Starting phenix.real_space_refine on Fri Sep 19 10:28:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi4_33851/09_2025/7yi4_33851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi4_33851/09_2025/7yi4_33851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yi4_33851/09_2025/7yi4_33851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi4_33851/09_2025/7yi4_33851.map" model { file = "/net/cci-nas-00/data/ceres_data/7yi4_33851/09_2025/7yi4_33851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi4_33851/09_2025/7yi4_33851.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 5 6.06 5 P 302 5.49 5 S 87 5.16 5 C 15143 2.51 5 N 4495 2.21 5 O 5319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25351 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4258 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 7, 'TRANS': 498} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2326 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "D" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2588 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 298} Chain breaks: 5 Chain: "F" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 178 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "H" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "I" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3076 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "P" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3115 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 853 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11022 SG CYS D 417 127.085 60.757 70.222 1.00548.42 S ATOM 11049 SG CYS D 420 128.395 57.216 70.769 1.00541.45 S ATOM 11305 SG CYS D 451 128.651 59.913 73.503 1.00488.09 S ATOM 9961 SG CYS D 263 92.512 95.032 76.495 1.00502.95 S ATOM 9978 SG CYS D 266 95.322 92.480 76.314 1.00506.17 S ATOM 10131 SG CYS D 286 96.001 95.688 78.071 1.00483.68 S ATOM 10266 SG CYS D 303 84.724 101.733 74.705 1.00517.62 S ATOM 10289 SG CYS D 306 80.870 104.261 73.937 1.00523.12 S ATOM 11210 SG CYS D 440 121.918 69.864 66.373 1.00572.63 S ATOM 11236 SG CYS D 443 124.633 69.527 63.545 1.00575.36 S ATOM 11425 SG CYS D 466 125.622 71.045 66.672 1.00567.07 S Time building chain proxies: 4.99, per 1000 atoms: 0.20 Number of scatterers: 25351 At special positions: 0 Unit cell: (177.53, 149.385, 145.055, 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 5 29.99 S 87 16.00 P 302 15.00 O 5319 8.00 N 4495 7.00 C 15143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 962.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 417 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 451 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 420 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 286 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 263 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 303 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 306 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 440 " Number of angles added : 9 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 21 sheets defined 59.4% alpha, 7.7% beta 147 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 678 through 694 Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 715 through 724 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.693A pdb=" N LEU A 778 " --> pdb=" O CYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.804A pdb=" N ALA A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 838 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 891 through 922 removed outlier: 3.784A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 removed outlier: 3.865A pdb=" N LEU A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 removed outlier: 4.081A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 Processing helix chain 'A' and resid 944 through 961 Processing helix chain 'A' and resid 983 through 999 Processing helix chain 'A' and resid 1003 through 1023 Processing helix chain 'A' and resid 1141 through 1164 removed outlier: 4.110A pdb=" N MET A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1174 removed outlier: 3.728A pdb=" N VAL A1168 " --> pdb=" O MET A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.954A pdb=" N MET A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1233 Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'A' and resid 1241 through 1259 Processing helix chain 'A' and resid 1259 through 1276 removed outlier: 3.501A pdb=" N SER A1276 " --> pdb=" O ASP A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1294 removed outlier: 4.240A pdb=" N ILE A1284 " --> pdb=" O ALA A1280 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 32 removed outlier: 4.077A pdb=" N GLY B 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.758A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 115 through 137 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.527A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 263 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 300 removed outlier: 4.321A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.505A pdb=" N GLY B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.935A pdb=" N ASN C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.637A pdb=" N ASP C 89 " --> pdb=" O