Starting phenix.real_space_refine on Sat Sep 12 19:10:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o7h_0641/09_2026/6o7h_0641.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o7h_0641/09_2026/6o7h_0641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o7h_0641/09_2026/6o7h_0641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o7h_0641/09_2026/6o7h_0641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o7h_0641/09_2026/6o7h_0641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o7h_0641/09_2026/6o7h_0641.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6o7h_0641/09_2026/6o7h_0641.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o7h_0641/09_2026/6o7h_0641.cif" } resolution = 2.9 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= 0.005 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 50 5.49 5 S 49 5.16 5 C 11014 2.51 5 N 3083 2.21 5 O 3377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17576 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6152 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1047 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 1 Chain: "D" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2265 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 1 Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 20, 'TRANS': 265} Chain: "G" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 589 Classifications: {'RNAv2': 27} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 398 Classifications: {'RNAv2': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 13} Chain: "F" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 313 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "F" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2223 Classifications: {'peptide': 322} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 106} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain breaks: 10 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'UNK:plan-1': 93, 'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNAv2': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna2p_pur': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3079 SG CYS A 389 57.900 85.339 89.908 1.00 26.12 S ATOM 3099 SG CYS A 392 53.925 83.414 90.176 1.00 20.38 S ATOM 3254 SG CYS A 413 55.553 86.020 92.716 1.00 30.17 S ATOM 3274 SG CYS A 416 56.496 82.553 92.693 1.00 30.70 S ATOM 8026 SG CYS C 113 73.888 99.035 65.322 1.00 24.94 S ATOM 8093 SG CYS C 122 74.316 98.299 61.726 1.00 18.20 S ATOM 8113 SG CYS C 125 71.610 95.804 64.201 1.00 17.21 S ATOM 10291 SG CYS D 113 93.830 71.709 67.401 1.00 32.50 S ATOM 10358 SG CYS D 122 96.213 71.721 64.605 1.00 31.10 S ATOM 10378 SG CYS D 125 91.608 70.721 64.658 1.00 23.12 S Time building chain proxies: 3.42, per 1000 atoms: 0.19 Number of scatterers: 17576 At special positions: 0 Unit cell: (127.413, 119.79, 150.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 49 16.00 P 50 15.00 O 3377 8.00 N 3083 7.00 C 11014 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 Links applied TRANS " UNK F 40 " - " ARG F 39 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 688.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " Number of angles added : 12 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 29 sheets defined 42.3% alpha, 15.8% beta 10 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.557A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 29 through 42 removed outlier: 3.893A pdb=" N GLN A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.778A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.591A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.764A pdb=" N PHE A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 105 removed outlier: 3.507A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 Processing helix chain 'A' and resid 171 through 184 Proline residue: A 177 - end of helix removed outlier: 3.730A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 255 through 282 removed outlier: 3.557A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 303 through 325 removed outlier: 3.697A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.572A pdb=" N LYS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.733A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.854A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.663A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.664A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.737A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.877A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.897A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.839A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 685 " --> pdb=" O TRP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 removed outlier: 4.526A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 4.355A pdb=" N TYR A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 755 Processing helix chain 'A' and resid 764 through 775 removed outlier: 4.309A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.835A pdb=" N MET B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 62 removed outlier: 4.203A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.555A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 132 removed outlier: 3.861A pdb=" N VAL B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 156 removed outlier: 3.616A pdb=" N LEU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 4.019A pdb=" N VAL B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.787A pdb=" N PHE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 70 removed outlier: 3.609A pdb=" N ARG C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.967A pdb=" N LEU C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.509A pdb=" N TRP C 156 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 223 removed outlier: 3.919A pdb=" N ASP C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.585A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.617A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 70 removed outlier: 3.799A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 151 through 159 removed outlier: 3.641A pdb=" N TRP D 156 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 247 through 254 removed outlier: 4.032A pdb=" N TYR D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.905A pdb=" N ILE D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.865A pdb=" N GLU D 284 " --> pdb=" O PHE D 280 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'E' and resid 20 through 36 Processing helix chain 'E' and