0) cc_final: 0.7528 (pp20) REVERT: C 244 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7400 (tp30) REVERT: C 246 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7476 (tm-30) REVERT: C 250 HIS cc_start: 0.7868 (t-90) cc_final: 0.7162 (t-90) REVERT: C 258 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7169 (mm-30) REVERT: C 262 LYS cc_start: 0.8050 (tmtm) cc_final: 0.7358 (ttpp) REVERT: C 266 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7403 (ttp80) REVERT: C 274 LYS cc_start: 0.8378 (tppt) cc_final: 0.8023 (tppt) REVERT: C 282 SER cc_start: 0.7755 (m) cc_final: 0.7388 (t) REVERT: C 288 LEU cc_start: 0.8896 (tp) cc_final: 0.8500 (tp) REVERT: C 292 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8071 (mmtm) REVERT: C 301 LYS cc_start: 0.8358 (ptpt) cc_final: 0.8076 (ptpp) REVERT: C 306 VAL cc_start: 0.8629 (t) cc_final: 0.8300 (p) REVERT: C 315 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7024 (tt0) REVERT: C 346 LEU cc_start: 0.8250 (tp) cc_final: 0.8000 (tp) REVERT: C 353 ASP cc_start: 0.7968 (t0) cc_final: 0.7645 (t0) REVERT: C 354 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7582 (ttp-110) REVERT: C 368 GLN cc_start: 0.7311 (tm-30) cc_final: 0.6681 (tm-30) REVERT: C 369 THR cc_start: 0.8013 (p) cc_final: 0.7674 (t) REVERT: C 373 ASP cc_start: 0.6285 (OUTLIER) cc_final: 0.6002 (t0) REVERT: C 394 ASP cc_start: 0.7954 (t0) cc_final: 0.7604 (t0) REVERT: C 395 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8260 (mmmm) REVERT: C 412 LEU cc_start: 0.8712 (mt) cc_final: 0.8463 (mm) REVERT: C 413 ASP cc_start: 0.8487 (m-30) cc_final: 0.8186 (m-30) REVERT: C 416 MET cc_start: 0.7178 (tpp) cc_final: 0.6778 (tpp) REVERT: C 418 LEU cc_start: 0.8796 (tt) cc_final: 0.8556 (tp) REVERT: C 423 GLN cc_start: 0.7677 (pm20) cc_final: 0.6593 (pt0) REVERT: C 424 GLU cc_start: 0.7405 (mp0) cc_final: 0.6734 (mp0) REVERT: C 431 TYR cc_start: 0.8090 (m-80) cc_final: 0.7482 (m-10) REVERT: C 438 ARG cc_start: 0.7816 (tpm170) cc_final: 0.7311 (tpm170) REVERT: C 441 LEU cc_start: 0.8296 (mt) cc_final: 0.7923 (mt) REVERT: C 473 MET cc_start: 0.7819 (mmt) cc_final: 0.7124 (mmt) REVERT: C 476 ASP cc_start: 0.7994 (t70) cc_final: 0.7737 (t0) REVERT: C 484 MET cc_start: 0.2936 (OUTLIER) cc_final: 0.2401 (tpt) REVERT: C 554 MET cc_start: 0.6539 (tpp) cc_final: 0.6148 (tpp) REVERT: C 684 SER cc_start: 0.7629 (p) cc_final: 0.7083 (p) REVERT: C 685 ASP cc_start: 0.7988 (t0) cc_final: 0.7710 (t0) REVERT: C 687 GLU cc_start: 0.6570 (pp20) cc_final: 0.6167 (pp20) REVERT: C 688 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7496 (mmm-85) REVERT: C 692 ARG cc_start: 0.8467 (tpp-160) cc_final: 0.8219 (mmp80) REVERT: B 19 GLU cc_start: 0.7643 (pp20) cc_final: 0.7051 (pp20) REVERT: B 24 PHE cc_start: 0.8552 (m-10) cc_final: 0.8322 (m-80) REVERT: B 29 LEU cc_start: 0.8323 (mp) cc_final: 0.8054 (mp) REVERT: B 32 ASP cc_start: 0.8056 (p0) cc_final: 0.7450 (p0) REVERT: B 46 LYS cc_start: 0.8805 (mttt) cc_final: 0.8465 (mttm) REVERT: B 57 ARG cc_start: 0.8524 (ptm160) cc_final: 0.8269 (ttm110) REVERT: B 61 MET cc_start: 0.7112 (tmm) cc_final: 0.6633 (tmm) REVERT: B 69 GLN cc_start: 0.7848 (tt0) cc_final: 0.7586 (tt0) REVERT: B 72 VAL cc_start: 0.8873 (m) cc_final: 0.8380 (p) REVERT: B 85 ILE cc_start: 0.8749 (mt) cc_final: 0.8427 (tp) REVERT: B 105 TYR cc_start: 0.7903 (t80) cc_final: 0.7701 (t80) REVERT: B 106 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7570 (mt-10) REVERT: B 112 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7404 (mm-40) REVERT: B 114 GLU cc_start: 0.6603 (tm-30) cc_final: 0.6314 (mm-30) REVERT: B 123 TYR cc_start: 0.7812 (t80) cc_final: 0.7117 (t80) REVERT: B 136 LEU cc_start: 0.8157 (mt) cc_final: 0.7896 (mm) REVERT: B 149 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7662 (tptm) REVERT: B 153 LYS cc_start: 0.8535 (tptm) cc_final: 0.7892 (ttmm) REVERT: B 154 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7469 (mtp85) REVERT: B 155 MET cc_start: 0.7921 (tpt) cc_final: 0.7426 (tpp) REVERT: B 170 MET cc_start: 0.7831 (mmm) cc_final: 0.7589 (mmm) REVERT: B 184 ASP cc_start: 0.8052 (t70) cc_final: 0.7580 (t0) REVERT: B 199 MET cc_start: 0.7629 (mmp) cc_final: 0.7345 (mmp) REVERT: B 203 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6972 (mm-30) REVERT: B 209 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7707 (mmt90) REVERT: B 212 TYR cc_start: 0.7865 (m-10) cc_final: 0.7554 (m-80) REVERT: B 242 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7883 (mmtt) REVERT: B 267 GLU cc_start: 0.7133 (tp30) cc_final: 0.6922 (tp30) REVERT: B 307 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8090 (mmtm) REVERT: B 361 PHE cc_start: 0.7658 (t80) cc_final: 0.7350 (t80) REVERT: B 363 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8319 (mmtp) REVERT: B 381 TYR cc_start: 0.7584 (m-80) cc_final: 0.6763 (m-80) REVERT: B 383 TYR cc_start: 0.5570 (m-80) cc_final: 0.5090 (m-80) REVERT: B 429 ASP cc_start: 0.8106 (m-30) cc_final: 0.7332 (m-30) REVERT: B 454 MET cc_start: 0.7406 (tpp) cc_final: 0.7061 (tpp) REVERT: B 469 ASP cc_start: 0.7631 (t70) cc_final: 0.7025 (t0) REVERT: B 472 PHE cc_start: 0.6070 (m-80) cc_final: 0.5374 (m-80) REVERT: B 502 TYR cc_start: 0.6751 (t80) cc_final: 0.6072 (t80) REVERT: B 534 LEU cc_start: 0.6250 (tp) cc_final: 0.5880 (tt) REVERT: F 28 LYS cc_start: 0.7979 (mmmm) cc_final: 0.7430 (mmmm) REVERT: F 35 ASP cc_start: 0.7414 (t0) cc_final: 0.7181 (t70) REVERT: F 47 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7849 (mmmt) REVERT: F 56 GLU cc_start: 0.7756 (mp0) cc_final: 0.7449 (mp0) REVERT: F 62 TYR cc_start: 0.8012 (t80) cc_final: 0.7243 (t80) REVERT: F 63 THR cc_start: 0.7449 (t) cc_final: 0.7128 (p) REVERT: F 64 MET cc_start: 0.7444 (tpt) cc_final: 0.7032 (tpt) REVERT: F 68 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8368 (mttm) REVERT: F 78 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7936 (ttm-80) REVERT: F 79 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6658 (tp30) REVERT: F 113 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7538 (tp40) REVERT: F 116 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8161 (tpp) REVERT: F 118 MET cc_start: 0.7530 (mtm) cc_final: 0.7167 (mtm) REVERT: F 126 MET cc_start: 0.8299 (tmt) cc_final: 0.7995 (tmm) REVERT: F 140 TYR cc_start: 0.8033 (t80) cc_final: 0.7160 (t80) REVERT: F 145 ILE cc_start: 0.8849 (mt) cc_final: 0.8573 (mm) REVERT: F 148 ARG cc_start: 0.8452 (ttp-170) cc_final: 0.8216 (ttm170) REVERT: F 150 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7553 (mm-40) REVERT: F 153 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7578 (mmt180) REVERT: F 154 TYR cc_start: 0.7144 (t80) cc_final: 0.5572 (t80) REVERT: F 160 HIS cc_start: 0.8144 (t-90) cc_final: 0.7933 (t-90) REVERT: F 167 ASP cc_start: 0.7125 (t0) cc_final: 0.6739 (t0) REVERT: F 168 MET cc_start: 0.7215 (ptp) cc_final: 0.6732 (ptp) REVERT: F 188 GLN cc_start: 0.7909 (tp40) cc_final: 0.7573 (tp40) REVERT: F 223 LYS cc_start: 0.7780 (tmtp) cc_final: 0.7450 (ttpt) REVERT: F 234 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.8001 (tt) REVERT: F 235 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8227 (mmmm) REVERT: F 236 LYS cc_start: 0.8388 (ttmt) cc_final: 0.7889 (ttmt) REVERT: F 240 ARG cc_start: 0.7924 (mmt180) cc_final: 0.7604 (tpp80) REVERT: F 243 GLU cc_start: 0.7589 (pp20) cc_final: 0.7121 (pp20) REVERT: F 246 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7209 (tp30) REVERT: F 249 MET cc_start: 0.7756 (ppp) cc_final: 0.7329 (ppp) REVERT: F 258 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7705 (mp0) REVERT: F 262 LYS cc_start: 0.8244 (tmtt) cc_final: 0.8022 (tmtt) REVERT: F 265 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7211 (mm-30) REVERT: F 266 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7861 (ttp80) REVERT: F 270 SER cc_start: 0.8519 (m) cc_final: 0.8081 (t) REVERT: F 274 LYS cc_start: 0.8244 (tppt) cc_final: 0.7721 (tmmt) REVERT: F 287 MET cc_start: 0.7679 (ptm) cc_final: 0.7274 (ppp) REVERT: F 295 ASP cc_start: 0.7343 (m-30) cc_final: 0.6824 (m-30) REVERT: F 303 PHE cc_start: 0.7961 (m-80) cc_final: 0.7341 (m-80) REVERT: F 311 LYS cc_start: 0.7866 (tmmt) cc_final: 0.7401 (ttmm) REVERT: F 322 ARG cc_start: 0.8175 (mmt90) cc_final: 0.7719 (mmt180) REVERT: F 323 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7672 (tm-30) REVERT: F 332 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6300 (pm20) REVERT: F 352 PHE cc_start: 0.8024 (m-80) cc_final: 0.7762 (m-80) REVERT: F 353 ASP cc_start: 0.7281 (t0) cc_final: 0.7028 (t0) REVERT: F 368 GLN cc_start: 0.7365 (tm-30) cc_final: 0.7112 (tm-30) REVERT: F 414 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8719 (mmtm) REVERT: F 423 GLN cc_start: 0.8102 (tt0) cc_final: 0.7579 (tt0) REVERT: F 457 LYS cc_start: 0.8241 (mmmt) cc_final: 0.7727 (mmtt) REVERT: F 539 TYR cc_start: 0.6404 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: F 551 GLN cc_start: 0.3190 (OUTLIER) cc_final: 0.2220 (pm20) REVERT: F 671 ARG cc_start: 0.6530 (tpt-90) cc_final: 0.6159 (tpt-90) REVERT: F 673 LYS cc_start: 0.8044 (pptt) cc_final: 0.7793 (pptt) REVERT: F 687 GLU cc_start: 0.4702 (OUTLIER) cc_final: 0.1947 (tt0) REVERT: D 30 VAL cc_start: 0.7577 (p) cc_final: 0.7064 (m) REVERT: D 42 CYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5722 (m) outliers start: 111 outliers final: 62 residues processed: 789 average time/residue: 0.1662 time to fit residues: 195.1860 Evaluate side-chains 767 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 691 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 539 TYR Chi-restraints excluded: chain F residue 551 GLN Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 687 GLU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 68 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 196 optimal weight: 0.4980 chunk 123 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 135 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN B 324 GLN B 357 GLN F 60 ASN F 106 ASN ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 729 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.167533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.141198 restraints weight = 49128.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.145469 restraints weight = 26875.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.148139 restraints weight = 16635.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.150093 restraints weight = 11340.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.151266 restraints weight = 8247.172| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22753 Z= 0.169 Angle : 0.702 13.011 30696 Z= 0.358 Chirality : 0.044 0.211 3385 Planarity : 0.004 0.054 3934 Dihedral : 4.627 27.720 3006 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.98 % Favored : 90.95 % Rotamer: Outliers : 4.65 % Allowed : 23.51 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.16), residues: 2718 helix: 0.76 (0.15), residues: 1261 sheet: -1.04 (0.31), residues: 262 loop : -2.43 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 397 TYR 0.023 0.002 TYR F 130 PHE 0.028 0.002 PHE B 56 TRP 0.023 0.002 TRP B 233 HIS 0.020 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00350 (22731) covalent geometry : angle 0.69613 (30684) hydrogen bonds : bond 0.04518 ( 1102) hydrogen bonds : angle 4.90267 ( 3228) metal coordination : bond 0.01391 ( 22) metal coordination : angle 4.46855 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 706 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7797 (pt) REVERT: A 13 TYR cc_start: 0.7180 (t80) cc_final: 0.6774 (t80) REVERT: A 20 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8072 (mm110) REVERT: A 22 LYS cc_start: 0.8595 (ttmt) cc_final: 0.7808 (ttmt) REVERT: A 23 LEU cc_start: 0.8441 (mt) cc_final: 0.8203 (tp) REVERT: A 26 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7438 (mt-10) REVERT: A 29 LEU cc_start: 0.8708 (mp) cc_final: 0.8419 (mm) REVERT: A 47 MET cc_start: 0.7453 (ttt) cc_final: 0.6879 (ttt) REVERT: A 57 ARG cc_start: 0.8361 (ptm160) cc_final: 0.7819 (ttm-80) REVERT: A 59 MET cc_start: 0.7708 (ttt) cc_final: 0.7398 (ttp) REVERT: A 66 GLU cc_start: 0.7912 (pm20) cc_final: 0.7280 (mp0) REVERT: A 84 ILE cc_start: 0.8677 (tp) cc_final: 0.8298 (tt) REVERT: A 87 THR cc_start: 0.8584 (t) cc_final: 0.8162 (p) REVERT: A 106 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 112 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8061 (tp40) REVERT: A 115 ASP cc_start: 0.7989 (p0) cc_final: 0.7298 (p0) REVERT: A 118 GLN cc_start: 0.8237 (tt0) cc_final: 0.7732 (tt0) REVERT: A 122 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 127 LYS cc_start: 0.8431 (tppt) cc_final: 0.7951 (mmmt) REVERT: A 147 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 149 LYS cc_start: 0.8152 (tttt) cc_final: 0.7744 (ttmt) REVERT: A 157 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6982 (mm-30) REVERT: A 159 LYS cc_start: 0.7301 (mtmt) cc_final: 0.7088 (mtmm) REVERT: A 170 MET cc_start: 0.6849 (mmp) cc_final: 0.6376 (mmp) REVERT: A 191 GLU cc_start: 0.7427 (pp20) cc_final: 0.7088 (tm-30) REVERT: A 196 GLU cc_start: 0.7781 (pp20) cc_final: 0.6843 (pp20) REVERT: A 199 MET cc_start: 