SER C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 124 Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.586A pdb=" N VAL C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 297 removed outlier: 5.251A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 316 removed outlier: 4.377A pdb=" N GLN C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.985A pdb=" N SER C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 369 removed outlier: 3.934A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 4.127A pdb=" N MET C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 168 through 175 removed outlier: 4.055A pdb=" N LEU D 171 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU D 173 " --> pdb=" O PHE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 removed outlier: 4.478A pdb=" N GLY D 186 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 330 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 344 through 346 No H-bonds generated for 'chain 'D' and resid 344 through 346' Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.806A pdb=" N THR D 405 " --> pdb=" O ASN D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 544 through 564 removed outlier: 3.580A pdb=" N LYS D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 549 " --> pdb=" O ASN D 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 563 Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 removed outlier: 3.814A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'I' and resid 16 through 22 Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 46 through 73 Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.516A pdb=" N LEU I 115 " --> pdb=" O GLN I 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 82 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 101 through 121 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 50 through 76 removed outlier: 3.708A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 46 through 73 Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 101 through 121 Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.152A pdb=" N ASN E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 4.118A pdb=" N ASP E 89 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 124 Processing helix chain 'G' and resid 44 through 55 removed outlier: 3.587A pdb=" N LEU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 75 Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 removed outlier: 3.853A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 removed outlier: 3.594A pdb=" N LYS K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER K 57 " --> pdb=" O ARG K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 77 removed outlier: 3.974A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 64 removed outlier: 7.008A pdb=" N VAL B 21 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR B 64 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR B 23 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 142 " --> pdb=" O MET B 305 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 307 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS B 210 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.522A pdb=" N PHE C 78 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.759A pdb=" N LEU C 15 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'D' and resid 364 through 366 Processing sheet with id=AA8, first strand: chain 'D' and resid 473 through 476 Processing sheet with id=AA9, first strand: chain 'D' and resid 505 through 506 removed outlier: 3.818A pdb=" N TYR D 506 " --> pdb=" O ILE D 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 45 through 46 removed outlier: 7.527A pdb=" N ARG H 45 " --> pdb=" O ILE G 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'H' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'H' and resid 96 through 97 removed outlier: 6.416A pdb=" N THR H 96 " --> pdb=" O THR M 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.738A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'I' and resid 100 through 102 Processing sheet with id=AB7, first strand: chain 'L' and resid 45 through 46 removed outlier: 7.939A pdb=" N ARG L 45 " --> pdb=" O ILE K 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AB9, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.185A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AC2, first strand: chain 'E' and resid 59 through 60 removed outlier: 3.677A pdb=" N GLN E 59 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE E 78 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE E 30 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS E 76 " --> pdb=" O ILE E 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 59 through 60 removed outlier: 3.677A pdb=" N GLN E 59 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA E 25 " --> pdb=" O CYS E 14 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS E 14 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 15 " --> pdb=" O ARG E 98 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 2997 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 6.51 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6819 1.34 - 1.46: 6865 1.46 - 1.58: 12052 1.58 - 1.70: 602 1.70 - 1.82: 137 Bond restraints: 26475 Sorted by