resid 37 through 50 removed outlier: 3.888A pdb=" N VAL E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.919A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 99 removed outlier: 3.569A pdb=" N ARG E 95 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.845A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 removed outlier: 3.554A pdb=" N PHE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 182 removed outlier: 3.755A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.591A pdb=" N UNK F 46 " --> pdb=" O UNK F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 4.304A pdb=" N UNK F 58 " --> pdb=" O UNK F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 132 removed outlier: 3.572A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.815A pdb=" N UNK F 141 " --> pdb=" O UNK F 137 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK F 142 " --> pdb=" O UNK F 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 142' Processing helix chain 'F' and resid 151 through 155 removed outlier: 4.183A pdb=" N UNK F 155 " --> pdb=" O UNK F 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 151 through 155' Processing helix chain 'F' and resid 160 through 169 removed outlier: 4.251A pdb=" N UNK F 166 " --> pdb=" O UNK F 162 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N UNK F 169 " --> pdb=" O UNK F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 187 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 256 through 263 removed outlier: 3.935A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.677A pdb=" N LYS F 276 " --> pdb=" O TRP F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.564A pdb=" N TRP F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 317 through 323 Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.837A pdb=" N MET F 344 " --> pdb=" O TRP F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 removed outlier: 4.113A pdb=" N LEU F 348 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 4.313A pdb=" N VAL F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 removed outlier: 4.224A pdb=" N LEU A 119 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.708A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA5, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 445 removed outlier: 4.265A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 430 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 580 through 586 removed outlier: 7.044A pdb=" N ILE A 580 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA A 595 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL A 582 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 593 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 589 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 620 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N PHE A 656 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 622 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.675A pdb=" N ARG A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.887A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.792A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.706A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB4, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB5, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.726A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.612A pdb=" N PHE D 194 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 85 through 88 removed outlier: 7.392A pdb=" N SER D 85 " --> pdb=" O PHE D 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB9, first strand: chain 'D' and resid 163 through 169 Processing sheet with id=AC1, first strand: chain 'D' and resid 231 through 232 removed outlier: 7.294A pdb=" N GLY D 232 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL F 211 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 58 through 61 removed outlier: 8.252A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'E' and resid 124 through 134 removed outlier: 3.646A pdb=" N VAL E 127 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 252 through 254 removed outlier: 4.608A pdb=" N TYR E 211 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 229 through 232 removed outlier: 3.535A pdb=" N LEU E 230 " --> pdb=" O PHE E 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC8, first strand: chain 'E' and resid 261 through 263 Processing sheet with id=AC9, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AD1, first strand: chain 'F' and resid 15 through 20 removed outlier: 5.565A pdb=" N ASN F 18 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 236 through 243 removed outlier: 3.718A pdb=" N ILE F 236 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.93 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: 4576 1.33 - 1.45: 3643 1.45 - 1.57: 9655 1.57 - 1.69: 97 1.69 - 1.81: 80 Bond restraints: 18051 Sorted by residual: bond pdb=" C5 A K 3 " pdb=" C6 A K 3 " ideal model delta sigma weight residual 1.406 1.324 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C5 A K 1 " pdb=" C6 A K 1 " ideal model delta sigma weight residual 1.406 1.328 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C5 A K 4 " pdb=" C6 A K 4 " ideal model delta sigma weight residual 1.406 1.329 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C5 A K 2 " pdb=" C6 A K 2 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" N ILE E 247 " pdb=" CA ILE E 247 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.05e+01 ... (remaining 18046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 24520 5.44 - 10.88: 105 10.88 - 16.32: 6 16.32 - 21.76: 2 21.76 - 27.20: 3 Bond angle restraints: 24636 Sorted by residual: angle pdb=" O3' A K 2 " pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 104.00 85.62 18.38 1.90e+00 2.77e-01 9.36e+01 angle pdb=" OP2 A K 3 " pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 110.70 83.50 27.20 3.00e+00 1.11e-01 8.22e+01 angle pdb=" OP1 A K 1 " pdb=" P A K 1 " pdb=" O5' A K 1 " ideal model delta sigma weight residual 110.70 87.41 23.29 3.00e+00 1.11e-01 6.03e+01 angle pdb=" OP2 A K 1 " pdb=" P A K 1 " pdb=" O5' A K 1 " ideal model delta sigma weight residual 110.70 88.26 22.44 3.00e+00 1.11e-01 5.60e+01 angle pdb=" N PRO A 113 " pdb=" CA PRO A 113 " pdb=" CB PRO A 113 " ideal model delta sigma weight residual 103.00 110.37 -7.37 1.10e+00 8.26e-01 4.49e+01 ... (remaining 24631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 9713 15.87 - 31.74: 608 31.74 - 47.61: 194 47.61 - 63.47: 94 63.47 - 79.34: 27 Dihedral angle restraints: 10636 sinusoidal: 4566 