0.7940 (mmm) cc_final: 0.7571 (mmp) REVERT: A 209 ARG cc_start: 0.7562 (mtm180) cc_final: 0.7149 (mtm180) REVERT: A 211 GLN cc_start: 0.7765 (pm20) cc_final: 0.7557 (pm20) REVERT: A 225 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5359 (mt) REVERT: A 267 GLU cc_start: 0.7506 (tp30) cc_final: 0.6969 (tp30) REVERT: A 291 GLN cc_start: 0.8184 (mp10) cc_final: 0.7788 (mp10) REVERT: A 294 LYS cc_start: 0.8520 (mmmm) cc_final: 0.8104 (mmmm) REVERT: A 297 LYS cc_start: 0.8133 (ptpt) cc_final: 0.7843 (ptpt) REVERT: A 311 VAL cc_start: 0.8310 (p) cc_final: 0.8102 (t) REVERT: A 352 TRP cc_start: 0.7820 (t60) cc_final: 0.7568 (t60) REVERT: A 357 GLN cc_start: 0.7587 (mm-40) cc_final: 0.6703 (mm-40) REVERT: A 358 ASN cc_start: 0.8228 (t0) cc_final: 0.7981 (t0) REVERT: A 361 PHE cc_start: 0.7189 (m-80) cc_final: 0.6351 (m-80) REVERT: A 382 ILE cc_start: 0.7313 (mm) cc_final: 0.7047 (mm) REVERT: A 383 TYR cc_start: 0.5687 (m-80) cc_final: 0.5329 (m-80) REVERT: A 454 MET cc_start: 0.7425 (tpp) cc_final: 0.7175 (tpp) REVERT: A 536 VAL cc_start: 0.7656 (m) cc_final: 0.7402 (p) REVERT: A 586 LEU cc_start: 0.8459 (mt) cc_final: 0.7976 (mp) REVERT: E 23 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7219 (mp0) REVERT: C 28 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7691 (tptp) REVERT: C 33 ILE cc_start: 0.8956 (mm) cc_final: 0.8674 (tt) REVERT: C 43 GLU cc_start: 0.7435 (tp30) cc_final: 0.6443 (tp30) REVERT: C 48 ASN cc_start: 0.8361 (t0) cc_final: 0.6797 (t0) REVERT: C 62 TYR cc_start: 0.8027 (t80) cc_final: 0.7614 (t80) REVERT: C 68 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8227 (mptt) REVERT: C 71 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 72 LYS cc_start: 0.8497 (tttt) cc_final: 0.8064 (tptm) REVERT: C 83 GLU cc_start: 0.7682 (tp30) cc_final: 0.7328 (tp30) REVERT: C 89 VAL cc_start: 0.7994 (m) cc_final: 0.7773 (t) REVERT: C 118 MET cc_start: 0.7314 (mtm) cc_final: 0.7089 (mtp) REVERT: C 124 MET cc_start: 0.2790 (tmm) cc_final: 0.2428 (tmm) REVERT: C 125 TYR cc_start: 0.4870 (t80) cc_final: 0.4573 (t80) REVERT: C 126 MET cc_start: 0.8075 (tmm) cc_final: 0.7818 (tmm) REVERT: C 127 ASP cc_start: 0.6728 (p0) cc_final: 0.6512 (p0) REVERT: C 153 ARG cc_start: 0.7845 (mtt180) cc_final: 0.7314 (mmm-85) REVERT: C 163 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7827 (mm110) REVERT: C 188 GLN cc_start: 0.8118 (tp40) cc_final: 0.7699 (tp40) REVERT: C 204 ASP cc_start: 0.7270 (t0) cc_final: 0.7003 (t0) REVERT: C 206 GLU cc_start: 0.6246 (mp0) cc_final: 0.5920 (mp0) REVERT: C 215 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: C 220 GLU cc_start: 0.6839 (tp30) cc_final: 0.6503 (tp30) REVERT: C 222 GLN cc_start: 0.7734 (tp40) cc_final: 0.7294 (tm-30) REVERT: C 224 PHE cc_start: 0.6703 (m-80) cc_final: 0.6003 (m-10) REVERT: C 235 LYS cc_start: 0.8338 (mmmt) cc_final: 0.7991 (ptpt) REVERT: C 238 GLU cc_start: 0.7419 (tp30) cc_final: 0.6529 (tm-30) REVERT: C 243 GLU cc_start: 0.8293 (pt0) cc_final: 0.7523 (pp20) REVERT: C 244 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7457 (tp30) REVERT: C 246 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7459 (tm-30) REVERT: C 250 HIS cc_start: 0.7960 (t-90) cc_final: 0.7306 (t-90) REVERT: C 258 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7254 (mm-30) REVERT: C 262 LYS cc_start: 0.8060 (tmtm) cc_final: 0.7402 (ttpp) REVERT: C 266 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7359 (ttp80) REVERT: C 274 LYS cc_start: 0.8393 (tppt) cc_final: 0.8008 (tppt) REVERT: C 282 SER cc_start: 0.7621 (m) cc_final: 0.7205 (t) REVERT: C 288 LEU cc_start: 0.8858 (tp) cc_final: 0.8578 (tp) REVERT: C 292 LYS cc_start: 0.8483 (mmmm) cc_final: 0.7977 (mmtm) REVERT: C 301 LYS cc_start: 0.8397 (ptpt) cc_final: 0.8070 (ptpp) REVERT: C 306 VAL cc_start: 0.8630 (t) cc_final: 0.8304 (p) REVERT: C 315 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7214 (tm-30) REVERT: C 346 LEU cc_start: 0.8253 (tp) cc_final: 0.8022 (tp) REVERT: C 353 ASP cc_start: 0.8004 (t0) cc_final: 0.7663 (t0) REVERT: C 354 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7695 (ttp-110) REVERT: C 368 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6666 (tm-30) REVERT: C 369 THR cc_start: 0.8118 (p) cc_final: 0.7761 (t) REVERT: C 373 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.6094 (t0) REVERT: C 394 ASP cc_start: 0.7956 (t0) cc_final: 0.7576 (t0) REVERT: C 395 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8207 (mmmm) REVERT: C 409 GLU cc_start: 0.8102 (pt0) cc_final: 0.7666 (pp20) REVERT: C 412 LEU cc_start: 0.8713 (mt) cc_final: 0.8456 (mm) REVERT: C 413 ASP cc_start: 0.8482 (m-30) cc_final: 0.7950 (m-30) REVERT: C 416 MET cc_start: 0.7161 (tpp) cc_final: 0.6879 (tpp) REVERT: C 418 LEU cc_start: 0.8816 (tt) cc_final: 0.8520 (tp) REVERT: C 423 GLN cc_start: 0.7683 (pm20) cc_final: 0.6606 (pt0) REVERT: C 424 GLU cc_start: 0.7402 (mp0) cc_final: 0.6681 (mp0) REVERT: C 431 TYR cc_start: 0.8265 (m-80) cc_final: 0.7542 (m-10) REVERT: C 438 ARG cc_start: 0.7839 (tpm170) cc_final: 0.7220 (tpm170) REVERT: C 441 LEU cc_start: 0.8303 (mt) cc_final: 0.7893 (mt) REVERT: C 473 MET cc_start: 0.7898 (mmt) cc_final: 0.7052 (mmt) REVERT: C 476 ASP cc_start: 0.8000 (t70) cc_final: 0.7720 (t0) REVERT: C 477 MET cc_start: 0.7782 (tmm) cc_final: 0.7568 (tmm) REVERT: C 554 MET cc_start: 0.6621 (tpp) cc_final: 0.6207 (tpp) REVERT: C 603 MET cc_start: 0.7739 (ptm) cc_final: 0.7466 (ptm) REVERT: C 684 SER cc_start: 0.7902 (p) cc_final: 0.7323 (p) REVERT: C 685 ASP cc_start: 0.8048 (t0) cc_final: 0.7843 (t0) REVERT: C 687 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6020 (pp20) REVERT: C 692 ARG cc_start: 0.8435 (tpp-160) cc_final: 0.8217 (mmp80) REVERT: B 19 GLU cc_start: 0.7662 (pp20) cc_final: 0.7048 (pp20) REVERT: B 24 PHE cc_start: 0.8642 (m-10) cc_final: 0.8394 (m-80) REVERT: B 29 LEU cc_start: 0.8313 (mp) cc_final: 0.8044 (mp) REVERT: B 32 ASP cc_start: 0.8067 (p0) cc_final: 0.7733 (p0) REVERT: B 46 LYS cc_start: 0.8836 (mttt) cc_final: 0.8508 (mttm) REVERT: B 57 ARG cc_start: 0.8544 (ptm160) cc_final: 0.8308 (ttm110) REVERT: B 61 MET cc_start: 0.7098 (tmm) cc_final: 0.6648 (tmm) REVERT: B 69 GLN cc_start: 0.7898 (tt0) cc_final: 0.7646 (tt0) REVERT: B 72 VAL cc_start: 0.8863 (m) cc_final: 0.8397 (p) REVERT: B 85 ILE cc_start: 0.8750 (mt) cc_final: 0.8426 (tp) REVERT: B 106 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 112 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7526 (mm-40) REVERT: B 114 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6385 (mm-30) REVERT: B 123 TYR cc_start: 0.7863 (t80) cc_final: 0.7197 (t80) REVERT: B 145 CYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7964 (m) REVERT: B 149 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7585 (tptm) REVERT: B 153 LYS cc_start: 0.8571 (tptm) cc_final: 0.7832 (ttmm) REVERT: B 154 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7464 (mtp85) REVERT: B 155 MET cc_start: 0.7831 (tpt) cc_final: 0.7408 (tpp) REVERT: B 170 MET cc_start: 0.7889 (mmm) cc_final: 0.7621 (mmm) REVERT: B 177 LEU cc_start: 0.7945 (tp) cc_final: 0.7703 (tp) REVERT: B 184 ASP cc_start: 0.8022 (t70) cc_final: 0.7616 (t0) REVERT: B 195 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7539 (ttt180) REVERT: B 199 MET cc_start: 0.7666 (mmp) cc_final: 0.7393 (mmp) REVERT: B 209 ARG cc_start: 0.8166 (mmt90) cc_final: 0.7676 (mmt90) REVERT: B 212 TYR cc_start: 0.7896 (m-10) cc_final: 0.7603 (m-80) REVERT: B 242 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7869 (mmtt) REVERT: B 267 GLU cc_start: 0.7021 (tp30) cc_final: 0.6719 (tp30) REVERT: B 269 MET cc_start: 0.6067 (mmp) cc_final: 0.5780 (mmp) REVERT: B 307 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8005 (mmtm) REVERT: B 363 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8255 (mmtp) REVERT: B 381 TYR cc_start: 0.7522 (m-80) cc_final: 0.6715 (m-80) REVERT: B 383 TYR cc_start: 0.5608 (m-80) cc_final: 0.5129 (m-80) REVERT: B 429 ASP cc_start: 0.8120 (m-30) cc_final: 0.7104 (m-30) REVERT: B 454 MET cc_start: 0.7404 (tpp) cc_final: 0.6913 (tpp) REVERT: B 469 ASP cc_start: 0.7618 (t70) cc_final: 0.6775 (t0) REVERT: B 470 LYS cc_start: 0.7142 (mttm) cc_final: 0.6830 (mtpp) REVERT: B 472 PHE cc_start: 0.6102 (m-80) cc_final: 0.5396 (m-80) REVERT: B 502 TYR cc_start: 0.6873 (t80) cc_final: 0.6548 (t80) REVERT: B 534 LEU cc_start: 0.6376 (tp) cc_final: 0.5983 (tt) REVERT: B 538 MET cc_start: 0.5877 (pmm) cc_final: 0.5613 (pmm) REVERT: B 583 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7302 (t) REVERT: F 28 LYS cc_start: 0.7764 (mmmm) cc_final: 0.7476 (mmmm) REVERT: F 35 ASP cc_start: 0.7451 (t0) cc_final: 0.7181 (t70) REVERT: F 56 GLU cc_start: 0.7970 (mp0) cc_final: 0.7525 (pm20) REVERT: F 60 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7979 (m-40) REVERT: F 62 TYR cc_start: 0.8073 (t80) cc_final: 0.7264 (t80) REVERT: F 63 THR cc_start: 0.7466 (t) cc_final: 0.7169 (p) REVERT: F 64 MET cc_start: 0.7555 (tpt) cc_final: 0.7058 (tpt) REVERT: F 68 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8366 (mttm) REVERT: F 78 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7924 (ttm-80) REVERT: F 79 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6586 (tp30) REVERT: F 103 GLN cc_start: 0.8456 (tp40) cc_final: 0.7948 (tp40) REVERT: F 113 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7490 (tp40) REVERT: F 116 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8250 (tpp) REVERT: F 118 MET cc_start: 0.7508 (mtm) cc_final: 0.7158 (mtm) REVERT: F 126 MET cc_start: 0.8085 (tmt) cc_final: 0.7450 (tmm) REVERT: F 140 TYR cc_start: 0.8036 (t80) cc_final: 0.6943 (t80) REVERT: F 145 ILE cc_start: 0.8859 (mt) cc_final: 0.8546 (mm) REVERT: F 148 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.8159 (ttm170) REVERT: F 150 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7511 (mm-40) REVERT: F 153 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7409 (mtt180) REVERT: F 154 TYR cc_start: 0.7171 (t80) cc_final: 0.5659 (t80) REVERT: F 158 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7733 (ttm-80) REVERT: F 167 ASP cc_start: 0.7190 (t0) cc_final: 0.6808 (t0) REVERT: F 168 MET cc_start: 0.7344 (ptp) cc_final: 0.6766 (ptp) REVERT: F 180 ARG cc_start: 0.7756 (ptp-110) cc_final: 0.7322 (ptp-110) REVERT: F 183 ILE cc_start: 0.8829 (mm) cc_final: 0.8554 (mm) REVERT: F 223 LYS cc_start: 0.7857 (tmtp) cc_final: 0.7541 (ptmt) REVERT: F 233 TYR cc_start: 0.7735 (t80) cc_final: 0.7269 (t80) REVERT: F 235 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8267 (mmmm) REVERT: F 240 ARG cc_start: 0.7878 (mmt180) cc_final: 0.7629 (tpp80) REVERT: F 243 GLU cc_start: 0.7625 (pp20) cc_final: 0.7155 (pp20) REVERT: F 246 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7216 (tp30) REVERT: F 249 MET cc_start: 0.7764 (ppp) cc_final: 0.7346 (ppp) REVERT: F 258 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7859 (mp0) REVERT: F 262 LYS cc_start: 0.8228 (tmtt) cc_final: 0.8021 (tmtt) REVERT: F 265 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7214 (mm-30) REVERT: F 266 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7858 (ttp80) REVERT: F 270 SER cc_start: 0.8572 (m) cc_final: 0.8096 (t) REVERT: F 272 HIS cc_start: 0.6468 (m170) cc_final: 0.6095 (m170) REVERT: F 274 LYS cc_start: 0.8354 (tppt) cc_final: 0.7828 (tmmt) REVERT: F 276 ILE cc_start: 0.7497 (tp) cc_final: 0.7239 (tt) REVERT: F 287 MET cc_start: 0.7673 (ptm) cc_final: 0.7203 (ppp) REVERT: F 295 ASP cc_start: 0.7361 (m-30) cc_final: 0.6820 (m-30) REVERT: F 303 PHE cc_start: 0.8009 (m-80) cc_final: 0.7436 (m-80) REVERT: F 311 LYS cc_start: 0.7880 (tmmt) cc_final: 0.7347 (ttmm) REVERT: F 322 ARG cc_start: 0.8184 (mmt90) cc_final: 0.7689 (mmt180) REVERT: F 332 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6330 (pm20) REVERT: F 352 PHE cc_start: 0.8050 (m-80) cc_final: 0.7782 (m-10) REVERT: F 353 ASP cc_start: 0.7270 (t0) cc_final: 0.7047 (t0) REVERT: F 368 GLN cc_start: 0.7377 (tm-30) cc_final: 0.7091 (tm-30) REVERT: F 370 ILE cc_start: 0.8736 (pt) cc_final: 0.8521 (pt) REVERT: F 414 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8684 (mmtm) REVERT: F 423 GLN cc_start: 0.7794 (tt0) cc_final: 0.7333 (tt0) REVERT: F 671 ARG cc_start: 0.6454 (tpt-90) cc_final: 0.5570 (tpt-90) REVERT: F 673 LYS cc_start: 0.8035 (pptt) cc_final: 0.7745 (pptt) REVERT: F 687 GLU cc_start: 0.4698 (OUTLIER) cc_final: 0.2003 (tt0) REVERT: D 42 CYS cc_start: 0.6255 (OUTLIER) cc_final: 0.5750 (m) outliers start: 115 outliers final: 72 residues processed: 767 average time/residue: 0.1596 time to fit residues: 183.7513 Evaluate side-chains 768 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 683 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 667 SER Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 687 GLU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 71 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 120 optimal weight: 0.3980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 113 GLN C 134 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN B 437 ASN F 60 ASN ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.167761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.141387 restraints weight = 49602.