residual: bond pdb=" CG MET B 47 " pdb=" SD MET B 47 " ideal model delta sigma weight residual 1.803 1.748 0.055 2.50e-02 1.60e+03 4.91e+00 bond pdb=" CB ARG E 110 " pdb=" CG ARG E 110 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CA MET B 305 " pdb=" CB MET B 305 " ideal model delta sigma weight residual 1.535 1.564 -0.029 2.09e-02 2.29e+03 1.88e+00 bond pdb=" N ALA M 47 " pdb=" CA ALA M 47 " ideal model delta sigma weight residual 1.463 1.454 0.009 6.90e-03 2.10e+04 1.62e+00 bond pdb=" CA LEU L 49 " pdb=" CB LEU L 49 " ideal model delta sigma weight residual 1.529 1.545 -0.016 1.34e-02 5.57e+03 1.40e+00 ... (remaining 26470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 36891 3.45 - 6.91: 99 6.91 - 10.36: 10 10.36 - 13.81: 7 13.81 - 17.27: 1 Bond angle restraints: 37008 Sorted by residual: angle pdb=" CA MET A1164 " pdb=" CB MET A1164 " pdb=" CG MET A1164 " ideal model delta sigma weight residual 114.10 125.18 -11.08 2.00e+00 2.50e-01 3.07e+01 angle pdb=" CA MET B 47 " pdb=" CB MET B 47 " pdb=" CG MET B 47 " ideal model delta sigma weight residual 114.10 124.46 -10.36 2.00e+00 2.50e-01 2.69e+01 angle pdb=" CA LEU L 49 " pdb=" CB LEU L 49 " pdb=" CG LEU L 49 " ideal model delta sigma weight residual 116.30 133.57 -17.27 3.50e+00 8.16e-02 2.43e+01 angle pdb=" N MET B 47 " pdb=" CA MET B 47 " pdb=" CB MET B 47 " ideal model delta sigma weight residual 110.40 117.37 -6.97 1.63e+00 3.76e-01 1.83e+01 angle pdb=" CB ARG E 110 " pdb=" CG ARG E 110 " pdb=" CD ARG E 110 " ideal model delta sigma weight residual 111.30 121.00 -9.70 2.30e+00 1.89e-01 1.78e+01 ... (remaining 37003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 13107 31.31 - 62.62: 1975 62.62 - 93.92: 73 93.92 - 125.23: 0 125.23 - 156.54: 1 Dihedral angle restraints: 15156 sinusoidal: 8247 harmonic: 6909 Sorted by residual: dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA MET B 61 " pdb=" C MET B 61 " pdb=" N GLU B 62 " pdb=" CA GLU B 62 " ideal model delta harmonic sigma weight residual 180.00 158.77 21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA MET A1194 " pdb=" C MET A1194 " pdb=" N GLY A1195 " pdb=" CA GLY A1195 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 15153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2941 0.035 - 0.069: 879 0.069 - 0.104: 188 0.104 - 0.139: 59 0.139 - 0.173: 9 Chirality restraints: 4076 Sorted by residual: chirality pdb=" CA MET B 47 " pdb=" N MET B 47 " pdb=" C MET B 47 " pdb=" CB MET B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA GLU C 255 " pdb=" N GLU C 255 " pdb=" C GLU C 255 " pdb=" CB GLU C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA GLU A 918 " pdb=" N GLU A 918 " pdb=" C GLU A 918 " pdb=" CB GLU A 918 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 4073 not shown) Planarity restraints: 3647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1164 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C MET A1164 " -0.047 2.00e-02 2.50e+03 pdb=" O MET A1164 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A1165 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO D 119 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA O -35 " -0.027 2.00e-02 2.50e+03 1.20e-02 3.97e+00 pdb=" N9 DA O -35 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA O -35 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA O -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA O -35 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA O -35 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA O -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA O -35 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA O -35 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA O -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA O -35 " 0.002 2.00e-02 2.50e+03 ... (remaining 3644 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 340 2.61 - 3.18: 21588 3.18 - 3.76: 45805 3.76 - 4.33: 60120 4.33 - 4.90: 90715 Nonbonded interactions: 218568 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.041 2.230 nonbonded pdb=" OG SER C 313 " pdb=" O LYS C 318 " model vdw 2.062 3.040 nonbonded pdb=" O2 DC O 70 " pdb=" N2 DG P -70 " model vdw 2.115 2.496 nonbonded pdb=" O2 DC O -21 " pdb=" N2 DG P 21 " model vdw 2.134 2.496 nonbonded pdb=" O2 DC O -50 " pdb=" N2 DG P 50 " model vdw 2.159 2.496 ... (remaining 218563 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 'G' and (resid 36 through 109 or (resid 110 through 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 134)) selection = chain 'K' } ncs_group { reference = chain 'H' selection = (chain 'L' and resid 23 through 101) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.760 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.004 0.055 26490 Z= 0.170 Angle : 0.614 17.267 37017 Z= 0.345 Chirality : 0.036 0.173 4076 Planarity : 0.004 0.068 3647 Dihedral : 23.495 156.538 10692 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.10 % Allowed : 19.33 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.18), residues: 2302 helix: 1.96 (0.15), residues: 1279 sheet: 0.32 (0.53), residues: 110 loop : -1.01 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 324 TYR 0.028 0.001 TYR L 88 PHE 0.014 0.001 PHE C 289 TRP 0.015 0.001 TRP A 912 HIS 0.017 