harmonic: 6070 Sorted by residual: dihedral pdb=" C4' A H 20 " pdb=" C3' A H 20 " pdb=" C2' A H 20 " pdb=" C1' A H 20 " ideal model delta sinusoidal sigma weight residual 36.34 -39.04 75.39 1 3.10e+00 1.04e-01 7.47e+02 dihedral pdb=" C4' C H 31 " pdb=" C3' C H 31 " pdb=" C2' C H 31 " pdb=" C1' C H 31 " ideal model delta sinusoidal sigma weight residual 36.34 -38.59 74.94 1 3.10e+00 1.04e-01 7.39e+02 dihedral pdb=" C4' A G 6 " pdb=" C3' A G 6 " pdb=" C2' A G 6 " pdb=" C1' A G 6 " ideal model delta sinusoidal sigma weight residual 36.34 -37.66 74.00 1 3.10e+00 1.04e-01 7.24e+02 ... (remaining 10633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2551 0.163 - 0.326: 165 0.326 - 0.489: 6 0.489 - 0.652: 0 0.652 - 0.816: 2 Chirality restraints: 2724 Sorted by residual: chirality pdb=" P A K 1 " pdb=" OP1 A K 1 " pdb=" OP2 A K 1 " pdb=" O5' A K 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.99 -0.82 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" P A K 3 " pdb=" OP1 A K 3 " pdb=" OP2 A K 3 " pdb=" O5' A K 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.96 -0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" C3' C G 11 " pdb=" C4' C G 11 " pdb=" O3' C G 11 " pdb=" C2' C G 11 " both_signs ideal model delta sigma weight residual False -2.50 -2.99 0.49 2.00e-01 2.50e+01 5.95e+00 ... (remaining 2721 not shown) Planarity restraints: 2993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 252 " 0.026 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C GLY A 252 " -0.091 2.00e-02 2.50e+03 pdb=" O GLY A 252 " 0.035 2.00e-02 2.50e+03 pdb=" N LYS A 253 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 71 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C MET A 71 " 0.077 2.00e-02 2.50e+03 pdb=" O MET A 71 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE A 72 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 47 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ALA E 47 " 0.076 2.00e-02 2.50e+03 pdb=" O ALA E 47 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE E 48 " -0.025 2.00e-02 2.50e+03 ... (remaining 2990 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 10 2.26 - 2.92: 6851 2.92 - 3.58: 23617 3.58 - 4.24: 42811 4.24 - 4.90: 71232 Nonbonded interactions: 144521 Sorted by model distance: nonbonded pdb=" O3' C H 35 " pdb=" P G H 101 " model vdw 1.596 3.400 nonbonded pdb=" P A K 1 " pdb=" O3' A K 4 " model vdw 1.628 3.400 nonbonded pdb=" O2' A K 1 " pdb=" OP1 A K 2 " model vdw 2.055 3.040 nonbonded pdb=" O5' A K 1 " pdb=" O3' A K 4 " model vdw 2.127 3.040 nonbonded pdb=" OE2 GLU A 180 " pdb=" OH TYR A 547 " model vdw 2.204 3.040 ... (remaining 144516 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 'C' and (resid 4 through 26 or resid 34 through 301)) selection = (chain 'D' and (resid 4 through 26 or resid 34 through 301)) } 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 individual isotropic 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: 1.060 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.240 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:5.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.007 0.210 18064 Z= 0.396 Angle : 1.212 28.884 24651 Z= 0.660 Chirality : 0.083 0.816 2724 Planarity : 0.007 0.061 2992 Dihedral : 13.681 79.343 6751 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 1.21 % Allowed : 4.83 % Favored : 93.96 % 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 are not related in a simple way. whole: -4.34 (0.15), residues: 2006 helix: -3.61 (0.12), residues: 771 sheet: -1.91 (0.27), residues: 290 loop : -2.44 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 212 TYR 0.029 0.003 TYR C 233 PHE 0.029 0.003 PHE A 502 TRP 0.023 0.002 TRP A 320 HIS 0.007 0.002 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.38 (18051) covalent geometry : angle 1.15982 / 0.66 (24636) hydrogen bonds : bond 0.28449 / 19.47 ( 640) hydrogen bonds : angle 10.28375 / 7.09 ( 1818) metal coordination : bond 0.13674 / 8.53 ( 12) metal coordination : angle 15.96816 / 7.92 ( 12) link_TRANS : bond 0.00937 / 0.49 ( 1) link_TRANS : angle 1.24286 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 445 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8305 (mtm) cc_final: 0.7894 (mtt) REVERT: A 158 VAL cc_start: 0.8439 (t) cc_final: 0.8144 (t) REVERT: A 159 LYS cc_start: 0.8553 (tmmt) cc_final: 0.8194 (tppt) REVERT: A 162 TRP cc_start: 0.8459 (t-100) cc_final: 0.8073 (t-100) REVERT: A 167 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7552 (mtmt) REVERT: A 170 LEU cc_start: 0.8991 (tp) cc_final: 0.8660 (tp) REVERT: A 297 MET cc_start: 0.8933 (ttt) cc_final: 0.8664 (ttt) REVERT: A 757 GLU cc_start: 0.7493 (pt0) cc_final: 0.6770 (pt0) outliers start: 20 outliers final: 5 residues processed: 460 average time/residue: 0.6878 time to fit residues: 347.2186 Evaluate side-chains 272 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain C residue 273 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS A 456 GLN A 668 HIS B 72 ASN C 37 ASN C 179 ASN D 22 HIS D 83 ASN D 106 ASN D 179 ASN D 183 ASN E 30 ASN F 18 ASN F 33 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.179707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133208 restraints weight = 19292.297| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.91 r_work: 0.3143 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18064 Z= 0.187 Angle : 0.936 17.707 24651 Z= 0.418 Chirality : 0.082 1.172 2724 Planarity : 0.006 0.052 2992 Dihedral : 11.206 172.993 2941 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.20 % Allowed : 15.93 % Favored : 80.87 % 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 are not related in a simple way. whole: -2.89 (0.16), residues: 2006 helix: -1.73 (0.16), residues: 791 sheet: -1.52 (0.27), residues: 283 loop : -2.13 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 157 TYR 0.021 0.002 TYR B 125 PHE 0.021 0.002 PHE E 15 TRP 0.018 0.001 TRP A 131 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (18051) covalent geometry : angle 0.93373 / 0.42 (24636) hydrogen bonds : bond 0.05377 / 3.69 ( 640) hydrogen bonds : angle 5.63943 / 3.98 ( 1818) metal coordination : bond 0.00743 / 0.42 ( 12) metal coordination : angle 3.36499 / 1.85 ( 12) link_TRANS : bond 0.00052 / 0.03 ( 1) link_TRANS : angle 0.35774 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8695 (tp) REVERT: A 21 GLN cc_start: 0.8215 (tm130) cc_final: 0.7862 (tm-30) REVERT: A 65 MET cc_start: 0.4291 (ptm) cc_final: 0.3891 (ptm) REVERT: A 71 MET cc_start: 0.8015 (mtm) cc_final: 