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.145860 restraints weight = 26398.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.148710 restraints weight = 16024.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.150610 restraints weight = 10712.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.151887 restraints weight = 7784.720| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22753 Z= 0.156 Angle : 0.708 13.763 30696 Z= 0.359 Chirality : 0.044 0.284 3385 Planarity : 0.004 0.054 3934 Dihedral : 4.606 26.277 3006 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.27 % Favored : 90.62 % Rotamer: Outliers : 4.57 % Allowed : 24.89 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.16), residues: 2718 helix: 0.74 (0.15), residues: 1259 sheet: -1.07 (0.31), residues: 262 loop : -2.42 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 46 TYR 0.023 0.002 TYR A 402 PHE 0.027 0.002 PHE C 419 TRP 0.036 0.002 TRP A 509 HIS 0.024 0.001 HIS F 490 Details of bonding type rmsd covalent geometry : bond 0.00332 (22731) covalent geometry : angle 0.70311 (30684) hydrogen bonds : bond 0.04410 ( 1102) hydrogen bonds : angle 4.90377 ( 3228) metal coordination : bond 0.01671 ( 22) metal coordination : angle 4.11950 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 704 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8247 (tp) cc_final: 0.7817 (pt) REVERT: A 13 TYR cc_start: 0.7222 (t80) cc_final: 0.6849 (t80) REVERT: A 20 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8144 (mm110) REVERT: A 22 LYS cc_start: 0.8546 (ttmt) cc_final: 0.7790 (ttmt) REVERT: A 26 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7414 (mt-10) REVERT: A 37 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8096 (m) REVERT: A 47 MET cc_start: 0.7484 (ttt) cc_final: 0.6837 (ttt) REVERT: A 57 ARG cc_start: 0.8355 (ptm160) cc_final: 0.7383 (ttm-80) REVERT: A 59 MET cc_start: 0.7584 (ttt) cc_final: 0.7356 (ttp) REVERT: A 66 GLU cc_start: 0.7865 (pm20) cc_final: 0.7440 (pm20) REVERT: A 84 ILE cc_start: 0.8619 (tp) cc_final: 0.8241 (tt) REVERT: A 87 THR cc_start: 0.8558 (t) cc_final: 0.8133 (p) REVERT: A 106 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 109 CYS cc_start: 0.8171 (t) cc_final: 0.6667 (t) REVERT: A 112 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8040 (tp40) REVERT: A 115 ASP cc_start: 0.7978 (p0) cc_final: 0.7140 (p0) REVERT: A 118 GLN cc_start: 0.8239 (tt0) cc_final: 0.7721 (tt0) REVERT: A 122 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 131 GLU cc_start: 0.7392 (pm20) cc_final: 0.7186 (pm20) REVERT: A 147 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7488 (mt-10) REVERT: A 149 LYS cc_start: 0.8128 (tttt) cc_final: 0.7727 (ttmt) REVERT: A 157 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6964 (mm-30) REVERT: A 170 MET cc_start: 0.6832 (mmp) cc_final: 0.6299 (mmp) REVERT: A 191 GLU cc_start: 0.7438 (pp20) cc_final: 0.7099 (tm-30) REVERT: A 196 GLU cc_start: 0.7710 (pp20) cc_final: 0.6979 (pp20) REVERT: A 199 MET cc_start: 0.7944 (mmm) cc_final: 0.7587 (mmp) REVERT: A 209 ARG cc_start: 0.7501 (mtm180) cc_final: 0.6812 (mtm-85) REVERT: A 211 GLN cc_start: 0.7855 (pm20) cc_final: 0.7486 (pm20) REVERT: A 217 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8042 (mp) REVERT: A 225 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5291 (mt) REVERT: A 228 VAL cc_start: 0.5140 (OUTLIER) cc_final: 0.4781 (p) REVERT: A 267 GLU cc_start: 0.7551 (tp30) cc_final: 0.7300 (tp30) REVERT: A 294 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8160 (mmmm) REVERT: A 297 LYS cc_start: 0.8168 (ptpt) cc_final: 0.7888 (ptpt) REVERT: A 311 VAL cc_start: 0.8344 (p) cc_final: 0.8129 (t) REVERT: A 357 GLN cc_start: 0.7590 (mm-40) cc_final: 0.6716 (mm-40) REVERT: A 358 ASN cc_start: 0.8294 (t0) cc_final: 0.8024 (t0) REVERT: A 361 PHE cc_start: 0.7204 (m-80) cc_final: 0.6308 (m-80) REVERT: A 382 ILE cc_start: 0.7270 (mm) cc_final: 0.7008 (mm) REVERT: A 383 TYR cc_start: 0.5729 (m-80) cc_final: 0.5398 (m-80) REVERT: A 434 MET cc_start: 0.2527 (tpt) cc_final: 0.2148 (tpt) REVERT: A 443 PHE cc_start: 0.8100 (t80) cc_final: 0.7758 (t80) REVERT: A 536 VAL cc_start: 0.7685 (m) cc_final: 0.7455 (p) REVERT: E 23 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7219 (mp0) REVERT: C 28 LYS cc_start: 0.8099 (mmmm) cc_final: 0.7684 (tptp) REVERT: C 33 ILE cc_start: 0.8934 (mm) cc_final: 0.8648 (tt) REVERT: C 43 GLU cc_start: 0.7322 (tp30) cc_final: 0.6677 (tp30) REVERT: C 62 TYR cc_start: 0.8017 (t80) cc_final: 0.7447 (t80) REVERT: C 64 MET cc_start: 0.7526 (tpt) cc_final: 0.7173 (tpp) REVERT: C 68 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8247 (mptt) REVERT: C 71 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 72 LYS cc_start: 0.8506 (tttt) cc_final: 0.8090 (tptm) REVERT: C 83 GLU cc_start: 0.7907 (tp30) cc_final: 0.7284 (tp30) REVERT: C 113 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7905 (tp40) REVERT: C 124 MET cc_start: 0.2848 (tmm) cc_final: 0.2280 (tmm) REVERT: C 125 TYR cc_start: 0.4948 (t80) cc_final: 0.4548 (t80) REVERT: C 126 MET cc_start: 0.8086 (tmm) cc_final: 0.7843 (tmm) REVERT: C 127 ASP cc_start: 0.6668 (p0) cc_final: 0.6268 (p0) REVERT: C 134 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8061 (t0) REVERT: C 153 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7373 (mmm-85) REVERT: C 163 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7829 (mm110) REVERT: C 188 GLN cc_start: 0.8126 (tp40) cc_final: 0.7726 (tp40) REVERT: C 191 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7082 (tmm) REVERT: C 199 SER cc_start: 0.8517 (t) cc_final: 0.8241 (p) REVERT: C 204 ASP cc_start: 0.7247 (t0) cc_final: 0.7046 (t0) REVERT: C 206 GLU cc_start: 0.6209 (mp0) cc_final: 0.5741 (mp0) REVERT: C 215 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7373 (mm-30) REVERT: C 222 GLN cc_start: 0.7567 (tp40) cc_final: 0.7188 (tm-30) REVERT: C 224 PHE cc_start: 0.6662 (m-80) cc_final: 0.5781 (m-10) REVERT: C 234 ILE cc_start: 0.8665 (mm) cc_final: 0.8364 (tp) REVERT: C 235 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7936 (ptpp) REVERT: C 238 GLU cc_start: 0.7423 (tp30) cc_final: 0.6581 (tm-30) REVERT: C 243 GLU cc_start: 0.8301 (pt0) cc_final: 0.7519 (pp20) REVERT: C 244 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7439 (tp30) REVERT: C 246 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 250 HIS cc_start: 0.8004 (t-90) cc_final: 0.7253 (t-90) REVERT: C 258 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7273 (mm-30) REVERT: C 262 LYS cc_start: 0.8054 (tmtm) cc_final: 0.7375 (ttpp) REVERT: C 266 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7321 (ttp80) REVERT: C 274 LYS cc_start: 0.8401 (tppt) cc_final: 0.7947 (tppt) REVERT: C 282 SER cc_start: 0.7633 (m) cc_final: 0.7138 (t) REVERT: C 288 LEU cc_start: 0.8848 (tp) cc_final: 0.8589 (tp) REVERT: C 292 LYS cc_start: 0.8337 (mmmm) cc_final: 0.7875 (mmtm) REVERT: C 301 LYS cc_start: 0.8364 (ptpt) cc_final: 0.7980 (ptpp) REVERT: C 306 VAL cc_start: 0.8640 (t) cc_final: 0.8322 (p) REVERT: C 314 CYS cc_start: 0.7510 (m) cc_final: 0.7242 (m) REVERT: C 346 LEU cc_start: 0.8242 (tp) cc_final: 0.8011 (tp) REVERT: C 353 ASP cc_start: 0.7949 (t0) cc_final: 0.7662 (t0) REVERT: C 354 ARG cc_start: 0.8032 (ttp-110) cc_final: 0.7690 (ttp-110) REVERT: C 368 GLN cc_start: 0.7335 (tm-30) cc_final: 0.6672 (tm-30) REVERT: C 369 THR cc_start: 0.8139 (p) cc_final: 0.7716 (t) REVERT: C 373 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.6104 (t0) REVERT: C 394 ASP cc_start: 0.7954 (t0) cc_final: 0.7573 (t0) REVERT: C 395 LYS cc_start: 0.8575 (mmtm) cc_final: 0.8204 (mmmm) REVERT: C 409 GLU cc_start: 0.8074 (pt0) cc_final: 0.7490 (pp20) REVERT: C 412 LEU cc_start: 0.8698 (mt) cc_final: 0.8440 (mm) REVERT: C 413 ASP cc_start: 0.8477 (m-30) cc_final: 0.7855 (m-30) REVERT: C 418 LEU cc_start: 0.8820 (tt) cc_final: 0.8524 (tp) REVERT: C 423 GLN cc_start: 0.7594 (pm20) cc_final: 0.6667 (pt0) REVERT: C 424 GLU cc_start: 0.7436 (mp0) cc_final: 0.6690 (mp0) REVERT: C 431 TYR cc_start: 0.8261 (m-80) cc_final: 0.7517 (m-10) REVERT: C 433 LYS cc_start: 0.7859 (pttp) cc_final: 0.7439 (ptmm) REVERT: C 438 ARG cc_start: 0.7770 (tpm170) cc_final: 0.6941 (tpm170) REVERT: C 441 LEU cc_start: 0.8232 (mt) cc_final: 0.7756 (mt) REVERT: C 473 MET cc_start: 0.7876 (mmt) cc_final: 0.6901 (mmt) REVERT: C 554 MET cc_start: 0.6649 (tpp) cc_final: 0.6227 (tpp) REVERT: C 603 MET cc_start: 0.7599 (ptm) cc_final: 0.7353 (ptm) REVERT: C 684 SER cc_start: 0.7665 (p) cc_final: 0.7293 (p) REVERT: C 685 ASP cc_start: 0.8071 (t0) cc_final: 0.7862 (t0) REVERT: C 687 GLU cc_start: 0.6491 (pp20) cc_final: 0.5997 (pp20) REVERT: C 692 ARG cc_start: 0.8427 (tpp-160) cc_final: 0.8210 (mmp80) REVERT: B 19 GLU cc_start: 0.7590 (pp20) cc_final: 0.6977 (pp20) REVERT: B 24 PHE cc_start: 0.8660 (m-10) cc_final: 0.8189 (m-80) REVERT: B 29 LEU cc_start: 0.8257 (mp) cc_final: 0.8014 (mp) REVERT: B 46 LYS cc_start: 0.8804 (mttt) cc_final: 0.8558 (mttm) REVERT: B 57 ARG cc_start: 0.8535 (ptm160) cc_final: 0.8256 (ttm110) REVERT: B 61 MET cc_start: 0.7102 (tmm) cc_final: 0.6601 (tmm) REVERT: B 69 GLN cc_start: 0.7853 (tt0) cc_final: 0.7615 (tt0) REVERT: B 72 VAL cc_start: 0.8828 (m) cc_final: 0.8381 (p) REVERT: B 85 ILE cc_start: 0.8738 (mt) cc_final: 0.8426 (tp) REVERT: B 103 GLN cc_start: 0.7545 (pm20) cc_final: 0.7226 (pm20) REVERT: B 106 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7318 (mp0) REVERT: B 112 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7330 (mm-40) REVERT: B 114 GLU cc_start: 0.6680 (tm-30) cc_final: 0.6347 (mm-30) REVERT: B 123 TYR cc_start: 0.7864 (t80) cc_final: 0.7207 (t80) REVERT: B 145 CYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7979 (m) REVERT: B 149 LYS cc_start: 0.8008 (ttmm) cc_final: 0.7430 (tptm) REVERT: B 153 LYS cc_start: 0.8545 (tptm) cc_final: 0.7965 (mmmm) REVERT: B 154 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7510 (mtp85) REVERT: B 155 MET cc_start: 0.7751 (tpt) cc_final: 0.7355 (tpp) REVERT: B 170 MET cc_start: 0.7880 (mmm) cc_final: 0.7618 (mmm) REVERT: B 177 LEU cc_start: 0.7913 (tp) cc_final: 0.7701 (tp) REVERT: B 184 ASP cc_start: 0.8005 (t70) cc_final: 0.7607 (t0) REVERT: B 195 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7391 (ttt180) REVERT: B 199 MET cc_start: 0.7765 (mmp) cc_final: 0.7397 (mmp) REVERT: B 209 ARG cc_start: 0.8109 (mmt90) cc_final: 0.7777 (mmt90) REVERT: B 212 TYR cc_start: 0.7914 (m-10) cc_final: 0.7615 (m-80) REVERT: B 242 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7819 (mmtt) REVERT: B 307 LYS cc_start: 0.8456 (mmtt) cc_final: 0.7987 (mmtm) REVERT: B 360 TRP cc_start: 0.7876 (m100) cc_final: 0.5976 (m100) REVERT: B 363 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8116 (mmmm) REVERT: B 381 TYR cc_start: 0.7444 (m-80) cc_final: 0.6692 (m-80) REVERT: B 383 TYR cc_start: 0.5627 (m-80) cc_final: 0.5187 (m-80) REVERT: B 429 ASP cc_start: 0.8128 (m-30) cc_final: 0.7003 (m-30) REVERT: B 430 CYS cc_start: 0.5672 (m) cc_final: 0.4840 (t) REVERT: B 454 MET cc_start: 0.7339 (tpp) cc_final: 0.6762 (tpp) REVERT: B 469 ASP cc_start: 0.7701 (t70) cc_final: 0.7007 (t70) REVERT: B 502 TYR cc_start: 0.6752 (t80) cc_final: 0.6167 (t80) REVERT: B 538 MET cc_start: 0.5817 (pmm) cc_final: 0.5616 (pmm) REVERT: B 583 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7627 (t) REVERT: F 28 LYS cc_start: 0.7784 (mmmm) cc_final: 0.7483 (mmmm) REVERT: F 35 ASP cc_start: 0.7541 (t0) cc_final: 0.7304 (t70) REVERT: F 45 GLN cc_start: 0.8060 (tt0) cc_final: 0.7748 (tp-100) REVERT: F 62 TYR cc_start: 0.8046 (t80) cc_final: 0.7195 (t80) REVERT: F 63 THR cc_start: 0.7415 (t) cc_final: 0.7114 (p) REVERT: F 64 MET cc_start: 0.7477 (tpt) cc_final: 0.7009 (tpt) REVERT: F 68 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8374 (mttm) REVERT: F 78 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7959 (ttm-80) REVERT: F 79 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6584 (tp30) REVERT: F 103 GLN cc_start: 0.8552 (tp40) cc_final: 0.8033 (tp40) REVERT: F 113 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7644 (tp40) REVERT: F 116 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8214 (tpp) REVERT: F 118 MET cc_start: 0.7400 (mtm) cc_final: 0.7120 (mtm) REVERT: F 126 MET cc_start: 0.8031 (tmt) cc_final: 0.7454 (tmm) REVERT: F 140 TYR cc_start: 0.8022 (t80) cc_final: 0.7226 (t80) REVERT: F 145 ILE cc_start: 0.8848 (mt) cc_final: 0.8506 (tt) REVERT: F 150 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7484 (mm-40) REVERT: F 153 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7575 (mmt180) REVERT: F 154 TYR cc_start: 0.7140 (t80) cc_final: 0.5668 (t80) REVERT: F 158 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7272 (ttm-80) REVERT: F 163 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7202 (mm110) REVERT: F 167 ASP cc_start: 0.7243 (t0) cc_final: 0.6862 (t0) REVERT: F 168 MET cc_start: 0.7361 (ptp) cc_final: 0.6817 (ptp) REVERT: F 183 ILE cc_start: 0.8831 (mm) cc_final: 0.8614 (mm) REVERT: F 223 LYS cc_start: 0.7882 (tmtp) cc_final: 0.7636 (ptmt) REVERT: F 233 TYR cc_start: 0.7594 (t80) cc_final: 0.7240 (t80) REVERT: F 235 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8176 (mmmm) REVERT: F 