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00353 (26475) covalent geometry : angle 0.61064 (37008) hydrogen bonds : bond 0.13308 ( 1409) hydrogen bonds : angle 5.27824 ( 3733) metal coordination : bond 0.01496 ( 15) metal coordination : angle 4.17566 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6705 (tpt) cc_final: 0.5145 (tmm) REVERT: B 47 MET cc_start: 0.3151 (pmm) cc_final: 0.2836 (pmm) REVERT: B 61 MET cc_start: 0.7266 (mpp) cc_final: 0.6687 (mpp) REVERT: B 306 MET cc_start: 0.9071 (mmm) cc_final: 0.8567 (tpp) REVERT: D 316 MET cc_start: 0.7751 (mmm) cc_final: 0.7473 (mmm) outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.1565 time to fit residues: 16.7755 Evaluate side-chains 61 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 258 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 GLN C 101 ASN D 116 ASN D 325 ASN D 503 GLN N 44 GLN E 80 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.035280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.022848 restraints weight = 392225.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.023191 restraints weight = 251814.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.023412 restraints weight = 186382.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.023572 restraints weight = 155878.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.023603 restraints weight = 138533.251| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26490 Z= 0.213 Angle : 0.575 9.798 37017 Z= 0.325 Chirality : 0.037 0.145 4076 Planarity : 0.004 0.047 3647 Dihedral : 26.278 154.792 5889 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.49 % Allowed : 18.03 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.18), residues: 2302 helix: 2.06 (0.14), residues: 1299 sheet: 0.29 (0.52), residues: 112 loop : -0.95 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 324 TYR 0.014 0.001 TYR E 38 PHE 0.011 0.001 PHE L 61 TRP 0.010 0.001 TRP A 912 HIS 0.006 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00451 (26475) covalent geometry : angle 0.57139 (37008) hydrogen bonds : bond 0.05953 ( 1409) hydrogen bonds : angle 4.17820 ( 3733) metal coordination : bond 0.00810 ( 15) metal coordination : angle 4.05108 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6835 (tpt) cc_final: 0.5052 (tmm) REVERT: A 773 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6137 (pmm) REVERT: B 19 ARG cc_start: 0.3244 (OUTLIER) cc_final: 0.1703 (mpp80) REVERT: B 61 MET cc_start: 0.7355 (mpp) cc_final: 0.6953 (mpp) REVERT: B 128 MET cc_start: 0.5618 (OUTLIER) cc_final: 0.5207 (mmm) REVERT: B 305 MET cc_start: 0.8420 (ppp) cc_final: 0.8076 (ppp) REVERT: B 315 MET cc_start: 0.2973 (pmm) cc_final: 0.2609 (pmm) REVERT: C 22 MET cc_start: 0.7845 (mpp) cc_final: 0.7188 (mpp) REVERT: D 316 MET cc_start: 0.8150 (mmm) cc_final: 0.7864 (mmm) REVERT: L 58 LEU cc_start: 0.9829 (OUTLIER) cc_final: 0.9589 (pp) REVERT: K 90 MET cc_start: 0.9188 (mmp) cc_final: 0.8861 (mmm) outliers start: 31 outliers final: 10 residues processed: 84 average time/residue: 0.1661 time to fit residues: 22.6723 Evaluate side-chains 73 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 540 THR Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 15 LYS Chi-restraints excluded: chain E residue 22 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 255 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 127 optimal weight: 50.0000 chunk 227 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 81 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.034974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.022501 restraints weight = 399124.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.022801 restraints weight = 254867.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.023008 restraints weight = 192540.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.023116 restraints weight = 161356.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.023208 restraints weight = 146999.054| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26490 Z= 0.200 Angle : 0.563 10.743 37017 Z= 0.317 Chirality : 0.037 0.169 4076 Planarity : 0.004 0.040 3647 Dihedral : 26.447 154.994 5889 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.02 % Allowed : 18.12 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.18), residues: 2302 helix: 2.08 (0.14), residues: 1302 sheet: 0.30 (0.52), residues: 106 loop : -0.85 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 110 TYR 0.013 0.001 TYR E 38 PHE 0.011 0.001 PHE L 61 TRP 0.013 0.001 TRP C 91 HIS 0.007 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00429 (26475) covalent geometry : angle 0.55925 (37008) hydrogen bonds : bond 0.05403 ( 1409) hydrogen bonds : angle 3.97055 ( 3733) metal coordination : bond 0.00745 ( 15) metal coordination : angle 4.07504 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 59 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6944 (tpt) cc_final: 0.5641 (tmm) REVERT: A 1194 MET cc_start: 0.4004 (tmm) cc_final: 0.3562 (ppp) REVERT: B 61 MET cc_start: 0.7701 (mpp) cc_final: 0.7331 (mpp) REVERT: B 128 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5421 (mmm) REVERT: B 305 MET cc_start: 0.8571 (ppp) cc_final: 0.8368 (ppp) REVERT: C 22 MET cc_start: 0.7481 (mpp) cc_final: 0.7007 (mmp) REVERT: C 256 MET cc_start: 0.9038 (ptp) cc_final: 0.8581 (ptp) REVERT: C 347 MET cc_start: 0.2076 (tpp) cc_final: 0.1736 (tpp) REVERT: D 316 MET cc_start: 0.8398 (mmm) cc_final: 0.8099 (mmm) REVERT: D 375 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6160 (pm20) REVERT: L 58 LEU cc_start: 0.9834 (OUTLIER) cc_final: 0.9606 (pp) outliers start: 42 outliers final: 20 residues processed: 95 average time/residue: 0.1554 time to fit residues: 23.9739 Evaluate side-chains 81 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 15 LYS Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 20.0000 chunk 61 optimal weight: 50.0000 chunk 245 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 237 optimal weight: 50.0000 chunk 57 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN E 82 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.035244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.022663 restraints weight = 393228.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.023034 restraints weight = 257080.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.023211 restraints weight = 194200.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.023349 restraints weight = 165792.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.023392 restraints weight = 149895.395| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26490 Z= 0.163 Angle : 0.540 11.222 37017 Z= 0.305 Chirality : 0.036 0.154 4076 Planarity : 0.004 0.040 3647 Dihedral : 26.389 154.465 5889 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.83 % Allowed : 18.56 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.18), residues: 2302 helix: 2.29 (0.14), residues: 1294 sheet: 0.13 (0.55), residues: 97 loop : -0.83 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 770 TYR 0.011 0.001 TYR E 81 PHE 0.010 0.001 PHE B 113 TRP 0.011 0.001 TRP A 775 HIS 0.014 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00346 (26475) covalent geometry : angle 0.53715 (37008) hydrogen bonds : bond 0.04725 ( 1409) hydrogen bonds : angle 3.81048 ( 3733) metal coordination : bond 0.00640 ( 15) metal coordination : angle 3.61863 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6700 (tpt) cc_final: 0.5286 (tmm) REVERT: A 773 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7028 (ppp) REVERT: A 1194 MET cc_start: 0.4277 (tmm) cc_final: 0.3723 (ppp) REVERT: B 19 ARG cc_start: 0.3908 (OUTLIER) cc_final: 0.3080 (mtm180) REVERT: B 61 MET cc_start: 0.7755 (mpp) cc_final: 0.7255 (mpp) REVERT: B 128 MET cc_start: 0.5807 (OUTLIER) cc_final: 0.5463 (mmm) REVERT: C 22 MET cc_start: 0.7290 (mpp) cc_final: 0.6301 (tpp) REVERT: C 256 MET cc_start: 0.9151 (ptp) cc_final: 0.8720 (ptp) REVERT: C 347 MET cc_start: 0.2181 (tpp) cc_final: 0.1716 (tpp) REVERT: D 316 MET cc_start: 0.8622 (mmm) cc_final: 0.8222 (mmm) REVERT: L 58 LEU cc_start: 0.9825 (OUTLIER) cc_final: 0.9585 (pp) outliers start: 38 outliers final: 18 residues processed: 91 average time/residue: 0.1775 time to fit residues: 25.9176 Evaluate side-chains 79 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 15 LYS Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 162 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 6 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 53 optimal weight: 50.0000 chunk 188 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS ** A1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.034151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.021741 restraints weight = 403991.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.022007 restraints weight = 283010.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.022148 restraints weight = 227015.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.022190 restraints weight = 197574.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.022269 restraints weight = 186992.917| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 26490 Z= 0.287 Angle : 0.638 10.783 37017 Z= 0.354 Chirality : 0.040 0.205 4076 Planarity : 0.004 0.040 3647 Dihedral : 26.798 155.508 5889 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.02 % Allowed : 18.99 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.18), residues: 2302 helix: 2.03 (0.14), residues: 1295 sheet: 0.23 (0.52), residues: 105 loop : -0.85 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 110 TYR 0.012 0.001 TYR D 442 PHE 0.018 0.002 PHE E 78 TRP 0.009 0.001 TRP E 88 HIS 0.008 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00619 (26475) covalent geometry : angle 0.63475 (37008) hydrogen bonds : bond 0.07858 ( 1409) hydrogen bonds : angle 4.11146 ( 3733) metal coordination : bond 0.01110 ( 15) metal coordination : angle 4.38699 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 59 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.7017 (tpt) cc_final: 0.6675 (tpt) REVERT: A 1194 MET cc_start: 0.4424 (tmm) cc_final: 0.3787 (ppp) REVERT: B 19 ARG cc_start: 0.3857 (OUTLIER) cc_final: 0.3172 (mpp80) REVERT: B 47 MET cc_start: 0.3872 (pmm) cc_final: 0.3536 (pmm) REVERT: B 61 MET cc_start: 0.7483 (mpp) cc_final: 0.6994 (mpp) REVERT: B 308 VAL cc_start: 0.9538 (OUTLIER) cc_final: 0.9269 (p) REVERT: B 315 MET cc_start: 0.4588 (pmm) cc_final: 0.3863 (pmm) REVERT: C 22 MET cc_start: 0.7223 (mpp) cc_final: 0.6879 (mmp) REVERT: C 296 MET cc_start: 0.9538 (pmm) cc_final: 0.8891 (tpt) REVERT: C 347 MET cc_start: 0.2407 (tpp) cc_final: 0.1725 (tpp) REVERT: D 316 MET cc_start: 0.8658 (mmm) cc_final: 0.8149 (mmm) REVERT: G 90 MET cc_start: 0.8916 (ptt) cc_final: 0.8621 (ptt) REVERT: K 120 MET cc_start: 0.9280 (mmm) cc_final: 0.8976 (mmm) outliers start: 42 outliers final: 30 residues processed: 94 average time/residue: 0.1616 time to fit residues: 25.4454 Evaluate side-chains 89 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain M residue 15 LYS Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 102 optimal weight: 7.9990 chunk 14 optimal weight: 40.0000 chunk 163 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 47 optimal weight: 40.0000 chunk 218 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 119 optimal weight: 40.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN D 346 HIS D 510 GLN E 59 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.035029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.022338 restraints weight = 391569.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.022592 restraints weight = 270418.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.022785 restraints weight = 211546.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.022914 restraints weight = 179617.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.022997 restraints weight = 162648.533| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26490 Z= 0.149 Angle : 0.551 12.106 37017 Z= 0.308 Chirality : 0.036 0.153 4076 Planarity : 0.003 0.042 3647 Dihedral : 26.688 154.810 5889 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.83 % Allowed : 19.18 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.18), residues: 2302 helix: 2.32 (0.14), residues: 1291 sheet: 0.22 (0.56), residues: 96 loop : -0.74 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 72 TYR 0.010 0.001 TYR E 38 PHE 0.011 0.001 PHE E 78 TRP 0.008 0.001 TRP C 91 HIS 0.004 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00317 (26475) covalent geometry : angle 0.54816 (37008) hydrogen bonds : bond 0.04459 ( 1409) hydrogen bonds : angle 3.80358 ( 3733) metal coordination : bond 0.00583 ( 15) metal coordination : angle 3.48568 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 57 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7147 (ppp) REVERT: A 1194 MET cc_start: 0.4266 (tmm) cc_final: 0.3967 (ppp) REVERT: B 19 ARG cc_start: 0.4259 (OUTLIER) cc_final: 0.2715 (mtm180) REVERT: B 47 MET cc_start: 0.3678 (pmm) cc_final: 0.3259 (pmm) REVERT: B 61 MET cc_start: 0.7503 (mpp) cc_final: 0.7062 (mpp) REVERT: B 128 MET cc_start: 0.5690 (OUTLIER) cc_final: 0.5317 (mmp) REVERT: B 204 MET cc_start: -0.1953 (mmm) cc_final: -0.2215 (mmm) REVERT: B 305 MET cc_start: 0.8427 (ppp) cc_final: 0.7870 (ppp) REVERT: C 22 MET cc_start: 0.7522 (mpp) cc_final: 0.6682 (tpp) REVERT: C 347 MET cc_start: 0.2550 (tpp) cc_final: 0.1862 (tpp) REVERT: D 316 MET cc_start: 0.8854 (mmm) cc_final: 0.8389 (mmm) REVERT: N 56 MET cc_start: 0.8999 (ppp) cc_final: 0.8656 (ppp) REVERT: G 90 MET cc_start: 0.8760 (ptt) cc_final: 0.8438 (ptt) REVERT: K 120 MET cc_start: 0.9287 (mmm) cc_final: 0.8940 (mmm) outliers start: 38 outliers final: 24 residues processed: 89 average time/residue: 0.1573 time to fit residues: 23.6056 Evaluate side-chains 84 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 81 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 16 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 175 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 40 optimal weight: 40.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** 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 = 0.3387 r_free = 0.3387 target = 0.034394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.022095 restraints weight = 398263.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.022327 restraints weight = 277716.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.022496 restraints weight = 219343.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.022646 restraints weight = 189690.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.022680 restraints weight = 170357.506| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26490 Z= 0.240 Angle : 0.598 11.745 37017 Z= 0.333 Chirality : 0.038 0.154 4076 Planarity : 0.004 0.041 3647 Dihedral : 26.762 154.993 5889 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.83 % Allowed : 19.52 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.18), residues: 2302 helix: 2.21 (0.14), residues: 1292 sheet: 0.24 (0.53), residues: 105 loop : -0.76 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 76 TYR 0.010 0.001 TYR C 326 PHE 0.014 0.001 PHE E 78 TRP 0.008 0.001 TRP D 464 HIS 0.005 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00517 (26475) covalent geometry : angle 0.59483 (37008) hydrogen bonds : bond 0.06451 ( 1409) hydrogen bonds : angle 3.97829 ( 3733) metal coordination : bond 0.00814 ( 15) metal coordination : angle 3.96382 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 57 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6807 (tpt) cc_final: 0.5549 (tmm) REVERT: A 1194 MET cc_start: 0.4485 (tmm) cc_final: 0.4150 (ppp) REVERT: B 19 ARG