0.7689 (mtt) REVERT: A 155 ARG cc_start: 0.8430 (ttm110) cc_final: 0.8081 (mtm-85) REVERT: A 159 LYS cc_start: 0.8606 (tmmt) cc_final: 0.7960 (tppt) REVERT: A 316 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8330 (tttp) REVERT: A 375 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7865 (ptmt) REVERT: A 501 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8281 (p) REVERT: A 507 MET cc_start: 0.8031 (mtp) cc_final: 0.7727 (mmt) REVERT: A 633 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7489 (mt) REVERT: A 635 ARG cc_start: 0.8503 (ttp-170) cc_final: 0.8251 (mtm180) REVERT: A 755 ARG cc_start: 0.7587 (mtp85) cc_final: 0.6910 (mtp85) REVERT: A 757 GLU cc_start: 0.7780 (pt0) cc_final: 0.7249 (pt0) REVERT: B 122 LYS cc_start: 0.8265 (mttt) cc_final: 0.7960 (mttt) REVERT: B 123 MET cc_start: 0.7583 (ttt) cc_final: 0.7265 (ttm) REVERT: C 237 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8380 (tptp) REVERT: D 1 MET cc_start: 0.7612 (tmt) cc_final: 0.7374 (tmt) REVERT: D 153 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: E 104 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8507 (tp) REVERT: E 176 MET cc_start: 0.9047 (mmm) cc_final: 0.8423 (mmp) REVERT: E 264 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7396 (tp30) REVERT: F 7 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6825 (mmtp) REVERT: F 128 LYS cc_start: 0.5756 (tptt) cc_final: 0.5496 (tttt) REVERT: F 131 LYS cc_start: 0.6012 (mmmm) cc_final: 0.5530 (mtpp) REVERT: F 276 LYS cc_start: 0.5434 (mtpp) cc_final: 0.4870 (mmmm) outliers start: 53 outliers final: 13 residues processed: 330 average time/residue: 0.6345 time to fit residues: 231.9703 Evaluate side-chains 284 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 243 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.170986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122997 restraints weight = 19477.089| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.14 r_work: 0.2965 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18064 Z= 0.220 Angle : 0.835 16.131 24651 Z= 0.388 Chirality : 0.068 1.022 2724 Planarity : 0.005 0.063 2992 Dihedral : 11.015 169.831 2933 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.77 % Allowed : 16.35 % Favored : 78.88 % 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 are not related in a simple way. whole: -2.08 (0.17), residues: 2006 helix: -0.80 (0.18), residues: 802 sheet: -1.18 (0.28), residues: 300 loop : -1.91 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 157 TYR 0.023 0.002 TYR A 265 PHE 0.031 0.002 PHE E 15 TRP 0.014 0.002 TRP A 131 HIS 0.008 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (18051) covalent geometry : angle 0.83231 / 0.39 (24636) hydrogen bonds : bond 0.05137 / 3.55 ( 640) hydrogen bonds : angle 5.32238 / 3.75 ( 1818) metal coordination : bond 0.01631 / 1.30 ( 12) metal coordination : angle 3.19792 / 1.72 ( 12) link_TRANS : bond 0.00061 / 0.03 ( 1) link_TRANS : angle 0.22060 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 267 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8177 (mpt180) cc_final: 0.7959 (mpt180) REVERT: A 65 MET cc_start: 0.4603 (ptm) cc_final: 0.4201 (ptp) REVERT: A 71 MET cc_start: 0.7936 (mtm) cc_final: 0.7617 (mtt) REVERT: A 157 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8299 (tp) REVERT: A 158 VAL cc_start: 0.8256 (t) cc_final: 0.7961 (t) REVERT: A 159 LYS cc_start: 0.8564 (tmmt) cc_final: 0.7974 (tppt) REVERT: A 316 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8343 (tttp) REVERT: A 375 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7943 (ptmt) REVERT: A 409 GLU cc_start: 0.7395 (mp0) cc_final: 0.7190 (mp0) REVERT: A 501 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 503 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: A 507 MET cc_start: 0.8216 (mtp) cc_final: 0.7973 (mmt) REVERT: A 513 ARG cc_start: 0.8142 (mpt180) cc_final: 0.7895 (mpt180) REVERT: A 630 ARG cc_start: 0.8577 (mmt180) cc_final: 0.7843 (mpt180) REVERT: A 633 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7812 (mt) REVERT: A 718 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7760 (ttp-170) REVERT: A 755 ARG cc_start: 0.7560 (mtp85) cc_final: 0.6981 (mtp85) REVERT: A 757 GLU cc_start: 0.7798 (pt0) cc_final: 0.7315 (pt0) REVERT: A 773 MET cc_start: 0.8654 (mtp) cc_final: 0.8311 (mtp) REVERT: B 122 LYS cc_start: 0.8269 (mttt) cc_final: 0.7964 (mttt) REVERT: B 123 MET cc_start: 0.7762 (ttt) cc_final: 0.7459 (ttm) REVERT: C 164 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: C 168 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: C 237 LYS cc_start: 0.8873 (ttpp) cc_final: 0.8470 (tptp) REVERT: C 263 ASP cc_start: 0.7893 (p0) cc_final: 0.7641 (p0) REVERT: D 1 MET cc_start: 0.7811 (tmt) cc_final: 0.7565 (tmt) REVERT: D 153 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: D 185 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7773 (ptp-170) REVERT: E 89 ARG cc_start: 0.7016 (ttm-80) cc_final: 0.6740 (ptm160) REVERT: E 92 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8280 (t) REVERT: E 129 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.8833 (t) REVERT: E 139 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8460 (mt0) REVERT: E 147 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: E 176 MET cc_start: 0.9146 (mmm) cc_final: 0.8356 (mmp) REVERT: E 264 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: F 117 LEU cc_start: 0.7885 (mt) cc_final: 0.7643 (mt) REVERT: F 215 LYS cc_start: 0.8595 (mptm) cc_final: 0.8146 (mmtp) REVERT: F 244 GLU cc_start: 0.7553 (pt0) cc_final: 0.7060 (pm20) outliers start: 79 outliers final: 23 residues processed: 322 average time/residue: 0.6324 time to fit residues: 225.6326 Evaluate side-chains 283 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 132 optimal weight: 0.0570 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 65 optimal weight: 0.0030 chunk 102 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.5708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.179334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133166 restraints weight = 19440.511| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.93 r_work: 0.3153 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18064 Z= 0.121 Angle : 0.686 12.185 24651 Z= 0.316 Chirality : 0.056 0.679 2724 Planarity : 0.004 0.047 2992 Dihedral : 10.873 169.433 2933 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.96 % Allowed : 19.07 % Favored : 77.97 % 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 