236 LYS cc_start: 0.8311 (ttmm) cc_final: 0.8078 (ttpp) REVERT: F 238 GLU cc_start: 0.8291 (tp30) cc_final: 0.7493 (tp30) REVERT: F 240 ARG cc_start: 0.7846 (mmt180) cc_final: 0.7630 (tpp80) REVERT: F 243 GLU cc_start: 0.7627 (pp20) cc_final: 0.7202 (pp20) REVERT: F 246 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7196 (tp30) REVERT: F 249 MET cc_start: 0.7763 (ppp) cc_final: 0.7346 (ppp) REVERT: F 258 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7875 (mp0) REVERT: F 262 LYS cc_start: 0.8232 (tmtt) cc_final: 0.7988 (tmtt) REVERT: F 265 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7163 (mm-30) REVERT: F 266 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7864 (ttp80) REVERT: F 270 SER cc_start: 0.8581 (m) cc_final: 0.8074 (t) REVERT: F 272 HIS cc_start: 0.6559 (m170) cc_final: 0.6174 (m170) REVERT: F 273 MET cc_start: 0.7380 (ttp) cc_final: 0.7017 (ttp) REVERT: F 274 LYS cc_start: 0.8391 (tppt) cc_final: 0.7865 (tmmt) REVERT: F 276 ILE cc_start: 0.7507 (tp) cc_final: 0.7217 (tt) REVERT: F 287 MET cc_start: 0.7627 (ptm) cc_final: 0.7155 (ppp) REVERT: F 311 LYS cc_start: 0.7767 (tmmt) cc_final: 0.7300 (ttmm) REVERT: F 322 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7669 (mmt180) REVERT: F 332 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6299 (pm20) REVERT: F 360 PHE cc_start: 0.7673 (m-80) cc_final: 0.7193 (m-80) REVERT: F 368 GLN cc_start: 0.7300 (tm-30) cc_final: 0.7036 (tm-30) REVERT: F 369 THR cc_start: 0.7984 (p) cc_final: 0.7637 (t) REVERT: F 414 LYS cc_start: 0.8921 (mmtm) cc_final: 0.8597 (mmtm) REVERT: F 423 GLN cc_start: 0.7616 (tt0) cc_final: 0.7136 (tt0) REVERT: F 484 MET cc_start: 0.2251 (mtp) cc_final: 0.2046 (mtp) REVERT: F 671 ARG cc_start: 0.6390 (tpt-90) cc_final: 0.5986 (tpt-90) REVERT: F 673 LYS cc_start: 0.8003 (pptt) cc_final: 0.7762 (pptt) REVERT: F 687 GLU cc_start: 0.4640 (OUTLIER) cc_final: 0.1950 (tt0) REVERT: D 42 CYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5817 (m) outliers start: 113 outliers final: 75 residues processed: 766 average time/residue: 0.1604 time to fit residues: 183.4556 Evaluate side-chains 776 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 685 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 687 GLU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 198 optimal weight: 0.0570 chunk 229 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 145 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 151 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 113 GLN C 135 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN F 60 ASN ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.168021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.141713 restraints weight = 49377.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.146140 restraints weight = 26236.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.148984 restraints weight = 15964.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.150868 restraints weight = 10673.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.152186 restraints weight = 7744.184| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22753 Z= 0.152 Angle : 0.724 16.415 30696 Z= 0.364 Chirality : 0.044 0.231 3385 Planarity : 0.004 0.055 3934 Dihedral : 4.613 25.128 3006 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.05 % Favored : 90.88 % Rotamer: Outliers : 4.86 % Allowed : 25.21 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.16), residues: 2718 helix: 0.72 (0.15), residues: 1261 sheet: -1.20 (0.30), residues: 273 loop : -2.40 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 383 TYR 0.024 0.002 TYR A 402 PHE 0.025 0.002 PHE B 537 TRP 0.071 0.002 TRP A 509 HIS 0.025 0.001 HIS F 490 Details of bonding type rmsd covalent geometry : bond 0.00325 (22731) covalent geometry : angle 0.71967 (30684) hydrogen bonds : bond 0.04385 ( 1102) hydrogen bonds : angle 4.91767 ( 3228) metal coordination : bond 0.01409 ( 22) metal coordination : angle 3.93413 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 696 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8232 (tp) cc_final: 0.7819 (pt) REVERT: A 13 TYR cc_start: 0.7210 (t80) cc_final: 0.6830 (t80) REVERT: A 22 LYS cc_start: 0.8548 (ttmt) cc_final: 0.7747 (ttmt) REVERT: A 26 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 37 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.7996 (m) REVERT: A 47 MET cc_start: 0.7483 (ttt) cc_final: 0.6841 (ttt) REVERT: A 57 ARG cc_start: 0.8390 (ptm160) cc_final: 0.7486 (ttm-80) REVERT: A 84 ILE cc_start: 0.8633 (tp) cc_final: 0.8239 (tt) REVERT: A 87 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8131 (p) REVERT: A 106 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 109 CYS cc_start: 0.8181 (t) cc_final: 0.6631 (t) REVERT: A 112 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8028 (tp40) REVERT: A 115 ASP cc_start: 0.7980 (p0) cc_final: 0.7118 (p0) REVERT: A 118 GLN cc_start: 0.8253 (tt0) cc_final: 0.7761 (tt0) REVERT: A 122 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 127 LYS cc_start: 0.8482 (mmmm) cc_final: 0.8153 (mmtm) REVERT: A 147 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7487 (mt-10) REVERT: A 149 LYS cc_start: 0.8127 (tttt) cc_final: 0.7704 (ttmt) REVERT: A 154 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7884 (ttm110) REVERT: A 157 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6966 (mm-30) REVERT: A 160 PHE cc_start: 0.5584 (OUTLIER) cc_final: 0.4278 (t80) REVERT: A 170 MET cc_start: 0.6812 (mmp) cc_final: 0.6415 (mmp) REVERT: A 191 GLU cc_start: 0.7508 (pp20) cc_final: 0.7167 (tm-30) REVERT: A 196 GLU cc_start: 0.7695 (pp20) cc_final: 0.7090 (pp20) REVERT: A 199 MET cc_start: 0.8090 (mmm) cc_final: 0.7757 (mmp) REVERT: A 209 ARG cc_start: 0.7419 (mtm180) cc_final: 0.7120 (mtm180) REVERT: A 211 GLN cc_start: 0.7934 (pm20) cc_final: 0.7463 (pm20) REVERT: A 225 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5532 (mt) REVERT: A 267 GLU cc_start: 0.7566 (tp30) cc_final: 0.7194 (tp30) REVERT: A 291 GLN cc_start: 0.8128 (mp10) cc_final: 0.7769 (mp10) REVERT: A 294 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8083 (mmmm) REVERT: A 297 LYS cc_start: 0.8174 (ptpt) cc_final: 0.7876 (ptpt) REVERT: A 311 VAL cc_start: 0.8348 (p) cc_final: 0.8108 (t) REVERT: A 357 GLN cc_start: 0.7620 (mm-40) cc_final: 0.6916 (mm-40) REVERT: A 361 PHE cc_start: 0.7233 (m-80) cc_final: 0.6343 (m-80) REVERT: A 382 ILE cc_start: 0.7283 (mm) cc_final: 0.7013 (mm) REVERT: A 383 TYR cc_start: 0.5760 (m-80) cc_final: 0.5532 (m-80) REVERT: A 430 CYS cc_start: 0.7055 (p) cc_final: 0.6694 (p) REVERT: A 434 MET cc_start: 0.2369 (tpt) cc_final: 0.2027 (tpt) REVERT: A 443 PHE cc_start: 0.8164 (t80) cc_final: 0.7783 (t80) REVERT: A 454 MET cc_start: 0.6251 (tpp) cc_final: 0.5830 (tpp) REVERT: A 502 TYR cc_start: 0.5779 (t80) cc_final: 0.3622 (t80) REVERT: A 536 VAL cc_start: 0.7690 (m) cc_final: 0.7441 (p) REVERT: E 23 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7227 (mp0) REVERT: C 28 LYS cc_start: 0.8096 (mmmm) cc_final: 0.7686 (tptp) REVERT: C 33 ILE cc_start: 0.8960 (mm) cc_final: 0.8660 (tt) REVERT: C 48 ASN cc_start: 0.8343 (t0) cc_final: 0.8125 (t0) REVERT: C 62 TYR cc_start: 0.7955 (t80) cc_final: 0.7371 (t80) REVERT: C 64 MET cc_start: 0.7560 (tpt) cc_final: 0.7171 (tpp) REVERT: C 68 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8248 (mptt) REVERT: C 71 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 72 LYS cc_start: 0.8460 (tttt) cc_final: 0.8066 (tptm) REVERT: C 83 GLU cc_start: 0.7786 (tp30) cc_final: 0.7312 (tp30) REVERT: C 113 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7769 (tp40) REVERT: C 124 MET cc_start: 0.2780 (tmm) cc_final: 0.2305 (tmm) REVERT: C 125 TYR cc_start: 0.4951 (t80) cc_final: 0.4504 (t80) REVERT: C 126 MET cc_start: 0.8084 (tmm) cc_final: 0.7853 (tmm) REVERT: C 127 ASP cc_start: 0.6646 (p0) cc_final: 0.6261 (p0) REVERT: C 153 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7402 (mmm-85) REVERT: C 163 GLN cc_start: 0.8433 (mm-40) cc_final: 0.7738 (mm110) REVERT: C 188 GLN cc_start: 0.8056 (tp40) cc_final: 0.7668 (tp40) REVERT: C 199 SER cc_start: 0.8515 (t) cc_final: 0.8208 (p) REVERT: C 206 GLU cc_start: 0.6175 (mp0) cc_final: 0.5669 (mp0) REVERT: C 220 GLU cc_start: 0.6866 (tp30) cc_final: 0.6399 (tp30) REVERT: C 222 GLN cc_start: 0.7559 (tp40) cc_final: 0.7185 (tm-30) REVERT: C 224 PHE cc_start: 0.6466 (m-80) cc_final: 0.5827 (m-10) REVERT: C 234 ILE cc_start: 0.8693 (mm) cc_final: 0.8256 (tp) REVERT: C 235 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7775 (mtmm) REVERT: C 238 GLU cc_start: 0.7432 (tp30) cc_final: 0.6589 (tm-30) REVERT: C 243 GLU cc_start: 0.8294 (pt0) cc_final: 0.7513 (pp20) REVERT: C 246 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7450 (tm-30) REVERT: C 250 HIS cc_start: 0.7978 (t-90) cc_final: 0.7246 (t-90) REVERT: C 258 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7001 (mp0) REVERT: C 262 LYS cc_start: 0.8054 (tmtm) cc_final: 0.7342 (ttpp) REVERT: C 265 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7135 (mm-30) REVERT: C 266 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7230 (ttp80) REVERT: C 274 LYS cc_start: 0.8407 (tppt) cc_final: 0.7908 (tppt) REVERT: C 282 SER cc_start: 0.7592 (m) cc_final: 0.7359 (m) REVERT: C 288 LEU cc_start: 0.8823 (tp) cc_final: 0.8552 (tp) REVERT: C 292 LYS cc_start: 0.8357 (mmmm) cc_final: 0.7897 (mmtm) REVERT: C 301 LYS cc_start: 0.8360 (ptpt) cc_final: 0.7999 (ptpp) REVERT: C 306 VAL cc_start: 0.8656 (t) cc_final: 0.8301 (p) REVERT: C 346 LEU cc_start: 0.8251 (tp) cc_final: 0.8032 (tp) REVERT: C 353 ASP cc_start: 0.8004 (t0) cc_final: 0.7705 (t0) REVERT: C 354 ARG cc_start: 0.8013 (ttp-110) cc_final: 0.7676 (ttp-110) REVERT: C 368 GLN cc_start: 0.7349 (tm-30) cc_final: 0.6668 (tm-30) REVERT: C 369 THR cc_start: 0.8181 (p) cc_final: 0.7778 (t) REVERT: C 373 ASP cc_start: 0.6634 (OUTLIER) cc_final: 0.6244 (t0) REVERT: C 386 GLU cc_start: 0.8346 (mp0) cc_final: 0.6482 (mp0) REVERT: C 394 ASP cc_start: 0.7968 (t0) cc_final: 0.7584 (t0) REVERT: C 395 LYS cc_start: 0.8573 (mmtm) cc_final: 0.8179 (mmmm) REVERT: C 409 GLU cc_start: 0.8074 (pt0) cc_final: 0.7469 (pp20) REVERT: C 412 LEU cc_start: 0.8685 (mt) cc_final: 0.8426 (mm) REVERT: C 413 ASP cc_start: 0.8480 (m-30) cc_final: 0.7869 (m-30) REVERT: C 418 LEU cc_start: 0.8824 (tt) cc_final: 0.8520 (tp) REVERT: C 423 GLN cc_start: 0.7560 (pm20) cc_final: 0.6753 (pt0) REVERT: C 424 GLU cc_start: 0.7472 (mp0) cc_final: 0.6684 (mp0) REVERT: C 431 TYR cc_start: 0.8257 (m-80) cc_final: 0.6832 (m-10) REVERT: C 438 ARG cc_start: 0.7760 (tpm170) cc_final: 0.6885 (tpm170) REVERT: C 441 LEU cc_start: 0.8220 (mt) cc_final: 0.7721 (mt) REVERT: C 473 MET cc_start: 0.7852 (mmt) cc_final: 0.6953 (mmt) REVERT: C 554 MET cc_start: 0.6641 (tpp) cc_final: 0.6233 (tpp) REVERT: C 603 MET cc_start: 0.7535 (ptm) cc_final: 0.7267 (ptm) REVERT: C 685 ASP cc_start: 0.8083 (t0) cc_final: 0.7841 (t0) REVERT: C 687 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5680 (pp20) REVERT: C 692 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.8151 (mmp80) REVERT: B 19 GLU cc_start: 0.7598 (pp20) cc_final: 0.6981 (pp20) REVERT: B 24 PHE cc_start: 0.8653 (m-10) cc_final: 0.8277 (m-80) REVERT: B 29 LEU cc_start: 0.8272 (mp) cc_final: 0.7969 (mt) REVERT: B 46 LYS cc_start: 0.8821 (mttt) cc_final: 0.8560 (mttm) REVERT: B 57 ARG cc_start: 0.8495 (ptm160) cc_final: 0.8174 (ttm110) REVERT: B 61 MET cc_start: 0.7118 (tmm) cc_final: 0.6599 (tmm) REVERT: B 69 GLN cc_start: 0.7840 (tt0) cc_final: 0.7637 (tt0) REVERT: B 72 VAL cc_start: 0.8773 (m) cc_final: 0.8406 (p) REVERT: B 85 ILE cc_start: 0.8730 (mt) cc_final: 0.8429 (tp) REVERT: B 87 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 103 GLN cc_start: 0.7544 (pm20) cc_final: 0.7332 (pm20) REVERT: B 106 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 112 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7347 (mm-40) REVERT: B 114 GLU cc_start: 0.6669 (tm-30) cc_final: 0.6363 (mm-30) REVERT: B 123 TYR cc_start: 0.7802 (t80) cc_final: 0.7176 (t80) REVERT: B 145 CYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8135 (m) REVERT: B 149 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7375 (tptm) REVERT: B 153 LYS cc_start: 0.8524 (tptm) cc_final: 0.7973 (mmmm) REVERT: B 154 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7636 (mtp85) REVERT: B 155 MET cc_start: 0.7784 (tpt) cc_final: 0.7390 (tpp) REVERT: B 170 MET cc_start: 0.7863 (mmm) cc_final: 0.7597 (mmm) REVERT: B 177 LEU cc_start: 0.7977 (tp) cc_final: 0.7763 (tp) REVERT: B 178 ILE cc_start: 0.8032 (tp) cc_final: 0.7804 (tp) REVERT: B 184 ASP cc_start: 0.7984 (t70) cc_final: 0.7593 (t0) REVERT: B 195 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7312 (ttt180) REVERT: B 199 MET cc_start: 0.7769 (mmp) cc_final: 0.7396 (mmp) REVERT: B 203 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6996 (mm-30) REVERT: B 209 ARG cc_start: 0.8163 (mmt90) cc_final: 0.7863 (mmt90) REVERT: B 212 TYR cc_start: 0.7943 (m-10) cc_final: 0.7631 (m-80) REVERT: B 215 SER cc_start: 0.8230 (m) cc_final: 0.7866 (p) REVERT: B 242 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7836 (mmtt) REVERT: B 267 GLU cc_start: 0.7006 (tp30) cc_final: 0.6753 (tp30) REVERT: B 307 LYS cc_start: 0.8396 (mmtt) cc_final: 0.7888 (mmtm) REVERT: B 360 TRP cc_start: 0.7699 (m100) cc_final: 0.6039 (m100) REVERT: B 363 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8056 (mmmm) REVERT: B 381 TYR cc_start: 0.7373 (m-80) cc_final: 0.6735 (m-80) REVERT: B 383 TYR cc_start: 0.5606 (m-80) cc_final: 0.5143 (m-80) REVERT: B 429 ASP cc_start: 0.8283 (m-30) cc_final: 0.7140 (m-30) REVERT: B 430 CYS cc_start: 0.5579 (m) cc_final: 0.4426 (t) REVERT: B 437 ASN cc_start: 0.6620 (m-40) cc_final: 0.6157 (m-40) REVERT: B 454 MET cc_start: 0.7229 (tpp) cc_final: 0.6730 (tpp) REVERT: B 469 ASP cc_start: 0.7603 (t70) cc_final: 0.6967 (t70) REVERT: B 470 LYS cc_start: 0.7136 (mttm) cc_final: 0.6868 (mtpp) REVERT: B 502 TYR cc_start: 0.6664 (t80) cc_final: 0.6368 (t80) REVERT: B 503 ASP cc_start: 0.7861 (t0) cc_final: 0.7613 (t0) REVERT: B 583 VAL cc_start: 0.7994 (OUTLIER) cc_final: 0.7245 (t) REVERT: F 28 LYS cc_start: 0.7785 (mmmm) cc_final: 0.7482 (mmmm) REVERT: F 35 ASP cc_start: 0.7565 (t0) cc_final: 0.7295 (t70) REVERT: F 53 SER cc_start: 0.7904 (t) cc_final: 0.6788 (t) REVERT: F 56 GLU cc_start: 0.7952 (mp0) cc_final: 0.6953 (pm20) REVERT: F 60 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7932 (m-40) REVERT: F 62 TYR cc_start: 0.8053 (t80) cc_final: 0.7177 (t80) REVERT: F 63 THR cc_start: 0.7473 (t) cc_final: 0.7190 (p) REVERT: F 64 MET cc_start: 0.7506 (tpt) cc_final: 0.7023 (tpt) REVERT: F 68 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8365 (mttm) REVERT: F 78 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7963 (ttm-80) REVERT: F 79 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6550 (tp30) REVERT: F 103 GLN cc_start: 0.8523 (tp40) cc_final: 0.8045 (tp40) REVERT: F 113 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7587 (tp40) REVERT: F 116 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8217 (tpp) REVERT: F 118 MET cc_start: 0.7397 (mtm) cc_final: 0.7132 (mtm) REVERT: F 124 MET cc_start: 0.4437 (tmm) cc_final: 0.3747 (tmm) REVERT: F 126 MET cc_start: 0.8064 (tmt) cc_final: 0.7591 (tmm) REVERT: F 140 TYR cc_start: 0.8015 (t80) cc_final: 0.7091 (t80) REVERT: F 145 ILE cc_start: 0.8757 (mt) cc_final: 0.8395 (tp) REVERT: F 150 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7480 (mm-40) REVERT: F 153 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7589 (mmt180) REVERT: F 154 TYR cc_start: 0.7166 (t80) cc_final: 0.5746 (t80) REVERT: F 158 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7426 (ttm-80) REVERT: F 163 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7200 (mm110) REVERT: F 167 ASP cc_start: 0.7238 (t0) cc_final: 0.6880 (t0) REVERT: F 168 MET cc_start: 0.7423 (ptp) cc_final: 0.6975 (ptp) REVERT: F 188 GLN cc_start: 0.8016 (tp40) cc_final: 0.7790 (tp40) REVERT: F 223 LYS cc_start: 0.7864 (tmtp) cc_final: 0.7633 (ptmt) REVERT: F 233 TYR cc_start: 0.7690 (t80) cc_final: 0.7320 (t80) REVERT: F 243 GLU cc_start: 0.7643 (pp20) cc_final: 0.7239 (pp20) REVERT: F 246 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7147 (tp30) REVERT: F 249 MET cc_start: 0.7768 (ppp) cc_final: 0.7316 (ppp) REVERT: F 258 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7530 (mp0) REVERT: F 262 LYS cc_start: 0.8221 (tmtt) cc_final: 0.7970 (tmtt) REVERT: F 265 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7191 (mm-30) REVERT: F 266 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7836 (ttp80) REVERT: F 270 SER cc_start: 0.8552 (m) cc_final: 0.8009 (t) REVERT: F 272 HIS cc_start: 0.6688 (m170) cc_final: 0.6322 (m170) REVERT: F 274 LYS cc_start: 0.8277 (tppt) cc_final: 0.7745 (tmmt) REVERT: F 276 ILE cc_start: 0.7351 (tp) cc_final: 0.7127 (tt) REVERT: F 287 MET cc_start: 0.7418 (ptm) cc_final: 0.7026 (ppp) REVERT: F 311 LYS cc_start: 0.7776 (tmmt) cc_final: 0.7265 (ttmm) REVERT: F 313 MET cc_start: 0.7364 (mmp) cc_final: 0.6863 (mmp) REVERT: F 317 MET cc_start: 0.7959 (ttp) cc_final: 0.7712 (ptt) REVERT: F 322 ARG cc_start: 0.8176 (mmt90) cc_final: 0.7692 (mmt180) REVERT: F 332 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6296 (pm20) REVERT: F 360 PHE cc_start: 0.7400 (m-80) cc_final: 0.7064 (m-80) REVERT: F 414 LYS cc_start: 0.8929 (mmtm) cc_final: 0.8629 (mmtm) REVERT: F 423 GLN cc_start: 0.7422 (tt0) cc_final: 0.7208 (pt0) REVERT: F 671 ARG cc_start: 0.6329 (tpt-90) cc_final: 0.5944 (tpt-90) REVERT: F 673 LYS cc_start: 0.7981 (pptt) cc_final: 0.7721 (pptt) REVERT: D 42 CYS cc_start: 0.6316 (OUTLIER) cc_final: 0.5882 (m) outliers start: 120 outliers final: 82 residues processed: 758 average time/residue: 0.1677 time to fit residues: 191.9794 Evaluate side-chains 777 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 679 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 729 GLN Chi-restraints excluded: chain C residue 734 PHE Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 184 ARG Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 CYS Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 98 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 205 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 243 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 165 HIS A 316 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 134 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN F 106 ASN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 ASN ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.168176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.142383 restraints weight = 48991.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.146702 restraints weight = 26526.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.149473 restraints weight = 16248.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.151337 restraints weight = 10938.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.152604 restraints weight = 7929.738| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22753 Z= 0.157 Angle : 0.737 14.854 30696 Z= 0.371 Chirality : 0.045 0.303 3385 Planarity : 0.004 0.058 3934 Dihedral : 4.606 25.469 3006 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.20 % Favored : 90.73 % Rotamer: Outliers : 4.33 % Allowed : 25.86 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.16), residues: 2718 helix: 0.67 (0.15), residues: 1262 sheet: -1.22 (0.30), residues: 269 loop : -2.42 (0.16), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 195 TYR 0.024 0.002 TYR B 105 PHE 0.049 0.002 PHE A 256 TRP 0.069 0.002 TRP A 509 HIS 0.023 0.001 HIS F 490 Details of bonding type rmsd covalent geometry : bond 0.00335 (22731) covalent geometry : angle 0.73313 (30684) hydrogen bonds : bond 0.04400 ( 1102) hydrogen bonds : angle 4.94010 ( 3228) metal coordination : bond 0.01339 ( 22) metal coordination : angle 3.85101 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 698 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8192 (tp) cc_final: 0.7805 (pt) REVERT: A 13 TYR cc_start: 0.7250 (t80) cc_final: 0.6823 (t80) REVERT: A 19 GLU cc_start: 0.7064 (pp20) cc_final: 0.6818 (pp20) REVERT: A 22 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8060 (ttmt) REVERT: A 26 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 27 GLN cc_start: 0.8325 (mt0) cc_final: 0.7990 (mt0) REVERT: A 37 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8106 (m) REVERT: A 46 LYS cc_start: 0.8523 (mttt) cc_final: 0.7695 (mmtt) REVERT: A 47 MET cc_start: 0.7419 (ttt) cc_final: 0.6787 (ttt) REVERT: A 57 ARG cc_start: 0.8399 (ptm160) cc_final: 0.7774 (ttp80) REVERT: A 60 PHE cc_start: 0.8335 (m-80) cc_final: 0.7397 (m-10) REVERT: A 84 ILE cc_start: 0.8619 (tp) cc_final: 0.8288 (tt) REVERT: A 87 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8199 (p) REVERT: A 106 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 109 CYS cc_start: 0.8167 (t) cc_final: 0.6579 (t) REVERT: A 112 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8038 (tp40) REVERT: A 115 ASP cc_start: 0.7963 (p0) cc_final: 0.7171 (p0) REVERT: A 118 GLN cc_start: 0.8249 (tt0) cc_final: 0.7798 (tt0) REVERT: A 122 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7553 (mm-30) REVERT: A 127 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8257 (mmtm) REVERT: A 129 ASN cc_start: 0.7580 (p0) cc_final: 0.7347 (p0) REVERT: A 155 MET cc_start: 0.7719 (tpp) cc_final: 0.7517 (tpp) REVERT: A 157 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7058 (mm-30) REVERT: A 159 LYS cc_start: 0.7649 (mmtt) cc_final: 0.7301 (mtmt) REVERT: A 170 MET cc_start: 0.6783 (mmp) cc_final: 0.6429 (mmp) REVERT: A 179 ASP cc_start: 0.7756 (t0) cc_final: 0.7287 (t70) REVERT: A 191 GLU cc_start: 0.7545 (pp20) cc_final: 0.7174 (tm-30) REVERT: A 196 GLU cc_start: 0.7552 (pp20) cc_final: 0.6654 (pp20) REVERT: A 199 MET cc_start: 0.8070 (mmm) cc_final: 0.7703 (mmp) REVERT: A 209 ARG cc_start: 0.7406 (mtm180) cc_final: 0.7089 (mtm180) REVERT: A 211 GLN cc_start: 0.7912 (pm20) cc_final: 0.7440 (pm20) REVERT: A 267 GLU cc_start: 0.7540 (tp30) cc_final: 0.7206 (tp30) REVERT: A 271 PHE cc_start: 0.7552 (m-80) cc_final: 0.7174 (m-80) REVERT: A 272 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7403 (tp) REVERT: A 291 GLN cc_start: 0.8122 (mp10) cc_final: 0.7791 (mp10) REVERT: A 294 LYS cc_start: 0.8520 (mmmm) cc_final: 0.8085 (mmmm) REVERT: A 297 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7813 (ptpp) REVERT: A 357 GLN cc_start: 0.7506 (mm-40) cc_final: 0.6749 (mm-40) REVERT: A 361 PHE cc_start: 0.7261 (m-80) cc_final: 0.6299 (m-80) REVERT: A 382 ILE cc_start: 0.7263 (mm) cc_final: 0.6995 (mm) REVERT: A 383 TYR cc_start: 0.5737 (m-80) cc_final: 0.5483 (m-80) REVERT: A 397 ARG cc_start: 0.7380 (ptp90) cc_final: 0.7138 (ptp90) REVERT: A 430 CYS cc_start: 0.7027 (p) cc_final: 0.6640 (p) REVERT: A 434 MET cc_start: 0.2300 (tpt) cc_final: 0.1988 (tpt) REVERT: A 443 PHE cc_start: 0.8242 (t80) cc_final: 0.7849 (t80) REVERT: A 454 MET cc_start: 0.6051 (tpp) cc_final: 0.5698 (tpp) REVERT: A 502 TYR cc_start: 0.5776 (t80) cc_final: 0.3613 (t80) REVERT: A 536 VAL cc_start: 0.7698 (m) cc_final: 0.7387 (p) REVERT: E 23 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7211 (mp0) REVERT: E 35 TRP cc_start: 0.3399 (m-10) cc_final: 0.3155 (m-10) REVERT: E 48 HIS cc_start: 0.5323 (t-90) cc_final: 0.4760 (t-90) REVERT: E 74 VAL cc_start: 0.6447 (OUTLIER) cc_final: 0.6236 (t) REVERT: C 28 LYS cc_start: 0.8075 (mmmm) cc_final: 0.7709 (tptp) REVERT: C 33 ILE cc_start: 0.9062 (mm) cc_final: 0.8778 (mm) REVERT: C 48 ASN cc_start: 0.8199 (t0) cc_final: 0.7991 (t0) REVERT: C 62 TYR cc_start: 0.7932 (t80) cc_final: 0.7344 (t80) REVERT: C 64 MET cc_start: 0.7524 (tpt) cc_final: 0.7060 (tpp) REVERT: C 68 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8226 (mptt) REVERT: C 71 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 72 LYS cc_start: 0.8459 (tttt) cc_final: 0.8076 (tptm) REVERT: C 83 GLU cc_start: 0.7781 (tp30) cc_final: 0.7349 (tp30) REVERT: C 124 MET cc_start: 0.2727 (tmm) cc_final: 0.2274 (tmm) REVERT: C 125 TYR cc_start: 0.4988 (t80) cc_final: 0.4476 (t80) REVERT: C 126 MET cc_start: 0.8090 (tmm) cc_final: 0.7845 (tmm) REVERT: C 127 ASP cc_start: 0.6558 (p0) cc_final: 0.6210 (p0) REVERT: C 134 ASN cc_start: 0.8422 (t160) cc_final: 0.8220 (t0) REVERT: C 153 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7356 (mmm-85) REVERT: C 163 GLN cc_start: 0.8452 (mm-40) cc_final: 0.7722 (mm110) REVERT: C 188 GLN cc_start: 0.8058 (tp40) cc_final: 0.7664 (tp40) REVERT: C 199 SER cc_start: 0.8489 (t) cc_final: 0.8190 (p) REVERT: C 206 GLU cc_start: 0.6171 (mp0) cc_final: 0.5627 (mp0) REVERT: C 222 GLN cc_start: 0.7523 (tp40) cc_final: 0.7153 (tm-30) REVERT: C 234 ILE cc_start: 0.8622 (mm) cc_final: 0.8157 (tp) REVERT: C 238 GLU cc_start: 0.7381 (tp30) cc_final: 0.6519 (tm-30) REVERT: C 243 GLU cc_start: 0.8297 (pt0) cc_final: 0.7523 (pp20) REVERT: C 246 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 250 HIS cc_start: 0.7991 (t-90) cc_final: 0.7226 (t-90) REVERT: C 258 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6957 (mp0) REVERT: C 262 LYS cc_start: 0.8062 (tmtm) cc_final: 0.7364 (ttpp) REVERT: C 265 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7141 (mm-30) REVERT: C 266 ARG cc_start: 0.7536 (ttp80) cc_final: 0.7183 (ttp80) REVERT: C 274 LYS cc_start: 0.8303 (tppt) cc_final: 0.7846 (tppt) REVERT: C 282 SER cc_start: 0.7604 (m) cc_final: 0.7390 (m) REVERT: C 292 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8046 (mmmm) REVERT: C 301 LYS cc_start: 0.8355 (ptpt) cc_final: 0.8102 (ptpp) REVERT: C 306 VAL cc_start: 0.8660 (t) cc_final: 0.8339 (p) REVERT: C 346 LEU cc_start: 0.8274 (tp) cc_final: 0.8032 (tp) REVERT: C 353 ASP cc_start: 0.7982 (t0) cc_final: 0.7669 (t0) REVERT: C 354 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7553 (ttp-110) REVERT: C 368 GLN cc_start: 0.7339 (tm-30) cc_final: 0.6755 (tm-30) REVERT: C 369 THR cc_start: 0.8227 (p) cc_final: 0.7796 (t) REVERT: C 373 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.6211 (t0) REVERT: C 386 GLU cc_start: 0.8310 (mp0) cc_final: 0.6375 (mp0) REVERT: C 394 ASP cc_start: 0.7923 (t0) cc_final: 0.7545 (t0) REVERT: C 395 LYS cc_start: 0.8565 (mmtm) cc_final: 0.8194 (mmmm) REVERT: C 409 GLU cc_start: 0.8136 (pt0) cc_final: 0.7778 (pp20) REVERT: C 412 