cc_start: 0.4319 (OUTLIER) cc_final: 0.2577 (mpp80) REVERT: B 47 MET cc_start: 0.3745 (pmm) cc_final: 0.3338 (pmm) REVERT: B 61 MET cc_start: 0.7617 (mpp) cc_final: 0.7264 (mpp) REVERT: B 305 MET cc_start: 0.8659 (ppp) cc_final: 0.7963 (ppp) REVERT: B 308 VAL cc_start: 0.9561 (OUTLIER) cc_final: 0.9309 (p) REVERT: C 22 MET cc_start: 0.7434 (mpp) cc_final: 0.7219 (mmp) REVERT: C 347 MET cc_start: 0.2339 (tpp) cc_final: 0.1581 (tpp) REVERT: D 300 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6470 (t0) REVERT: D 316 MET cc_start: 0.8888 (mmm) cc_final: 0.8429 (mmm) REVERT: G 90 MET cc_start: 0.8914 (ptt) cc_final: 0.8559 (ptt) REVERT: K 120 MET cc_start: 0.9274 (mmm) cc_final: 0.8957 (mmm) outliers start: 38 outliers final: 25 residues processed: 90 average time/residue: 0.1494 time to fit residues: 22.7289 Evaluate side-chains 85 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 81 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 50.0000 chunk 254 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 67 optimal weight: 40.0000 chunk 144 optimal weight: 50.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN A1254 HIS E 59 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.034772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.022174 restraints weight = 391808.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.022501 restraints weight = 271563.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.022660 restraints weight = 209795.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.022732 restraints weight = 182928.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.022793 restraints weight = 169477.811| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26490 Z= 0.171 Angle : 0.570 12.259 37017 Z= 0.316 Chirality : 0.037 0.144 4076 Planarity : 0.003 0.042 3647 Dihedral : 26.757 154.322 5889 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.59 % Allowed : 20.19 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.18), residues: 2302 helix: 2.29 (0.14), residues: 1291 sheet: 0.13 (0.56), residues: 95 loop : -0.69 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 76 TYR 0.015 0.001 TYR L 88 PHE 0.016 0.001 PHE B 324 TRP 0.008 0.001 TRP E 91 HIS 0.006 0.001 HIS A1254 Details of bonding type rmsd covalent geometry : bond 0.00365 (26475) covalent geometry : angle 0.56757 (37008) hydrogen bonds : bond 0.04944 ( 1409) hydrogen bonds : angle 3.84953 ( 3733) metal coordination : bond 0.00602 ( 15) metal coordination : angle 3.63092 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6587 (tpt) cc_final: 0.5229 (tmm) REVERT: A 773 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7272 (ppp) REVERT: A 1194 MET cc_start: 0.4531 (tmm) cc_final: 0.4166 (ppp) REVERT: B 19 ARG cc_start: 0.4800 (OUTLIER) cc_final: 0.2879 (mpp80) REVERT: B 47 MET cc_start: 0.3630 (pmm) cc_final: 0.3352 (pmm) REVERT: B 61 MET cc_start: 0.7745 (mpp) cc_final: 0.7378 (mpp) REVERT: B 288 MET cc_start: 0.7117 (tpt) cc_final: 0.5925 (tpt) REVERT: B 305 MET cc_start: 0.8633 (ppp) cc_final: 0.7927 (ppp) REVERT: B 308 VAL cc_start: 0.9483 (OUTLIER) cc_final: 0.9249 (p) REVERT: C 22 MET cc_start: 0.7631 (mpp) cc_final: 0.6944 (tpp) REVERT: C 347 MET cc_start: 0.2284 (tpp) cc_final: 0.1475 (tpp) REVERT: D 300 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6510 (t0) REVERT: D 316 MET cc_start: 0.8952 (mmm) cc_final: 0.8373 (mmm) REVERT: G 90 MET cc_start: 0.8848 (ptt) cc_final: 0.8477 (ptt) REVERT: K 120 MET cc_start: 0.9254 (mmm) cc_final: 0.8934 (mmm) outliers start: 33 outliers final: 26 residues processed: 86 average time/residue: 0.1618 time to fit residues: 23.0956 Evaluate side-chains 87 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 81 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 235 optimal weight: 50.0000 chunk 113 optimal weight: 30.0000 chunk 84 optimal weight: 50.0000 chunk 210 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 31 optimal weight: 0.0050 chunk 237 optimal weight: 4.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.034707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.022209 restraints weight = 394344.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.022477 restraints weight = 268915.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.022575 restraints weight = 210255.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.022727 restraints weight = 186094.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.022816 restraints weight = 170635.672| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26490 Z= 0.176 Angle : 0.578 12.454 37017 Z= 0.318 Chirality : 0.037 0.139 4076 Planarity : 0.003 0.042 3647 Dihedral : 26.681 153.326 5889 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.59 % Allowed : 20.10 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.18), residues: 2302 helix: 2.32 (0.14), residues: 1298 sheet: 0.17 (0.56), residues: 95 loop : -0.72 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 72 TYR 0.014 0.001 TYR L 88 PHE 0.010 0.001 PHE E 78 TRP 0.008 0.001 TRP E 91 HIS 0.010 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00376 (26475) covalent geometry : angle 0.57603 (37008) hydrogen bonds : bond 0.05162 ( 1409) hydrogen bonds : angle 3.81904 ( 3733) metal coordination : bond 