are not related in a simple way. whole: -1.46 (0.18), residues: 2006 helix: -0.13 (0.18), residues: 803 sheet: -1.01 (0.29), residues: 289 loop : -1.69 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 74 TYR 0.013 0.001 TYR A 552 PHE 0.018 0.001 PHE B 181 TRP 0.019 0.001 TRP A 131 HIS 0.004 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (18051) covalent geometry : angle 0.68474 / 0.32 (24636) hydrogen bonds : bond 0.03980 / 2.75 ( 640) hydrogen bonds : angle 4.83411 / 3.42 ( 1818) metal coordination : bond 0.00406 / 0.21 ( 12) metal coordination : angle 2.16276 / 1.19 ( 12) link_TRANS : bond 0.00011 / 0.01 ( 1) link_TRANS : angle 0.20553 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4548 (ptm) cc_final: 0.4256 (ptp) REVERT: A 71 MET cc_start: 0.8209 (mtm) cc_final: 0.7766 (mtt) REVERT: A 158 VAL cc_start: 0.8265 (t) cc_final: 0.8009 (t) REVERT: A 159 LYS cc_start: 0.8592 (tmmt) cc_final: 0.8029 (tppt) REVERT: A 297 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8921 (ttt) REVERT: A 375 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7811 (ptmt) REVERT: A 443 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8310 (tt) REVERT: A 501 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8069 (p) REVERT: A 503 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: A 513 ARG cc_start: 0.8119 (mpt180) cc_final: 0.7918 (mpt180) REVERT: A 552 TYR cc_start: 0.7864 (m-80) cc_final: 0.7599 (m-80) REVERT: A 630 ARG cc_start: 0.8451 (mmt180) cc_final: 0.7778 (mpt180) REVERT: A 633 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7661 (mt) REVERT: A 755 ARG cc_start: 0.7535 (mtp85) cc_final: 0.6914 (mtp85) REVERT: A 757 GLU cc_start: 0.7695 (pt0) cc_final: 0.7197 (pt0) REVERT: A 773 MET cc_start: 0.8523 (mtp) cc_final: 0.8141 (mtp) REVERT: B 122 LYS cc_start: 0.8292 (mttt) cc_final: 0.7946 (mttt) REVERT: B 123 MET cc_start: 0.7821 (ttt) cc_final: 0.7502 (ttm) REVERT: C 168 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: C 236 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8248 (m) REVERT: C 237 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8374 (tptp) REVERT: C 263 ASP cc_start: 0.7661 (p0) cc_final: 0.7365 (p0) REVERT: D 107 ARG cc_start: 0.8088 (mpt-90) cc_final: 0.7796 (mpt-90) REVERT: D 185 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7748 (ptp-170) REVERT: E 3 LYS cc_start: 0.8953 (mtpm) cc_final: 0.8733 (ttpp) REVERT: E 139 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8451 (mt0) REVERT: E 147 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: F 117 LEU cc_start: 0.7796 (mt) cc_final: 0.7577 (mt) REVERT: F 301 MET cc_start: 0.6370 (ttm) cc_final: 0.5493 (tpp) outliers start: 49 outliers final: 16 residues processed: 289 average time/residue: 0.6548 time to fit residues: 209.7247 Evaluate side-chains 264 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 HIS C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.174632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126700 restraints weight = 19159.139| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.00 r_work: 0.3035 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18064 Z= 0.176 Angle : 0.729 11.667 24651 Z= 0.339 Chirality : 0.060 0.893 2724 Planarity : 0.005 0.058 2992 Dihedral : 10.786 167.304 2933 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.62 % Allowed : 19.07 % Favored : 77.31 % 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 are not related in a simple way. whole: -1.32 (0.18), residues: 2006 helix: 0.03 (0.19), residues: 809 sheet: -1.05 (0.27), residues: 315 loop : -1.61 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 74 TYR 0.015 0.002 TYR A 265 PHE 0.021 0.002 PHE B 181 TRP 0.014 0.001 TRP F 393 HIS 0.006 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (18051) covalent geometry : angle 0.72703 / 0.34 (24636) hydrogen bonds : bond 0.04278 / 2.99 ( 640) hydrogen bonds : angle 4.87501 / 3.46 ( 1818) metal coordination : bond 0.01195 / 0.93 ( 12) metal coordination : angle 2.41549 / 1.32 ( 12) link_TRANS : bond 0.00039 / 0.02 ( 1) link_TRANS : angle 0.17023 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4631 (ptm) cc_final: 0.4352 (ptp) REVERT: A 71 MET cc_start: 0.8174 (mtm) cc_final: 0.7786 (mtt) REVERT: A 91 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8816 (tt) REVERT: A 158 VAL cc_start: 0.8262 (t) cc_final: 0.7995 (t) REVERT: A 159 LYS cc_start: 0.8578 (tmmt) cc_final: 0.7984 (tppt) REVERT: A 341 ARG cc_start: 0.9088 (ptm-80) cc_final: 0.8743 (ptm-80) REVERT: A 375 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7872 (ptmt) REVERT: A 630 ARG cc_start: 0.8568 (mmt180) cc_final: 0.7831 (mpt180) REVERT: A 633 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7687 (mt) REVERT: A 755 ARG cc_start: 0.7470 (mtp85) cc_final: 0.6858 (mtp85) REVERT: A 757 GLU cc_start: 0.7653 (pt0) cc_final: 0.7083 (pt0) REVERT: A 773 MET cc_start: 0.8680 (mtp) cc_final: 0.8258 (mtp) REVERT: B 122 LYS cc_start: 0.8296 (mttt) cc_final: 0.7898 (mttt) REVERT: B 123 MET cc_start: 0.7802 (ttt) cc_final: 0.7493 (ttm) REVERT: C 157 ARG cc_start: 0.7432 (mtt-85) cc_final: 0.7221 (mtm-85) REVERT: C 168 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: C 236 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8446 (m) REVERT: C 237 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8431 (tptp) REVERT: C 263 ASP cc_start: 0.7780 (p0) cc_final: 0.7450 (p0) REVERT: C 267 LYS cc_start: 0.8420 (pttt) cc_final: 0.7471 (ptmm) REVERT: D 85 SER cc_start: 0.8825 (t) cc_final: 0.8562 (p) REVERT: D 94 GLN cc_start: 0.7402 (tp40) cc_final: 0.6987 (tp-100) REVERT: D 107 ARG cc_start: 0.8131 (mpt-90) cc_final: 0.7825 (mpt-90) REVERT: D 185 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7711 (ptp-170) REVERT: D 267 LYS cc_start: 0.8496 (pttm) cc_final: 0.8082 (pttp) REVERT: E 3 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8679 (ttpp) REVERT: E 147 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: F 98 MET cc_start: 0.5844 (ptp) cc_final: 0.5511 (ptp) REVERT: F 117 LEU cc_start: 0.7904 (mt) cc_final: 0.7650 (mt) REVERT: F 301 MET cc_start: 0.6357 (ttm) cc_final: 0.5420 (tpp) outliers start: 60 outliers final: 25 residues processed: 285 average time/residue: 0.6479 time to fit residues: 204.4512 Evaluate side-chains 267 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN E 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.177936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130973 restraints weight = 19227.534| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.87 