LEU cc_start: 0.8675 (mt) cc_final: 0.8411 (mm) REVERT: C 413 ASP cc_start: 0.8458 (m-30) cc_final: 0.7947 (m-30) REVERT: C 418 LEU cc_start: 0.8840 (tt) cc_final: 0.8526 (tp) REVERT: C 423 GLN cc_start: 0.7527 (pm20) cc_final: 0.6772 (pt0) REVERT: C 424 GLU cc_start: 0.7459 (mp0) cc_final: 0.6714 (mp0) REVERT: C 431 TYR cc_start: 0.8261 (m-80) cc_final: 0.6802 (m-10) REVERT: C 438 ARG cc_start: 0.7753 (tpm170) cc_final: 0.6867 (tpm170) REVERT: C 441 LEU cc_start: 0.8242 (mt) cc_final: 0.7701 (mt) REVERT: C 473 MET cc_start: 0.7832 (mmt) cc_final: 0.6948 (mmt) REVERT: C 554 MET cc_start: 0.6630 (tpp) cc_final: 0.6233 (tpp) REVERT: C 685 ASP cc_start: 0.8117 (t0) cc_final: 0.7861 (t0) REVERT: C 692 ARG cc_start: 0.8402 (tpp-160) cc_final: 0.8156 (mmp80) REVERT: B 19 GLU cc_start: 0.7586 (pp20) cc_final: 0.6974 (pp20) REVERT: B 24 PHE cc_start: 0.8632 (m-10) cc_final: 0.8303 (m-80) REVERT: B 29 LEU cc_start: 0.8245 (mp) cc_final: 0.7946 (mt) REVERT: B 46 LYS cc_start: 0.8841 (mttt) cc_final: 0.8597 (mttm) REVERT: B 57 ARG cc_start: 0.8492 (ptm160) cc_final: 0.8095 (ttm170) REVERT: B 61 MET cc_start: 0.7107 (tmm) cc_final: 0.6577 (tmm) REVERT: B 72 VAL cc_start: 0.8763 (m) cc_final: 0.8404 (p) REVERT: B 85 ILE cc_start: 0.8736 (mt) cc_final: 0.8435 (tp) REVERT: B 103 GLN cc_start: 0.7545 (pm20) cc_final: 0.7326 (pm20) REVERT: B 105 TYR cc_start: 0.8045 (t80) cc_final: 0.7788 (t80) REVERT: B 106 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 112 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7344 (mm-40) REVERT: B 114 GLU cc_start: 0.6642 (tm-30) cc_final: 0.6315 (mm-30) REVERT: B 123 TYR cc_start: 0.7813 (t80) cc_final: 0.7220 (t80) REVERT: B 145 CYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8110 (m) REVERT: B 149 LYS cc_start: 0.7914 (ttmm) cc_final: 0.7516 (tptm) REVERT: B 153 LYS cc_start: 0.8462 (tptm) cc_final: 0.7800 (ttmm) REVERT: B 155 MET cc_start: 0.7796 (tpt) cc_final: 0.7403 (tpp) REVERT: B 170 MET cc_start: 0.7833 (mmm) cc_final: 0.7551 (mmm) REVERT: B 177 LEU cc_start: 0.7959 (tp) cc_final: 0.7734 (tp) REVERT: B 178 ILE cc_start: 0.7952 (tp) cc_final: 0.7626 (mm) REVERT: B 184 ASP cc_start: 0.7947 (t70) cc_final: 0.7501 (t0) REVERT: B 195 ARG cc_start: 0.7821 (ttp-170) cc_final: 0.7298 (ttt180) REVERT: B 199 MET cc_start: 0.7712 (mmp) cc_final: 0.7362 (mmp) REVERT: B 209 ARG cc_start: 0.8139 (mmt90) cc_final: 0.7600 (mmt90) REVERT: B 212 TYR cc_start: 0.7834 (m-10) cc_final: 0.7516 (m-80) REVERT: B 215 SER cc_start: 0.8249 (m) cc_final: 0.7897 (p) REVERT: B 242 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7920 (mmtt) REVERT: B 307 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7873 (mmtm) REVERT: B 360 TRP cc_start: 0.7837 (m100) cc_final: 0.5946 (m100) REVERT: B 363 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7921 (mmtp) REVERT: B 381 TYR cc_start: 0.7339 (m-80) cc_final: 0.6868 (m-80) REVERT: B 383 TYR cc_start: 0.5539 (m-80) cc_final: 0.5125 (m-80) REVERT: B 429 ASP cc_start: 0.8284 (m-30) cc_final: 0.7136 (m-30) REVERT: B 430 CYS cc_start: 0.5598 (m) cc_final: 0.4863 (t) REVERT: B 437 ASN cc_start: 0.6526 (m-40) cc_final: 0.6028 (m-40) REVERT: B 454 MET cc_start: 0.7182 (tpp) cc_final: 0.6656 (tpp) REVERT: B 469 ASP cc_start: 0.7530 (t70) cc_final: 0.6796 (t70) REVERT: B 470 LYS cc_start: 0.7234 (mttm) cc_final: 0.6946 (mtpp) REVERT: B 502 TYR cc_start: 0.6601 (t80) cc_final: 0.6357 (t80) REVERT: B 503 ASP cc_start: 0.7889 (t0) cc_final: 0.7616 (t0) REVERT: B 526 ARG cc_start: 0.6007 (mmm-85) cc_final: 0.5432 (mmm-85) REVERT: B 583 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7561 (t) REVERT: F 28 LYS cc_start: 0.7797 (mmmm) cc_final: 0.7481 (mmmm) REVERT: F 35 ASP cc_start: 0.7546 (t0) cc_final: 0.7277 (t70) REVERT: F 53 SER cc_start: 0.7968 (t) cc_final: 0.6846 (t) REVERT: F 56 GLU cc_start: 0.7915 (mp0) cc_final: 0.6939 (pm20) REVERT: F 60 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7821 (m-40) REVERT: F 62 TYR cc_start: 0.8028 (t80) cc_final: 0.7406 (t80) REVERT: F 63 THR cc_start: 0.7431 (t) cc_final: 0.7176 (p) REVERT: F 64 MET cc_start: 0.7470 (tpt) cc_final: 0.6962 (tpt) REVERT: F 68 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8372 (mttm) REVERT: F 78 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7956 (ttm-80) REVERT: F 79 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6520 (tp30) REVERT: F 103 GLN cc_start: 0.8536 (tp40) cc_final: 0.8023 (tp40) REVERT: F 113 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7591 (tp40) REVERT: F 116 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8231 (tpp) REVERT: F 118 MET cc_start: 0.7353 (mtm) cc_final: 0.7091 (mtm) REVERT: F 124 MET cc_start: 0.4443 (tmm) cc_final: 0.3721 (tmm) REVERT: F 126 MET cc_start: 0.8036 (tmt) cc_final: 0.7611 (tmm) REVERT: F 140 TYR cc_start: 0.7998 (t80) cc_final: 0.7082 (t80) REVERT: F 145 ILE cc_start: 0.8784 (mt) cc_final: 0.8398 (tp) REVERT: F 150 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7459 (mm-40) REVERT: F 153 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7540 (mmt180) REVERT: F 154 TYR cc_start: 0.7099 (t80) cc_final: 0.5812 (t80) REVERT: F 158 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7197 (ttm-80) REVERT: F 163 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7191 (mm110) REVERT: F 167 ASP cc_start: 0.7273 (t0) cc_final: 0.6924 (t0) REVERT: F 168 MET cc_start: 0.7706 (ptp) cc_final: 0.7325 (ptp) REVERT: F 188 GLN cc_start: 0.8011 (tp40) cc_final: 0.7795 (tp40) REVERT: F 206 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7172 (tm-30) REVERT: F 223 LYS cc_start: 0.7864 (tmtp) cc_final: 0.7438 (ptpp) REVERT: F 233 TYR cc_start: 0.7717 (t80) cc_final: 0.7175 (t80) REVERT: F 235 LYS cc_start: 0.8433 (mmtp) cc_final: 0.8120 (mppt) REVERT: F 238 GLU cc_start: 0.8215 (tp30) cc_final: 0.7503 (tp30) REVERT: F 246 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7148 (tp30) REVERT: F 249 MET cc_start: 0.7663 (ppp) cc_final: 0.7182 (ppp) REVERT: F 258 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7758 (mp0) REVERT: F 262 LYS cc_start: 0.8203 (tmtt) cc_final: 0.7938 (tmtt) REVERT: F 265 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7213 (mm-30) REVERT: F 266 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7842 (ttp80) REVERT: F 270 SER cc_start: 0.8545 (m) cc_final: 0.7987 (t) REVERT: F 272 HIS cc_start: 0.6603 (m170) cc_final: 0.6189 (m170) REVERT: F 274 LYS cc_start: 0.8260 (tppt) cc_final: 0.7771 (tmmt) REVERT: F 276 ILE cc_start: 0.7371 (tp) cc_final: 0.7140 (tp) REVERT: F 311 LYS cc_start: 0.7878 (tmmt) cc_final: 0.7325 (ttmm) REVERT: F 313 MET cc_start: 0.7514 (mmp) cc_final: 0.6979 (mmm) REVERT: F 322 ARG cc_start: 0.8172 (mmt90) cc_final: 0.7695 (mmt180) REVERT: F 332 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6314 (pm20) REVERT: F 346 LEU cc_start: 0.7714 (tp) cc_final: 0.7374 (pp) REVERT: F 369 THR cc_start: 0.8303 (t) cc_final: 0.7299 (p) REVERT: F 414 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8532 (mmtm) REVERT: F 671 ARG cc_start: 0.6335 (tpt-90) cc_final: 0.6082 (tpt-90) REVERT: F 673 LYS cc_start: 0.8001 (pptt) cc_final: 0.7748 (pptt) REVERT: F 687 GLU cc_start: 0.4667 (OUTLIER) cc_final: 0.2110 (tt0) REVERT: D 42 CYS cc_start: 0.6369 (OUTLIER) cc_final: 0.6013 (m) outliers start: 107 outliers final: 78 residues processed: 753 average time/residue: 0.1807 time to fit residues: 203.4190 Evaluate side-chains 777 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 686 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 734 PHE Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 687 GLU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 212 optimal weight: 0.0270 chunk 207 optimal weight: 0.3980 chunk 231 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 100 ASN C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.166433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.140064 restraints weight = 49597.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.144538 restraints weight = 26686.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.147408 restraints weight = 16297.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.149329 restraints weight = 10926.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.150669 restraints weight = 7922.111| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22753 Z= 0.183 Angle : 0.779 14.597 30696 Z= 0.396 Chirality : 0.046 0.342 3385 Planarity : 0.005 0.059 3934 Dihedral : 4.751 25.339 3006 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.31 % Favored : 90.58 % Rotamer: Outliers : 4.17 % Allowed : 26.71 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.16), residues: 2718 helix: 0.53 (0.14), residues: 1263 sheet: -1.18 (0.30), residues: 264 loop : -2.41 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 46 TYR 0.031 0.002 TYR A 164 PHE 0.041 0.002 PHE A 256 TRP 0.077 0.002 TRP A 509 HIS 0.023 0.001 HIS F 490 Details of bonding type rmsd covalent geometry : bond 0.00384 (22731) covalent geometry : angle 0.77477 (30684) hydrogen bonds : bond 0.04628 ( 1102) hydrogen bonds : angle 5.03751 ( 3228) metal coordination : bond 0.01331 ( 22) metal coordination : angle 4.21803 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 709 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8255 (tp) cc_final: 0.7872 (pt) REVERT: A 13 TYR cc_start: 0.7347 (t80) cc_final: 0.6994 (t80) REVERT: A 22 LYS cc_start: 0.8553 (ttmt) cc_final: 0.7782 (ttmt) REVERT: A 26 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7292 (mt-10) REVERT: A 27 GLN cc_start: 0.8353 (mt0) cc_final: 0.7966 (mt0) REVERT: A 37 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.7915 (m) REVERT: A 46 LYS cc_start: 0.8546 (mttt) cc_final: 0.8298 (mtmt) REVERT: A 47 MET cc_start: 0.7475 (ttt) cc_final: 0.6904 (ttt) REVERT: A 49 LEU cc_start: 0.8224 (mt) cc_final: 0.7910 (mt) REVERT: A 57 ARG cc_start: 0.8420 (ptm160) cc_final: 0.8023 (ttm-80) REVERT: A 59 MET cc_start: 0.7398 (ttp) cc_final: 0.7036 (ttp) REVERT: A 60 PHE cc_start: 0.8280 (m-80) cc_final: 0.7834 (m-10) REVERT: A 84 ILE cc_start: 0.8640 (tp) cc_final: 0.8277 (tt) REVERT: A 87 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8183 (p) REVERT: A 106 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 109 CYS cc_start: 0.8198 (t) cc_final: 0.6639 (t) REVERT: A 112 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8063 (tp40) REVERT: A 115 ASP cc_start: 0.7980 (p0) cc_final: 0.7398 (p0) REVERT: A 118 GLN cc_start: 0.8255 (tt0) cc_final: 0.7961 (tt0) REVERT: A 122 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 127 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8236 (mmtm) REVERT: A 157 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6969 (mm-30) REVERT: A 159 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7451 (mtmt) REVERT: A 170 MET cc_start: 0.6853 (mmp) cc_final: 0.6387 (mmp) REVERT: A 195 ARG cc_start: 0.7861 (ttm170) cc_final: 0.6849 (ttm-80) REVERT: A 196 GLU cc_start: 0.7651 (pp20) cc_final: 0.7276 (pp20) REVERT: A 199 MET cc_start: 0.8144 (mmm) cc_final: 0.7729 (mmp) REVERT: A 209 ARG cc_start: 0.7474 (mtm180) cc_final: 0.7156 (mtm180) REVERT: A 211 GLN cc_start: 0.7965 (pm20) cc_final: 0.7558 (pm20) REVERT: A 225 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5530 (mt) REVERT: A 267 GLU cc_start: 0.7601 (tp30) cc_final: 0.7292 (tp30) REVERT: A 271 PHE cc_start: 0.7605 (m-80) cc_final: 0.7380 (m-10) REVERT: A 272 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7472 (tp) REVERT: A 291 GLN cc_start: 0.8175 (mp10) cc_final: 0.7830 (mp10) REVERT: A 294 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8174 (mmmm) REVERT: A 297 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7835 (ptpp) REVERT: A 357 GLN cc_start: 0.7602 (mm-40) cc_final: 0.6858 (mm-40) REVERT: A 361 PHE cc_start: 0.7269 (m-80) cc_final: 0.6294 (m-80) REVERT: A 382 ILE cc_start: 0.7305 (mm) cc_final: 0.7038 (mm) REVERT: A 397 ARG cc_start: 0.7465 (ptp90) cc_final: 0.7206 (ptp90) REVERT: A 430 CYS cc_start: 0.7067 (p) cc_final: 0.6657 (p) REVERT: A 443 PHE cc_start: 0.8322 (t80) cc_final: 0.7870 (t80) REVERT: A 454 MET cc_start: 0.6153 (tpp) cc_final: 0.5870 (tpp) REVERT: A 502 TYR cc_start: 0.5704 (t80) cc_final: 0.3596 (t80) REVERT: A 536 VAL cc_start: 0.7745 (m) cc_final: 0.7423 (p) REVERT: E 23 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7230 (mp0) REVERT: E 35 TRP cc_start: 0.3412 (m-10) cc_final: 0.3169 (m-10) REVERT: E 48 HIS cc_start: 0.5385 (t-90) cc_final: 0.4822 (t-90) REVERT: C 28 LYS cc_start: 0.8111 (mmmm) cc_final: 0.7757 (tptp) REVERT: C 33 ILE cc_start: 0.9155 (mm) cc_final: 0.8812 (mm) REVERT: C 35 ASP cc_start: 0.7407 (t0) cc_final: 0.7207 (m-30) REVERT: C 62 TYR cc_start: 0.7989 (t80) cc_final: 0.7304 (t80) REVERT: C 64 MET cc_start: 0.7593 (tpt) cc_final: 0.7106 (tpp) REVERT: C 68 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8216 (mptt) REVERT: C 71 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7598 (tm-30) REVERT: C 72 LYS cc_start: 0.8498 (tttt) cc_final: 0.8067 (tptm) REVERT: C 83 GLU cc_start: 0.7804 (tp30) cc_final: 0.7379 (tp30) REVERT: C 124 MET cc_start: 0.3027 (tmm) cc_final: 0.2696 (tmm) REVERT: C 125 TYR cc_start: 0.5061 (t80) cc_final: 0.4652 (t80) REVERT: C 