0.00570 ( 15) metal coordination : angle 3.45338 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6435 (tpt) cc_final: 0.5071 (tmm) REVERT: A 773 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7308 (ppp) REVERT: A 1194 MET cc_start: 0.4621 (tmm) cc_final: 0.4245 (ppp) REVERT: B 47 MET cc_start: 0.3740 (pmm) cc_final: 0.3461 (pmm) REVERT: B 61 MET cc_start: 0.7648 (mpp) cc_final: 0.7284 (mpp) REVERT: B 305 MET cc_start: 0.8569 (ppp) cc_final: 0.8003 (ppp) REVERT: B 308 VAL cc_start: 0.9439 (OUTLIER) cc_final: 0.9183 (p) REVERT: C 22 MET cc_start: 0.7524 (mpp) cc_final: 0.6801 (tpp) REVERT: C 347 MET cc_start: 0.2255 (tpp) cc_final: 0.1338 (tpp) REVERT: D 300 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6526 (t0) REVERT: D 316 MET cc_start: 0.9008 (mmm) cc_final: 0.8178 (mpp) REVERT: G 90 MET cc_start: 0.8869 (ptt) cc_final: 0.8514 (ptt) REVERT: K 120 MET cc_start: 0.9261 (mmm) cc_final: 0.8952 (mmm) outliers start: 33 outliers final: 28 residues processed: 85 average time/residue: 0.1593 time to fit residues: 23.3948 Evaluate side-chains 88 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 81 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 166 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 3 optimal weight: 0.9980 chunk 118 optimal weight: 50.0000 chunk 112 optimal weight: 0.0570 overall best weight: 3.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 GLN D 535 GLN E 59 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.034988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.022360 restraints weight = 388763.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.022744 restraints weight = 252898.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.022909 restraints weight = 191741.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.023030 restraints weight = 164207.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.023090 restraints weight = 150076.907| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26490 Z= 0.144 Angle : 0.558 12.837 37017 Z= 0.307 Chirality : 0.036 0.139 4076 Planarity : 0.003 0.042 3647 Dihedral : 26.551 151.212 5889 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.44 % Allowed : 20.10 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.18), residues: 2302 helix: 2.42 (0.14), residues: 1292 sheet: 0.41 (0.56), residues: 94 loop : -0.63 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 76 TYR 0.018 0.001 TYR L 88 PHE 0.010 0.001 PHE B 113 TRP 0.009 0.001 TRP A 775 HIS 0.012 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00304 (26475) covalent geometry : angle 0.55641 (37008) hydrogen bonds : bond 0.04277 ( 1409) hydrogen bonds : angle 3.71591 ( 3733) metal coordination : bond 0.00489 ( 15) metal coordination : angle 3.04452 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6279 (tpt) cc_final: 0.4954 (tmm) REVERT: A 773 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7408 (ppp) REVERT: A 1194 MET cc_start: 0.4615 (tmm) cc_final: 0.4237 (ppp) REVERT: B 47 MET cc_start: 0.3767 (pmm) cc_final: 0.3506 (pmm) REVERT: B 61 MET cc_start: 0.7716 (mpp) cc_final: 0.7380 (mpp) REVERT: B 305 MET cc_start: 0.8574 (ppp) cc_final: 0.7580 (ppp) REVERT: C 22 MET cc_start: 0.7715 (mpp) cc_final: 0.6875 (tpp) REVERT: C 347 MET cc_start: 0.2680 (tpp) cc_final: 0.1681 (tpp) REVERT: D 300 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.6644 (t0) REVERT: D 316 MET cc_start: 0.9015 (mmm) cc_final: 0.8175 (mpp) REVERT: G 90 MET cc_start: 0.8919 (ptt) cc_final: 0.8583 (ptt) REVERT: K 120 MET cc_start: 0.9288 (mmm) cc_final: 0.8873 (mmm) outliers start: 30 outliers final: 26 residues processed: 86 average time/residue: 0.1577 time to fit residues: 22.9768 Evaluate side-chains 88 residues out of total 2081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 219 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.034778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.022174 restraints weight = 385213.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.022521 restraints weight = 257958.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.022679 restraints weight = 199246.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.022801 restraints weight = 172274.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.022872 restraints weight = 157139.604| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26490 Z= 0.172 Angle : 0.573 12.398 37017 Z= 0.315 Chirality : 0.036 0.175 4076 Planarity : 0.003 0.042 3647 Dihedral : 26.553 151.016 5889 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.35 % Allowed : 20.34 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.18), residues: 2302 helix: 2.41 (0.14), residues: 1293 sheet: 0.38 (0.57), residues: 93 loop : -0.60 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 72 TYR 0.015 0.001 TYR L 88 PHE 0.022 0.001 PHE B 324 TRP 0.008 0.001 TRP A 775 HIS 0.010 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00368 (26475) covalent geometry : angle 0.57060 (37008) hydrogen bonds : bond 0.04930 ( 1409) hydrogen bonds : angle 3.74369 ( 3733) metal coordination : bond 0.00523 ( 15) metal coordination : angle 3.21589 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5723.72 seconds wall clock time: 99 minutes 12.03 seconds (5952.03 seconds total)