r_work: 0.3089 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18064 Z= 0.132 Angle : 0.678 11.234 24651 Z= 0.313 Chirality : 0.056 0.734 2724 Planarity : 0.004 0.048 2992 Dihedral : 10.737 169.788 2931 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.08 % Allowed : 19.92 % Favored : 77.01 % 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 are not related in a simple way. whole: -1.04 (0.18), residues: 2006 helix: 0.31 (0.19), residues: 806 sheet: -0.93 (0.27), residues: 315 loop : -1.49 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 74 TYR 0.014 0.001 TYR A 552 PHE 0.013 0.001 PHE E 159 TRP 0.018 0.001 TRP F 393 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (18051) covalent geometry : angle 0.67658 / 0.31 (24636) hydrogen bonds : bond 0.03869 / 2.69 ( 640) hydrogen bonds : angle 4.70170 / 3.35 ( 1818) metal coordination : bond 0.00567 / 0.40 ( 12) metal coordination : angle 2.15075 / 1.18 ( 12) link_TRANS : bond 0.00010 / 0.01 ( 1) link_TRANS : angle 0.18039 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4697 (ptm) cc_final: 0.4432 (ptp) REVERT: A 71 MET cc_start: 0.8095 (mtm) cc_final: 0.7654 (mtt) REVERT: A 91 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8825 (tp) REVERT: A 159 LYS cc_start: 0.8601 (tmmt) cc_final: 0.7973 (tppt) REVERT: A 341 ARG cc_start: 0.9067 (ptm-80) cc_final: 0.8715 (ptm-80) REVERT: A 375 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7844 (ptmt) REVERT: A 407 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: A 501 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8073 (p) REVERT: A 552 TYR cc_start: 0.7988 (m-80) cc_final: 0.7691 (m-80) REVERT: A 630 ARG cc_start: 0.8553 (mmt180) cc_final: 0.7746 (mpt180) REVERT: A 633 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7514 (mt) REVERT: A 755 ARG cc_start: 0.7449 (mtp85) cc_final: 0.6830 (mtp85) REVERT: A 757 GLU cc_start: 0.7561 (pt0) cc_final: 0.6971 (pt0) REVERT: A 773 MET cc_start: 0.8615 (mtp) cc_final: 0.8233 (mtp) REVERT: A 775 VAL cc_start: 0.6604 (OUTLIER) cc_final: 0.6205 (m) REVERT: B 122 LYS cc_start: 0.8288 (mttt) cc_final: 0.7877 (mttt) REVERT: B 123 MET cc_start: 0.7721 (ttt) cc_final: 0.7483 (ttm) REVERT: C 107 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8005 (ttp-110) REVERT: C 157 ARG cc_start: 0.7414 (mtt-85) cc_final: 0.7205 (mtm-85) REVERT: C 168 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: C 236 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8318 (m) REVERT: C 237 LYS cc_start: 0.8767 (ttpp) cc_final: 0.8368 (tptp) REVERT: C 263 ASP cc_start: 0.7728 (p0) cc_final: 0.7308 (p0) REVERT: C 267 LYS cc_start: 0.8474 (pttt) cc_final: 0.7541 (ptmm) REVERT: D 85 SER cc_start: 0.8812 (t) cc_final: 0.8557 (p) REVERT: D 94 GLN cc_start: 0.7405 (tp40) cc_final: 0.6999 (tp-100) REVERT: D 107 ARG cc_start: 0.8144 (mpt-90) cc_final: 0.7747 (mtt90) REVERT: D 185 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7658 (ptp-170) REVERT: E 3 LYS cc_start: 0.8906 (mtpm) cc_final: 0.8618 (ttpp) REVERT: E 129 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.8853 (t) REVERT: E 147 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: E 176 MET cc_start: 0.9020 (mmm) cc_final: 0.8426 (mmp) REVERT: F 117 LEU cc_start: 0.7875 (mt) cc_final: 0.7652 (mt) REVERT: F 301 MET cc_start: 0.6364 (ttm) cc_final: 0.5396 (tpp) outliers start: 51 outliers final: 23 residues processed: 282 average time/residue: 0.6100 time to fit residues: 190.7130 Evaluate side-chains 269 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 3 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 146 optimal weight: 0.0060 chunk 127 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 overall best weight: 0.4834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.180114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133547 restraints weight = 19364.013| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.88 r_work: 0.3159 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18064 Z= 0.111 Angle : 0.649 10.728 24651 Z= 0.299 Chirality : 0.054 0.549 2724 Planarity : 0.004 0.048 2992 Dihedral : 10.534 170.250 2931 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.72 % Allowed : 19.98 % Favored : 77.31 % 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 are not related in a simple way. whole: -0.70 (0.19), residues: 2006 helix: 0.68 (0.19), residues: 795 sheet: -0.93 (0.27), residues: 315 loop : -1.29 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 262 TYR 0.012 0.001 TYR A 552 PHE 0.013 0.001 PHE E 159 TRP 0.022 0.001 TRP F 393 HIS 0.004 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (18051) covalent geometry : angle 0.64747 / 0.30 (24636) hydrogen bonds : bond 0.03582 / 2.48 ( 640) hydrogen bonds : angle 4.51320 / 3.22 ( 1818) metal coordination : bond 0.00447 / 0.25 ( 12) metal coordination : angle 2.10889 / 1.15 ( 12) link_TRANS : bond 0.00001 / 0.00 ( 1) link_TRANS : angle 0.18237 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.5505 (pm20) cc_final: 0.5187 (pm20) REVERT: A 39 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7768 (mpt180) REVERT: A 65 MET cc_start: 0.4362 (ptm) cc_final: 0.3996 (ptp) REVERT: A 71 MET cc_start: 0.8086 (mtm) cc_final: 0.7649 (mtt) REVERT: A 91 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8832 (tp) REVERT: A 159 LYS cc_start: 0.8604 (tmmt) cc_final: 0.7989 (tppt) REVERT: A 160 ARG cc_start: 0.7236 (mmm-85) cc_final: 0.6983 (mtm180) REVERT: A 375 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7844 (ptmt) REVERT: A 443 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8057 (tt) REVERT: A 501 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8078 (p) REVERT: A 552 TYR cc_start: 0.8079 (m-80) cc_final: 0.7776 (m-80) REVERT: A 577 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7821 (tt0) REVERT: A 629 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: A 630 ARG cc_start: 0.8521 (mmt180) cc_final: 0.7685 (mpt180) REVERT: A 755 ARG cc_start: 0.7447 (mtp85) cc_final: 0.6813 (mtp85) REVERT: A 757 GLU cc_start: 0.7604 (pt0) cc_final: 0.7021 (pt0) REVERT: A 773 MET cc_start: 0.8654 (mtp) cc_final: 0.8224 (mtp) REVERT: B 122 LYS cc_start: 0.8252 (mttt) cc_final: 0.7902 (mttt) REVERT: B 123 MET cc_start: 0.7722 (ttt) cc_final: 0.7288 (ttm) REVERT: C 107 ARG cc_start: 0.8408 (ttp80) cc_final: 0.7939 (ttp-110) REVERT: C 168 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: C 236 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8249 (m) REVERT: C 237 LYS cc_start: 0.8776 (ttpp) cc_final: 