126 MET cc_start: 0.8149 (tmm) cc_final: 0.7941 (tmm) REVERT: C 153 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7382 (mmm-85) REVERT: C 163 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7906 (mm110) REVERT: C 188 GLN cc_start: 0.8087 (tp40) cc_final: 0.7734 (tp40) REVERT: C 191 MET cc_start: 0.8172 (tpp) cc_final: 0.7787 (tpp) REVERT: C 199 SER cc_start: 0.8520 (t) cc_final: 0.8236 (m) REVERT: C 206 GLU cc_start: 0.6242 (mp0) cc_final: 0.5655 (mp0) REVERT: C 222 GLN cc_start: 0.7562 (tp40) cc_final: 0.7133 (tm-30) REVERT: C 224 PHE cc_start: 0.6613 (m-10) cc_final: 0.5706 (m-10) REVERT: C 234 ILE cc_start: 0.8609 (mm) cc_final: 0.8061 (tp) REVERT: C 238 GLU cc_start: 0.7498 (tp30) cc_final: 0.6578 (tm-30) REVERT: C 246 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7511 (tm-30) REVERT: C 247 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7777 (ttm110) REVERT: C 250 HIS cc_start: 0.8009 (t-90) cc_final: 0.7234 (t-90) REVERT: C 258 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7019 (mp0) REVERT: C 262 LYS cc_start: 0.8082 (tmtm) cc_final: 0.7396 (ttmm) REVERT: C 265 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7150 (mm-30) REVERT: C 266 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7300 (ttp80) REVERT: C 274 LYS cc_start: 0.8405 (tppt) cc_final: 0.7697 (tppt) REVERT: C 282 SER cc_start: 0.7742 (m) cc_final: 0.7511 (m) REVERT: C 292 LYS cc_start: 0.8552 (mmmm) cc_final: 0.7956 (mmtm) REVERT: C 301 LYS cc_start: 0.8326 (ptpt) cc_final: 0.8094 (ptpp) REVERT: C 306 VAL cc_start: 0.8724 (t) cc_final: 0.8381 (p) REVERT: C 314 CYS cc_start: 0.7512 (m) cc_final: 0.7295 (m) REVERT: C 346 LEU cc_start: 0.8301 (tp) cc_final: 0.8067 (tp) REVERT: C 353 ASP cc_start: 0.8017 (t0) cc_final: 0.7762 (t0) REVERT: C 368 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6809 (tm-30) REVERT: C 369 THR cc_start: 0.8204 (p) cc_final: 0.7785 (t) REVERT: C 373 ASP cc_start: 0.6614 (OUTLIER) cc_final: 0.6354 (t0) REVERT: C 386 GLU cc_start: 0.8360 (mp0) cc_final: 0.6564 (mp0) REVERT: C 394 ASP cc_start: 0.7952 (t0) cc_final: 0.7570 (t0) REVERT: C 395 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8213 (mmmm) REVERT: C 409 GLU cc_start: 0.8192 (pt0) cc_final: 0.7787 (pp20) REVERT: C 412 LEU cc_start: 0.8705 (mt) cc_final: 0.8440 (mm) REVERT: C 413 ASP cc_start: 0.8497 (m-30) cc_final: 0.7989 (m-30) REVERT: C 418 LEU cc_start: 0.8833 (tt) cc_final: 0.8540 (tp) REVERT: C 423 GLN cc_start: 0.7543 (pm20) cc_final: 0.6746 (pt0) REVERT: C 424 GLU cc_start: 0.7445 (mp0) cc_final: 0.6691 (mp0) REVERT: C 431 TYR cc_start: 0.8363 (m-80) cc_final: 0.6851 (m-10) REVERT: C 554 MET cc_start: 0.6659 (tpp) cc_final: 0.6247 (tpp) REVERT: C 603 MET cc_start: 0.7545 (ptm) cc_final: 0.7307 (ptm) REVERT: C 685 ASP cc_start: 0.8190 (t0) cc_final: 0.7953 (t0) REVERT: C 692 ARG cc_start: 0.8432 (tpp-160) cc_final: 0.8180 (mmp80) REVERT: B 19 GLU cc_start: 0.7644 (pp20) cc_final: 0.7028 (pp20) REVERT: B 24 PHE cc_start: 0.8671 (m-10) cc_final: 0.8335 (m-80) REVERT: B 29 LEU cc_start: 0.8302 (mp) cc_final: 0.8069 (mp) REVERT: B 46 LYS cc_start: 0.8830 (mttt) cc_final: 0.8487 (mttm) REVERT: B 57 ARG cc_start: 0.8561 (ptm160) cc_final: 0.8163 (ttm170) REVERT: B 61 MET cc_start: 0.7138 (tmm) cc_final: 0.6598 (tmm) REVERT: B 69 GLN cc_start: 0.7909 (tt0) cc_final: 0.7639 (pt0) REVERT: B 72 VAL cc_start: 0.8627 (m) cc_final: 0.8343 (p) REVERT: B 85 ILE cc_start: 0.8773 (mt) cc_final: 0.8535 (tp) REVERT: B 103 GLN cc_start: 0.7569 (pm20) cc_final: 0.7357 (pm20) REVERT: B 106 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7904 (mt-10) REVERT: B 112 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7139 (mm-40) REVERT: B 114 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6375 (mm-30) REVERT: B 123 TYR cc_start: 0.7873 (t80) cc_final: 0.7239 (t80) REVERT: B 149 LYS cc_start: 0.7917 (ttmm) cc_final: 0.7524 (tptm) REVERT: B 153 LYS cc_start: 0.8546 (tptm) cc_final: 0.7877 (ttmm) REVERT: B 155 MET cc_start: 0.7866 (tpt) cc_final: 0.7478 (tpp) REVERT: B 177 LEU cc_start: 0.7970 (tp) cc_final: 0.7756 (tp) REVERT: B 178 ILE cc_start: 0.7922 (tp) cc_final: 0.7549 (mm) REVERT: B 184 ASP cc_start: 0.7966 (t70) cc_final: 0.7514 (t0) REVERT: B 195 ARG cc_start: 0.7901 (ttp-170) cc_final: 0.7180 (ttt180) REVERT: B 199 MET cc_start: 0.7793 (mmp) cc_final: 0.7422 (mmp) REVERT: B 209 ARG cc_start: 0.8204 (mmt90) cc_final: 0.7915 (mmt90) REVERT: B 212 TYR cc_start: 0.7675 (m-10) cc_final: 0.7407 (m-80) REVERT: B 215 SER cc_start: 0.8291 (m) cc_final: 0.7961 (p) REVERT: B 242 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7871 (mmtt) REVERT: B 307 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7790 (mmtm) REVERT: B 363 LYS cc_start: 0.8396 (mmtt) cc_final: 0.7938 (mmtp) REVERT: B 381 TYR cc_start: 0.7414 (m-80) cc_final: 0.6867 (m-80) REVERT: B 383 TYR cc_start: 0.5647 (m-80) cc_final: 0.5219 (m-80) REVERT: B 429 ASP cc_start: 0.8279 (m-30) cc_final: 0.7046 (m-30) REVERT: B 430 CYS cc_start: 0.5441 (m) cc_final: 0.4329 (t) REVERT: B 454 MET cc_start: 0.7263 (tpp) cc_final: 0.6721 (tpp) REVERT: B 469 ASP cc_start: 0.7685 (t70) cc_final: 0.6966 (t70) REVERT: B 470 LYS cc_start: 0.7144 (mttm) cc_final: 0.6864 (mtpp) REVERT: B 502 TYR cc_start: 0.6581 (t80) cc_final: 0.6341 (t80) REVERT: B 503 ASP cc_start: 0.7886 (t0) cc_final: 0.7538 (t0) REVERT: B 526 ARG cc_start: 0.6108 (mmm-85) cc_final: 0.5465 (mmm-85) REVERT: F 28 LYS cc_start: 0.7831 (mmmm) cc_final: 0.7517 (mmmm) REVERT: F 35 ASP cc_start: 0.7608 (t0) cc_final: 0.7365 (t70) REVERT: F 45 GLN cc_start: 0.8091 (tt0) cc_final: 0.7787 (tp-100) REVERT: F 53 SER cc_start: 0.8030 (t) cc_final: 0.6307 (t) REVERT: F 56 GLU cc_start: 0.7942 (mp0) cc_final: 0.7122 (pm20) REVERT: F 62 TYR cc_start: 0.8108 (t80) cc_final: 0.7454 (t80) REVERT: F 63 THR cc_start: 0.7474 (t) cc_final: 0.7203 (p) REVERT: F 64 MET cc_start: 0.7480 (tpt) cc_final: 0.7042 (tpt) REVERT: F 68 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8398 (mttm) REVERT: F 78 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7933 (ttm-80) REVERT: F 79 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6567 (tp30) REVERT: F 103 GLN cc_start: 0.8571 (tp40) cc_final: 0.8072 (tp40) REVERT: F 113 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7537 (tp40) REVERT: F 116 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8276 (tpp) REVERT: F 117 VAL cc_start: 0.8271 (t) cc_final: 0.7905 (p) REVERT: F 118 MET cc_start: 0.7421 (mtm) cc_final: 0.7117 (mtm) REVERT: F 124 MET cc_start: 0.4956 (tmm) cc_final: 0.4122 (tmm) REVERT: F 126 MET cc_start: 0.8013 (tmt) cc_final: 0.7615 (tmm) REVERT: F 140 TYR cc_start: 0.8031 (t80) cc_final: 0.7147 (t80) REVERT: F 145 ILE cc_start: 0.8800 (mt) cc_final: 0.8530 (mm) REVERT: F 150 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7521 (mm-40) REVERT: F 153 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7590 (mmt180) REVERT: F 154 TYR cc_start: 0.7151 (t80) cc_final: 0.5916 (t80) REVERT: F 158 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7149 (ttm-80) REVERT: F 163 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7218 (mm110) REVERT: F 167 ASP cc_start: 0.7374 (t0) cc_final: 0.7039 (t0) REVERT: F 206 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7207 (tm-30) REVERT: F 223 LYS cc_start: 0.7875 (tmtp) cc_final: 0.7659 (ptmm) REVERT: F 233 TYR cc_start: 0.7809 (t80) cc_final: 0.7292 (t80) REVERT: F 238 GLU cc_start: 0.8233 (tp30) cc_final: 0.7555 (tp30) REVERT: F 246 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7122 (tp30) REVERT: F 249 MET cc_start: 0.7628 (ppp) cc_final: 0.7187 (ppp) REVERT: F 258 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7823 (mp0) REVERT: F 262 LYS cc_start: 0.8231 (tmtt) cc_final: 0.7962 (tmtt) REVERT: F 265 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7236 (mm-30) REVERT: F 266 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7858 (ttp80) REVERT: F 270 SER cc_start: 0.8556 (m) cc_final: 0.8016 (t) REVERT: F 272 HIS cc_start: 0.6690 (m170) cc_final: 0.6288 (m170) REVERT: F 274 LYS cc_start: 0.8399 (tppt) cc_final: 0.8048 (tmmt) REVERT: F 276 ILE cc_start: 0.7612 (tp) cc_final: 0.7386 (tp) REVERT: F 311 LYS cc_start: 0.7896 (tmmt) cc_final: 0.7332 (ttmm) REVERT: F 313 MET cc_start: 0.7599 (mmp) cc_final: 0.6358 (mmm) REVERT: F 322 ARG cc_start: 0.8204 (mmt90) cc_final: 0.7721 (mmt180) REVERT: F 332 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6349 (pm20) REVERT: F 365 LEU cc_start: 0.7834 (tp) cc_final: 0.7495 (tp) REVERT: F 414 LYS cc_start: 0.8938 (mmtm) cc_final: 0.8611 (mmtm) REVERT: F 461 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6915 (mm-30) REVERT: F 536 ARG cc_start: 0.7117 (ptt180) cc_final: 0.6779 (ptt180) REVERT: F 671 ARG cc_start: 0.6382 (tpt-90) cc_final: 0.6099 (tpt-90) REVERT: F 673 LYS cc_start: 0.8055 (pptt) cc_final: 0.7814 (pptt) REVERT: F 687 GLU cc_start: 0.4662 (OUTLIER) cc_final: 0.2177 (tt0) REVERT: D 42 CYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6423 (m) outliers start: 103 outliers final: 75 residues processed: 763 average time/residue: 0.1831 time to fit residues: 208.6088 Evaluate side-chains 784 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 699 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 734 PHE Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 667 SER Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 687 GLU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 30 optimal weight: 0.5980 chunk 165 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 146 optimal weight: 0.0870 chunk 181 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 261 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.166782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.141111 restraints weight = 49023.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.145390 restraints weight = 26416.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.148169 restraints weight = 16182.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.150033 restraints weight = 10852.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.151292 restraints weight = 7858.513| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22753 Z= 0.183 Angle : 0.790 14.031 30696 Z= 0.402 Chirality : 0.046 0.347 3385 Planarity : 0.005 0.060 3934 Dihedral : 4.819 26.829 3006 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.57 % Favored : 90.32 % Rotamer: Outliers : 3.68 % Allowed : 27.48 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.16), residues: 2718 helix: 0.48 (0.14), residues: 1263 sheet: -1.16 (0.31), residues: 264 loop : -2.41 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 46 TYR 0.028 0.002 TYR A 164 PHE 0.033 0.002 PHE B 537 TRP 0.086 0.003 TRP A 509 HIS 0.024 0.001 HIS F 490 Details of bonding type rmsd covalent geometry : bond 0.00388 (22731) covalent geometry : angle 0.78550 (30684) hydrogen bonds : bond 0.04653 ( 1102) hydrogen bonds : angle 5.08296 ( 3228) metal coordination : bond 0.01333 ( 22) metal coordination : angle 4.15833 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 716 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8223 (tp) cc_final: 0.7848 (pt) REVERT: A 13 TYR cc_start: 0.7374 (t80) cc_final: 0.6953 (t80) REVERT: A 19 GLU cc_start: 0.7115 (pp20) cc_final: 0.6782 (pp20) REVERT: A 22 LYS cc_start: 0.8562 (ttmt) cc_final: 0.7755 (ttmt) REVERT: A 26 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7317 (mt-10) REVERT: A 27 GLN cc_start: 0.8306 (mt0) cc_final: 0.7900 (mt0) REVERT: A 46 LYS cc_start: 0.8538 (mttt) cc_final: 0.7927 (mmtp) REVERT: A 47 MET cc_start: 0.7487 (ttt) cc_final: 0.6962 (ttt) REVERT: A 49 LEU cc_start: 0.8207 (mt) cc_final: 0.7961 (mt) REVERT: A 57 ARG cc_start: 0.8410 (ptm160) cc_final: 0.7972 (ttm-80) REVERT: A 60 PHE cc_start: 0.8314 (m-80) cc_final: 0.7334 (m-10) REVERT: A 73 HIS cc_start: 0.7469 (m-70) cc_final: 0.7018 (m-70) REVERT: A 84 ILE cc_start: 0.8646 (tp) cc_final: 0.8291 (tt) REVERT: A 87 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8207 (p) REVERT: A 88 TYR cc_start: 0.8524 (t80) cc_final: 0.7441 (t80) REVERT: A 90 TYR cc_start: 0.8081 (m-80) cc_final: 0.7640 (m-80) REVERT: A 102 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6942 (mm-30) REVERT: A 106 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 109 CYS cc_start: 0.8169 (t) cc_final: 0.6576 (t) REVERT: A 112 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8071 (tp40) REVERT: A 115 ASP cc_start: 0.7962 (p0) cc_final: 0.7177 (p0) REVERT: A 118 GLN cc_start: 0.8258 (tt0) cc_final: 0.7994 (tt0) REVERT: A 122 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 127 LYS cc_start: 0.8606 (mmmm) cc_final: 0.8173 (mmtm) REVERT: A 157 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6974 (mm-30) REVERT: A 159 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7502 (mtmt) REVERT: A 170 MET cc_start: 0.6782 (mmp) cc_final: 0.6429 (mmp) REVERT: A 195 ARG cc_start: 0.7855 (ttm170) cc_final: 0.6853 (ttm-80) REVERT: A 196 GLU cc_start: 0.7526 (pp20) cc_final: 0.7203 (pp20) REVERT: A 199 MET cc_start: 0.8091 (mmm) cc_final: 0.7721 (mmp) REVERT: A 209 ARG cc_start: 0.7465 (mtm180) cc_final: 0.7145 (mtm180) REVERT: A 211 GLN cc_start: 0.7944 (pm20) cc_final: 0.7538 (pm20) REVERT: A 225 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5520 (mt) REVERT: A 267 GLU cc_start: 0.7614 (tp30) cc_final: 0.7309 (tp30) REVERT: A 272 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7534 (tp) REVERT: A 291 GLN cc_start: 0.8136 (mp10) cc_final: 0.7789 (mp10) REVERT: A 294 LYS cc_start: 0.8443 (mmmm) cc_final: 0.8065 (mmmm) REVERT: A 297 LYS cc_start: 0.8118 (ptpt) cc_final: 0.7771 (ptpp) REVERT: A 357 GLN cc_start: 0.7528 (mm-40) cc_final: 0.6701 (mm-40) REVERT: A 360 TRP cc_start: 0.7958 (m100) cc_final: 0.5722 (m100) REVERT: A 361 PHE cc_start: 0.7254 (m-80) cc_final: 0.6224 (m-80) REVERT: A 397 ARG cc_start: 0.7425 (ptp90) cc_final: 0.7207 (ptp90) REVERT: A 430 CYS cc_start: 0.7251 (p) cc_final: 0.6838 (p) REVERT: A 443 PHE cc_start: 0.8316 (t80) cc_final: 0.7873 (t80) REVERT: A 502 TYR cc_start: 0.5722 (t80) cc_final: 0.5162 (t80) REVERT: A 536 VAL cc_start: 0.7736 (m) cc_final: 0.7427 (p) REVERT: E 23 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7238 (mp0) REVERT: E 48 HIS cc_start: 0.5503 (t-90) cc_final: 0.4975 (t-90) REVERT: C 28 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7767 (tptp) REVERT: C 33 ILE cc_start: 0.9145 (mm) cc_final: 0.8815 (mm) REVERT: C 35 ASP cc_start: 0.7564 (t0) cc_final: 0.7309 (m-30) REVERT: C 49 ASN cc_start: 0.8106 (p0) cc_final: 0.7614 (p0) REVERT: C 62 TYR cc_start: 0.7965 (t80) cc_final: 0.7311 (t80) REVERT: C 64 MET cc_start: 0.7539 (tpt) cc_final: 0.7020 (tpp) REVERT: C 68 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8453 (mptt) REVERT: C 71 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7578 (tm-30) REVERT: C 72 LYS cc_start: 0.8491 (tttt) cc_final: 0.8059 (tptm) REVERT: C 83 GLU cc_start: 0.7656 (tp30) cc_final: 0.7215 (tp30) REVERT: C 124 MET cc_start: 0.2976 (tmm) cc_final: 0.2700 (tmm) REVERT: C 125 TYR cc_start: 0.5059 (t80) cc_final: 0.4671 (t80) REVERT: C 153 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7592 (mmm-85) REVERT: C 163 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7854 (mm110) REVERT: C 188 GLN cc_start: 0.8092 (tp40) cc_final: 0.7716 (tp40) REVERT: C 191 MET cc_start: 0.8105 (tpp) cc_final: 0.7703 (ttm) REVERT: C 206 GLU cc_start: 0.6295 (mp0) cc_final: 0.5703 (mp0) REVERT: C 222 GLN cc_start: 0.7525 (tp40) cc_final: 0.7072 (tm-30) REVERT: C 234 ILE cc_start: 0.8560 (mm) cc_final: 0.8010 (tp) REVERT: C 238 GLU cc_start: 0.7537 (tp30) cc_final: 0.6512 (tm-30) REVERT: C 246 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7481 (tm-30) REVERT: C 247 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7764 (ttm110) REVERT: C 250 HIS cc_start: 0.7980 (t-90) cc_final: 0.7196 (t-90) REVERT: C 258 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7028 (mp0) REVERT: C 262 LYS cc_start: 0.8081 (tmtm) cc_final: 0.7392 (ttmm) REVERT: C 265 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7196 (mm-30) REVERT: C 266 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7258 (ttp80) REVERT: C 274 LYS cc_start: 0.8394 (tppt) cc_final: 0.7678 (tppt) REVERT: C 282 SER cc_start: 0.7713 (m) cc_final: 0.7485 (m) REVERT: C 292 LYS cc_start: 0.8461 (mmmm) cc_final: 0.8078 (mmtt) REVERT: C 301 LYS cc_start: 0.8324 (ptpt) cc_final: 0.7957 (ptpp) REVERT: C 306 VAL cc_start: 0.8759 (t) cc_final: 0.8410 (p) REVERT: C 346 LEU cc_start: 0.8308 (tp) cc_final: 0.8081 (tp) REVERT: C 353 ASP cc_start: 0.7997 (t0) cc_final: 0.7698 (t0) REVERT: C 354 ARG cc_start: 0.7959 (ttp-110) cc_final: 0.7716 (ptp-170) REVERT: C 368 GLN cc_start: 0.7412 (tm-30) cc_final: 0.6688 (tm-30) REVERT: C 369 THR cc_start: 0.8211 (p) cc_final: 0.7846 (t) REVERT: C 373 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6391 (t0) REVERT: C 386 GLU cc_start: 0.8334 (mp0) cc_final: 0.6499 (mp0) REVERT: C 394 ASP cc_start: 0.7862 (t0) cc_final: 0.7494 (t0) REVERT: C 395 LYS cc_start: 0.8602 (mmtm) cc_final: 0.8205 (mmmm) REVERT: C 409 GLU cc_start: 0.8124 (pt0) cc_final: 0.7756 (pp20) REVERT: C 412 LEU cc_start: 0.8722 (mt) cc_final: 0.8448 (mm) REVERT: C 413 ASP cc_start: 0.8531 (m-30) cc_final: 0.8028 (m-30) REVERT: C 418 LEU cc_start: 0.8798 (tt) cc_final: 0.8531 (tp) REVERT: C 423 GLN cc_start: 0.7544 (pm20) cc_final: 0.6826 (pt0) REVERT: C 424 GLU cc_start: 0.7432 (mp0) cc_final: 0.6683 (mp0) REVERT: C 431 TYR cc_start: 0.8351 (m-80) cc_final: 0.6820 (m-10) REVERT: C 438 ARG cc_start: 0.7890 (tpm170) cc_final: 0.7203 (tpm170) REVERT: C 473 MET cc_start: 0.7656 (mmt) cc_final: 0.6589 (tpp) REVERT: C 554 MET cc_start: 0.6602 (tpp) cc_final: 0.6218 (tpp) REVERT: C 603 MET cc_start: 0.7771 (ptm) cc_final: 0.7416 (ptm) REVERT: C 692 ARG cc_start: 0.8406 (tpp-160) cc_final: 0.8133 (mmp80) REVERT: B 19 GLU cc_start: 0.7608 (pp20) cc_final: 0.7005 (pp20) REVERT: B 24 PHE cc_start: 0.8658 (m-10) cc_final: 0.8336 (m-80) REVERT: B 37 VAL cc_start: 0.8668 (t) cc_final: 0.7810 (m) REVERT: B 46 LYS cc_start: 0.8837 (mttt) cc_final: 0.8518 (mttm) REVERT: B 57 ARG cc_start: 0.8544 (ptm160) cc_final: 0.8102 (ttm170) REVERT: B 61 MET cc_start: 0.7114 (tmm) cc_final: 0.6543 (tmm) REVERT: B 69 GLN cc_start: 0.7823 (tt0) cc_final: 0.7622 (tt0) REVERT: B 72 VAL cc_start: 0.8621 (m) cc_final: 0.8344 (p) REVERT: B 85 ILE cc_start: 0.8759 (mt) cc_final: 0.8534 (tp) REVERT: B 106 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 112 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7142 (mm-40) REVERT: B 114 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6388 (mm-30) REVERT: B 123 TYR cc_start: 0.7874 (t80) cc_final: 0.7241 (t80) REVERT: B 149 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7549 (tptm) REVERT: B 155 MET cc_start: 0.7881 (tpt) cc_final: 0.7430 (tpp) REVERT: B 171 GLN cc_start: 0.7976 (pt0) cc_final: 0.7345 (pm20) REVERT: B 177 LEU cc_start: 0.7958 (tp) cc_final: 0.7737 (tp) REVERT: B 178 ILE cc_start: 0.7893 (tp) cc_final: 0.7495 (mm) REVERT: B 184 ASP cc_start: 0.7922 (t70) cc_final: 0.7496 (t0) REVERT: B 191 GLU cc_start: 0.7692 (pm20) cc_final: 0.7067 (pp20) REVERT: B 195 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.6765 (ttp80) REVERT: B 199 MET cc_start: 0.7771 (mmp) cc_final: 0.7427 (mmp) REVERT: B 209 ARG cc_start: 0.8165 (mmt90) cc_final: 0.7874 (mmt90) REVERT: B 212 TYR cc_start: 0.7667 (m-10) cc_final: 0.7394 (m-80) REVERT: B 215 SER cc_start: 0.8378 (m) cc_final: 0.8053 (p) REVERT: B 242 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7892 (mmtt) REVERT: B 307 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7736 (mmtm) REVERT: B 361 PHE cc_start: 0.7878 (t80) cc_final: 0.7677 (t80) REVERT: B 363 LYS cc_start: 0.8412 (mmtt) cc_final: 0.7911 (mmtp) REVERT: B 381 TYR cc_start: 0.7435 (m-80) cc_final: 0.6855 (m-80) REVERT: B 383 TYR cc_start: 0.5592 (m-80) cc_final: 0.5216 (m-80) REVERT: B 429 ASP cc_start: 0.8290 (m-30) cc_final: 0.7860 (m-30) REVERT: B 430 CYS cc_start: 0.5585 (m) cc_final: 0.4796 (t) REVERT: B 454 MET cc_start: 0.7187 (tpp) cc_final: 0.6605 (tpp) REVERT: B 469 ASP cc_start: 0.7682 (t70) cc_final: 0.6969 (t70) REVERT: B 470 LYS cc_start: 0.7210 (mttm) cc_final: 0.6914 (mtpp) REVERT: B 502 TYR cc_start: 0.6628 (t80) cc_final: 0.6418 (t80) REVERT: B 503 ASP cc_start: 0.7919 (t0) cc_final: 0.7550 (t0) REVERT: B 537 PHE cc_start: 0.6586 (t80) cc_final: 0.6363 (t80) REVERT: F 28 LYS cc_start: 0.7848 (mmmm) cc_final: 0.7542 (mmmm) REVERT: F 45 GLN cc_start: 0.8095 (tt0) cc_final: 0.7776 (tp-100) REVERT: F 53 SER cc_start: 0.8220 (t) cc_final: 0.7994 (t) REVERT: F 56 GLU cc_start: 0.8048 (mp0) cc_final: 0.7700 (mp0) REVERT: F 62 TYR cc_start: 0.8102 (t80) cc_final: 0.7285 (t80) REVERT: F 63 THR cc_start: 0.7591 (t) cc_final: 0.7318 (p) REVERT: F 64 MET cc_start: 0.7476 (tpt) cc_final: 0.7100 (tpt) REVERT: F 68 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8404 (mttm) REVERT: F 78 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7962 (ttm-80) REVERT: F 79 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6554 (tp30) REVERT: F 103 GLN cc_start: 0.8562 (tp40) cc_final: 0.8057 (tp40) REVERT: F 113 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7520 (tp40) REVERT: F 116 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8267 (tpp) REVERT: F 117 VAL cc_start: 0.8275 (t) cc_final: 0.7881 (p) REVERT: F 118 MET cc_start: 0.7505 (mtm) cc_final: 0.7194 (mtm) REVERT: F 124 MET cc_start: 0.4946 (tmm) cc_final: 0.4083 (tmm) REVERT: F 126 MET cc_start: 0.8019 (tmt) cc_final: 0.7640 (tmm) REVERT: F 140 TYR cc_start: 0.8021 (t80) cc_final: 0.7159 (t80) REVERT: F 145 ILE cc_start: 0.8804 (mt) cc_final: 0.8420 (tp) REVERT: F 150 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7513 (mm-40) REVERT: F 153 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7577 (mmt180) REVERT: F 154 TYR cc_start: 0.7118 (t80) cc_final: 0.5931 (t80) REVERT: F 158 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7064 (ttm-80) REVERT: F 163 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7233 (mm110) REVERT: F 167 ASP cc_start: 0.7423 (t0) cc_final: 0.7094 (t0) REVERT: F 168 MET cc_start: 0.7622 (ptp) cc_final: 0.7354 (ptp) REVERT: F 206 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7240 (tm-30) REVERT: F 223 LYS cc_start: 0.7841 (tmtp) cc_final: 0.7451 (ptpp) REVERT: F 233 TYR cc_start: 0.7773 (t80) cc_final: 0.7204 (t80) REVERT: F 238 GLU cc_start: 0.8155 (tp30) cc_final: 0.7539 (tp30) REVERT: F 246 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7114 (tp30) REVERT: F 249 MET cc_start: 0.7625 (ppp) cc_final: 0.7179 (ppp) REVERT: F 258 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7852 (mp0) REVERT: F 265 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7213 (mm-30) REVERT: F 266 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7869 (ttp80) REVERT: F 270 SER cc_start: 0.8548 (m) cc_final: 0.7982 (t) REVERT: F 272 HIS cc_start: 0.6425 (m170) cc_final: 0.6092 (m170) REVERT: F 274 LYS cc_start: 0.8349 (tppt) cc_final: 0.8046 (tmmt) REVERT: F 276 ILE cc_start: 0.7654 (tp) cc_final: 0.7393 (tp) REVERT: F 296 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6791 (mm) REVERT: F 311 LYS cc_start: 0.7882 (tmmt) cc_final: 0.7340 (ttmm) REVERT: F 313 MET cc_start: 0.7381 (mmp) cc_final: 0.6967 (mmm) REVERT: F 322 ARG cc_start: 0.8254 (mmt90) cc_final: 0.7786 (mmt180) REVERT: F 332 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: F 360 PHE cc_start: 0.7508 (m-80) cc_final: 0.7066 (t80) REVERT: F 378 LEU cc_start: 0.5088 (OUTLIER) cc_final: 0.4415 (mt) REVERT: F 414 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8669 (mmtm) REVERT: F 536 ARG cc_start: 0.7093 (ptt180) cc_final: 0.6748 (ptt180) REVERT: F 671 ARG cc_start: 0.6413 (tpt-90) cc_final: 0.6089 (tpt-90) REVERT: F 673 LYS cc_start: 0.8063 (pptt) cc_final: 0.7814 (pptt) REVERT: F 687 GLU cc_start: 0.4716 (OUTLIER) cc_final: 0.2138 (tt0) REVERT: D 42 CYS cc_start: 0.6461 (OUTLIER) cc_final: 0.6220 (m) REVERT: D 68 CYS cc_start: 0.5386 (OUTLIER) cc_final: 0.4720 (t) outliers start: 91 outliers final: 75 residues processed: 762 average time/residue: 0.1812 time to fit residues: 205.8809 Evaluate side-chains 786 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 699 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 729 GLN Chi-restraints excluded: chain C residue 734 PHE Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 665 PHE Chi-restraints excluded: chain F residue 667 SER Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 687 GLU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 68 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 143 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 254 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 146 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 158 HIS ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 113 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.165125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.139070 restraints weight = 48972.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.143371 restraints weight = 26598.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.146161 restraints weight = 16357.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.147963 restraints weight = 11021.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.149282 restraints weight = 8067.122| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22753 Z= 0.195 Angle : 0.814 13.536 30696 Z= 0.416 Chirality : 0.047 0.346 3385 Planarity : 0.005 0.063 3934 Dihedral : 4.896 26.723 3006 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.79 % Favored : 90.10 % Rotamer: Outliers : 4.01 % Allowed : 27.44 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.16), residues: 2718 helix: 0.44 (0.14), residues: 1261 sheet: -1.23 (0.31), residues: 268 loop : -2.47 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 46 TYR 0.029 0.002 TYR A 164 PHE 0.030 0.002 PHE B 537 TRP 0.090 0.003 TRP A 509 HIS 0.026 0.002 HIS F 490 Details of bonding type rmsd covalent geometry : bond 0.00409 (22731) covalent geometry : angle 0.80945 (30684) hydrogen bonds : bond 0.04794 ( 1102) hydrogen bonds : angle 5.13882 ( 3228) metal coordination : bond 0.01395 ( 22) metal coordination : angle 4.41309 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5328.53 seconds wall clock time: 92 minutes 37.73 seconds (5557.73 seconds total)