0.8380 (tptp) REVERT: C 263 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7341 (p0) REVERT: D 85 SER cc_start: 0.8718 (t) cc_final: 0.8470 (p) REVERT: D 94 GLN cc_start: 0.7394 (tp40) cc_final: 0.6967 (tp-100) REVERT: D 107 ARG cc_start: 0.8139 (mpt-90) cc_final: 0.7684 (mtt90) REVERT: E 3 LYS cc_start: 0.8884 (mtpm) cc_final: 0.8598 (ttpp) REVERT: E 35 ILE cc_start: 0.8865 (pt) cc_final: 0.8639 (mt) REVERT: E 129 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.8844 (t) REVERT: E 147 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: E 262 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8245 (ttm110) REVERT: F 301 MET cc_start: 0.6350 (ttm) cc_final: 0.5390 (tpp) outliers start: 45 outliers final: 22 residues processed: 276 average time/residue: 0.6253 time to fit residues: 191.7616 Evaluate side-chains 262 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 160 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 173 optimal weight: 0.3980 chunk 122 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 111 optimal weight: 0.0370 chunk 139 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133021 restraints weight = 19290.286| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.87 r_work: 0.3115 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18064 Z= 0.114 Angle : 0.648 10.487 24651 Z= 0.300 Chirality : 0.053 0.561 2724 Planarity : 0.004 0.080 2992 Dihedral : 10.508 169.658 2931 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.78 % Allowed : 20.70 % Favored : 76.52 % 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 are not related in a simple way. whole: -0.52 (0.19), residues: 2006 helix: 0.93 (0.19), residues: 782 sheet: -0.92 (0.27), residues: 315 loop : -1.24 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 74 TYR 0.011 0.001 TYR A 727 PHE 0.013 0.001 PHE E 159 TRP 0.025 0.001 TRP F 393 HIS 0.006 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (18051) covalent geometry : angle 0.64706 / 0.30 (24636) hydrogen bonds : bond 0.03553 / 2.47 ( 640) hydrogen bonds : angle 4.46446 / 3.19 ( 1818) metal coordination : bond 0.00457 / 0.29 ( 12) metal coordination : angle 2.07021 / 1.12 ( 12) link_TRANS : bond 0.00004 / 0.00 ( 1) link_TRANS : angle 0.17595 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7533 (mpt180) REVERT: A 65 MET cc_start: 0.4388 (ptm) cc_final: 0.4009 (ptp) REVERT: A 71 MET cc_start: 0.8101 (mtm) cc_final: 0.7644 (mtt) REVERT: A 91 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8798 (tp) REVERT: A 159 LYS cc_start: 0.8607 (tmmt) cc_final: 0.7925 (tppt) REVERT: A 160 ARG cc_start: 0.7185 (mmm-85) cc_final: 0.6936 (mtm180) REVERT: A 375 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7820 (ptmt) REVERT: A 501 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8048 (p) REVERT: A 552 TYR cc_start: 0.8064 (m-80) cc_final: 0.7760 (m-80) REVERT: A 577 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7840 (tt0) REVERT: A 630 ARG cc_start: 0.8472 (mmt180) cc_final: 0.7646 (mpt180) REVERT: A 755 ARG cc_start: 0.7395 (mtp85) cc_final: 0.6733 (mtp85) REVERT: A 757 GLU cc_start: 0.7595 (pt0) cc_final: 0.6990 (pt0) REVERT: A 773 MET cc_start: 0.8627 (mtp) cc_final: 0.8234 (mtp) REVERT: B 123 MET cc_start: 0.7733 (ttt) cc_final: 0.7414 (ttm) REVERT: C 107 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7870 (ttp-110) REVERT: C 168 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 236 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8265 (m) REVERT: C 237 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8377 (tptp) REVERT: C 263 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7268 (p0) REVERT: D 85 SER cc_start: 0.8672 (t) cc_final: 0.8433 (p) REVERT: D 94 GLN cc_start: 0.7394 (tp40) cc_final: 0.6998 (tp-100) REVERT: D 107 ARG cc_start: 0.8008 (mpt-90) cc_final: 0.7638 (mtt90) REVERT: D 199 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8549 (m-40) REVERT: E 3 LYS cc_start: 0.8884 (mtpm) cc_final: 0.8588 (ttpp) REVERT: E 129 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.8843 (t) REVERT: E 147 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: F 301 MET cc_start: 0.6330 (ttm) cc_final: 0.5315 (tpp) outliers start: 46 outliers final: 20 residues processed: 267 average time/residue: 0.6335 time to fit residues: 187.7462 Evaluate side-chains 253 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 142 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.0020 chunk 41 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.177997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131321 restraints weight = 19294.872| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.91 r_work: 0.3069 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18064 Z= 0.126 Angle : 0.654 10.119 24651 Z= 0.304 Chirality : 0.054 0.603 2724 Planarity : 0.004 0.075 2992 Dihedral : 10.508 168.353 2931 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.51 % Rotamer: Outliers : 2.60 % Allowed : 20.76 % Favored : 76.64 % 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 are not related in a simple way. whole: -0.43 (0.19), residues: 2006 helix: 1.02 (0.19), residues: 784 sheet: -0.85 (0.27), residues: 317 loop : -1.22 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 74 TYR 0.012 0.001 TYR E 90 PHE 0.015 0.001 PHE E 159 TRP 0.030 0.001 TRP F 393 HIS 0.007 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (18051) covalent geometry : angle 0.65281 / 0.30 (24636) hydrogen bonds : bond 0.03645 / 2.54 ( 640) hydrogen bonds : angle 4.48056 / 3.20 ( 1818) metal coordination : bond 0.00614 / 0.45 ( 12) metal coordination : angle 2.12854 / 1.16 ( 12) link_TRANS : bond 0.00010 / 0.01 ( 1) link_TRANS : angle 0.15718 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7548 (mpt180) REVERT: A 65 MET cc_start: 0.4455 (ptm) cc_final: 0.4198 (ptp) REVERT: A 71 MET cc_start: 0.8091 (mtm) cc_final: 0.7769 (mtt) REVERT: A 91 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8794 (tp) REVERT: A 159 LYS cc_start: 0.8579 (tmmt) cc_final: 0.7938 (tppt) REVERT: A 375 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7867 (ptmt) REVERT: A 443 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8282 (tt) REVERT: A 501 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8045 (p) REVERT: A 577 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7867 (tt0) REVERT: A 630 ARG cc_start: 0.8482 (mmt180) cc_final: 0.7650 (mpt180) REVERT: A 755 ARG cc_start: 0.7457 (mtp85) cc_final: 0.6793 (mtp85) REVERT: A 757 GLU cc_start: 0.7630 (pt0) cc_final: 0.7046 (pt0) REVERT: A 773 MET cc_start: 0.8646 (mtp) cc_final: 0.8240 (mtp) REVERT: B 123 MET cc_start: 0.7823 (ttt) cc_final: 0.7471 (ttm) REVERT: C 107 ARG cc_start: 0.8378 (ttp80) cc_final: 0.7930 (ttp-110) REVERT: C 157 ARG cc_start: 0.7527 (mtm-85) cc_final: 0.7174 (mtm-85) REVERT: C 168 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: C 236 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8319 (m) REVERT: C 237 LYS cc_start: 0.8820 (ttpp) cc_final: 0.8408 (tptp) REVERT: C 263 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7322 (p0) REVERT: D 85 SER cc_start: 0.8677 (t) cc_final: 0.8438 (p) REVERT: D 94 GLN cc_start: 0.7364 (tp40) cc_final: 0.6971 (tp-100) REVERT: D 107 ARG cc_start: 0.8026 (mpt-90) cc_final: 0.7536 (mtt90) REVERT: E 129 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.8849 (t) REVERT: E 147 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: E 262 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8060 (ttm-80) REVERT: F 117 LEU cc_start: 0.8096 (mt) cc_final: 0.7873 (mt) REVERT: F 215 LYS cc_start: 0.8607 (mptm) cc_final: 0.8125 (mmtp) REVERT: F 301 MET cc_start: 0.6301 (ttm) cc_final: 0.5334 (tpp) outliers start: 43 outliers final: 21 residues processed: 265 average time/residue: 0.6827 time to fit residues: 200.4491 Evaluate side-chains 254 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 115 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 79 optimal weight: 0.0570 chunk 88 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 456 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.177695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131321 restraints weight = 19124.234| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.87 r_work: 0.3115 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18064 Z= 0.131 Angle : 0.658 10.245 24651 Z= 0.306 Chirality : 0.054 0.597 2724 Planarity : 0.004 0.069 2992 Dihedral : 10.511 166.774 2931 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Rotamer: Outliers : 2.29 % Allowed : 21.42 % Favored : 76.28 % 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 are not related in a simple way. whole: -0.42 (0.19), residues: 2006 helix: 1.04 (0.19), residues: 785 sheet: -0.78 (0.27), residues: 311 loop : -1.26 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 74 TYR 0.015 0.001 TYR A 552 PHE 0.014 0.001 PHE E 159 TRP 0.031 0.001 TRP F 393 HIS 0.007 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (18051) covalent geometry : angle 0.65600 / 0.31 (24636) hydrogen bonds : bond 0.03663 / 2.55 ( 640) hydrogen bonds : angle 4.50139 / 3.21 ( 1818) metal coordination : bond 0.00633 / 0.46 ( 12) metal coordination : angle 2.20250 / 1.20 ( 12) link_TRANS : bond 0.00015 / 0.01 ( 1) link_TRANS : angle 0.16391 / 0.08 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4540 (ptm) cc_final: 0.4288 (ptp) REVERT: A 71 MET cc_start: 0.8165 (mtm) cc_final: 0.7894 (mtt) REVERT: A 91 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8795 (tp) REVERT: A 159 LYS cc_start: 0.8613 (tmmt) cc_final: 0.8004 (tppt) REVERT: A 375 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7843 (ptmt) REVERT: A 501 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8033 (p) REVERT: A 503 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: A 552 TYR cc_start: 0.8082 (m-80) cc_final: 0.7794 (m-80) REVERT: A 577 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7890 (tt0) REVERT: A 630 ARG cc_start: 0.8503 (mmt180) cc_final: 0.7655 (mpt180) REVERT: A 633 ILE cc_start: 0.7761 (tp) cc_final: 0.7282 (mt) REVERT: A 755 ARG cc_start: 0.7475 (mtp85) cc_final: 0.6802 (mtp85) REVERT: A 757 GLU cc_start: 0.7624 (pt0) cc_final: 0.7029 (pt0) REVERT: A 773 MET cc_start: 0.8662 (mtp) cc_final: 0.8191 (mtp) REVERT: B 123 MET cc_start: 0.7865 (ttt) cc_final: 0.7557 (ttm) REVERT: C 107 ARG cc_start: 0.8369 (ttp80) cc_final: 0.7883 (ttp-110) REVERT: C 157 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7217 (mtm-85) REVERT: C 168 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: C 236 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8281 (m) REVERT: C 237 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8410 (tptp) REVERT: C 263 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7428 (p0) REVERT: D 85 SER cc_start: 0.8681 (t) cc_final: 0.8437 (p) REVERT: D 94 GLN cc_start: 0.7383 (tp40) cc_final: 0.6998 (tp-100) REVERT: D 107 ARG cc_start: 0.7974 (mpt-90) cc_final: 0.7529 (mtt90) REVERT: E 129 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.8853 (t) REVERT: E 147 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: E 262 ARG cc_start: 0.8557 (ttm110) cc_final: 0.8295 (ttm110) REVERT: F 117 LEU cc_start: 0.8131 (mt) cc_final: 0.7917 (mt) REVERT: F 215 LYS cc_start: 0.8638 (mptm) cc_final: 0.8206 (mmtp) REVERT: F 301 MET cc_start: 0.6307 (ttm) cc_final: 0.5428 (tpp) REVERT: F 302 LYS cc_start: 0.6282 (mmmt) cc_final: 0.5763 (mmtt) outliers start: 38 outliers final: 20 residues processed: 251 average time/residue: 0.6896 time to fit residues: 191.9506 Evaluate side-chains 253 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 52 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 0.0030 chunk 144 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 456 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132511 restraints weight = 19296.738| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.90 r_work: 0.3100 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18064 Z= 0.115 Angle : 0.639 10.240 24651 Z= 0.298 Chirality : 0.053 0.525 2724 Planarity : 0.004 0.049 2992 Dihedral : 10.429 165.940 2931 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Rotamer: Outliers : 2.11 % Allowed : 21.61 % Favored : 76.28 % 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 are not related in a simple way. whole: -0.33 (0.19), residues: 2006 helix: 1.16 (0.19), residues: 782 sheet: -0.69 (0.28), residues: 301 loop : -1.25 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 341 TYR 0.015 0.001 TYR A 552 PHE 0.012 0.001 PHE E 159 TRP 0.033 0.001 TRP F 393 HIS 0.007 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (18051) covalent geometry : angle 0.63797 / 0.30 (24636) hydrogen bonds : bond 0.03474 / 2.42 ( 640) hydrogen bonds : angle 4.44549 / 3.17 ( 1818) metal coordination : bond 0.00476 / 0.29 ( 12) metal coordination : angle 2.10199 / 1.14 ( 12) link_TRANS : bond 0.00000 / 0.00 ( 1) link_TRANS : angle 0.16155 / 0.08 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6621.89 seconds wall clock time: 113 minutes 15.66 seconds (6795.66 seconds total)