Starting phenix.real_space_refine on Sun Aug 9 18:25:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p4a_17403/08_2026/8p4a_17403.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4a_17403/08_2026/8p4a_17403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p4a_17403/08_2026/8p4a_17403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4a_17403/08_2026/8p4a_17403.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4a_17403/08_2026/8p4a_17403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4a_17403/08_2026/8p4a_17403.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8p4a_17403/08_2026/8p4a_17403.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p4a_17403/08_2026/8p4a_17403.cif" } resolution = 3.6 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 86 5.49 5 Mg 1 5.21 5 S 222 5.16 5 C 22912 2.51 5 N 6426 2.21 5 O 7018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36673 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11142 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1337} Chain breaks: 3 Chain: "P" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 405 Classifications: {'RNAv2': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "B" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8928 Classifications: {'peptide': 1116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1062} Chain breaks: 6 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2070 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 998 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1305 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 591 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 Chain: "T" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 785 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "M" Number of atoms: 4083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4083 Classifications: {'peptide': 507} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 477} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 768 SG CYS A 111 100.182 55.697 135.873 1.00194.06 S ATOM 796 SG CYS A 114 103.497 53.982 137.853 1.00204.54 S ATOM 464 SG CYS A 71 111.340 68.027 91.175 1.00167.86 S ATOM 486 SG CYS A 74 109.892 64.857 89.530 1.00164.59 S ATOM 533 SG CYS A 81 107.518 67.750 90.273 1.00154.12 S ATOM 20044 SG CYS B1119 106.846 52.672 98.178 1.00160.36 S ATOM 20066 SG CYS B1122 106.866 53.229 100.989 1.00150.21 S ATOM 20181 SG CYS B1137 108.911 54.983 98.807 1.00164.49 S ATOM 21168 SG CYS C 88 76.439 90.574 36.043 1.00180.61 S ATOM 21181 SG CYS C 90 79.033 92.113 38.399 1.00189.59 S ATOM 21216 SG CYS C 94 76.912 94.255 36.084 1.00161.86 S ATOM 21238 SG CYS C 97 75.398 92.618 39.154 1.00161.06 S ATOM 28482 SG CYS I 17 56.334 100.268 158.172 1.00197.04 S ATOM 28506 SG CYS I 20 59.763 100.505 156.556 1.00199.23 S ATOM 28667 SG CYS I 39 58.693 97.154 157.602 1.00196.03 S ATOM 28692 SG CYS I 42 59.295 99.841 160.300 1.00204.97 S ATOM 29044 SG CYS I 86 23.618 105.453 128.447 1.00168.40 S ATOM 29068 SG CYS I 89 23.352 108.306 127.868 1.00178.30 S ATOM 29272 SG CYS I 114 25.481 106.905 125.512 1.00176.35 S ATOM 29307 SG CYS I 119 26.789 108.780 128.157 1.00181.99 S ATOM 29418 SG CYS J 7 52.080 97.206 59.754 1.00127.09 S ATOM 29442 SG CYS J 10 49.597 95.461 57.056 1.00133.91 S ATOM 29706 SG CYS J 44 48.471 95.930 60.349 1.00137.18 S ATOM 29712 SG CYS J 45 49.318 98.997 58.062 1.00136.71 S ATOM 30893 SG CYS L 22 88.160 122.559 73.849 1.00175.09 S ATOM 31010 SG CYS L 36 91.310 121.403 73.461 1.00175.60 S Time building chain proxies: 6.84, per 1000 atoms: 0.19 Number of scatterers: 36673 At special positions: 0 Unit cell: (166.95, 140.7, 180.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 222 16.00 P 86 15.00 Mg 1 11.99 O 7018 8.00 N 6426 7.00 C 22912 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: 2.40 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1122 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1137 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1119 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 39 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 27 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB MET M 30 " Number of C-beta restraints generated: 8216 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 53 sheets defined 37.3% alpha, 18.5% beta 25 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 98 through 110 removed outlier: 4.150A pdb=" N LYS A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.598A pdb=" N LYS A 149 " --> pdb=" O TYR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.570A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.586A pdb=" N MET A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 248' Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.644A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.381A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.154A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 4.082A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.835A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.914A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 757 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.726A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.802A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 4.049A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1160 Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.733A pdb=" N TRP A1192 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A1194 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1224 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.607A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1296 removed outlier: 4.163A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A1296 " --> pdb=" O MET A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.898A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.625A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1435 through 1445 Processing helix chain 'A' and resid 1454 through 1461 Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.135A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.178A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 4.093A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 4.111A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 335 through 346 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.730A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 removed outlier: 4.528A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 583 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.617A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.641A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.603A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.511A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 711 removed outlier: 3.740A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 711' Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.879A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.611A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.639A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.557A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.752A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.600A pdb=" N GLN D 19 " --> pdb=" O ASP D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.664A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR D 28 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.678A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.827A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 97 removed outlier: 4.039A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.587A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 137' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.515A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.507A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.822A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.535A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.056A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 6 through 10 removed outlier: 3.954A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 10' Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.602A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 removed outlier: 3.513A pdb=" N GLU K 114 " --> pdb=" O LYS K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 23 Processing helix chain 'M' and resid 19 through 22 Processing helix chain 'M' and resid 32 through 37 removed outlier: 4.184A pdb=" N SER M 37 " --> pdb=" O PRO M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 53 removed outlier: 4.289A pdb=" N TYR M 53 " --> pdb=" O MET M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 57 Processing helix chain 'M' and resid 76 through 83 removed outlier: 3.513A pdb=" N GLU M 80 " --> pdb=" O ARG M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 117 removed outlier: 4.227A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG M 116 " --> pdb=" O ARG M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 144 Processing helix chain 'M' and resid 148 through 160 removed outlier: 3.759A pdb=" N VAL M 153 " --> pdb=" O ILE M 149 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE M 156 " --> pdb=" O ALA M 152 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA M 157 " --> pdb=" O VAL M 153 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN M 158 " --> pdb=" O ALA M 154 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA M 159 " --> pdb=" O THR M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 178 Processing helix chain 'M' and resid 246 through 262 removed outlier: 3.537A pdb=" N GLU M 252 " --> pdb=" O PRO M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 286 removed outlier: 3.504A pdb=" N LEU M 286 " --> pdb=" O LEU M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 371 through 375 Processing helix chain 'M' and resid 376 through 388 Processing helix chain 'M' and resid 388 through 398 removed outlier: 3.558A pdb=" N ARG M 392 " --> pdb=" O ILE M 388 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR M 398 " --> pdb=" O GLU M 394 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 425 removed outlier: 4.370A pdb=" N LEU M 424 " --> pdb=" O SER M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 504 through 510 removed outlier: 4.180A pdb=" N TYR M 510 " --> pdb=" O GLU M 506 " (cutoff:3.500A) Processing helix chain 'M' and resid 538 through 549 Processing helix chain 'M' and resid 554 through 564 removed outlier: 5.006A pdb=" N GLU M 560 " --> pdb=" O GLU M 556 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N PHE M 561 " --> pdb=" O MET M 557 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.542A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.696A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 5.812A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.772A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.140A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.979A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.205A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.205A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.881A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB8, first strand: chain 'A' and resid 1308 through 1310 Processing sheet with id=AB9, first strand: chain 'A' and resid 1243 through 1246 removed outlier: 3.674A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC2, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.317A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AC5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.286A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.714A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 223 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD1, first strand: chain 'B' and resid 550 through 552 removed outlier: 5.293A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.633A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.633A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD5, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD6, first strand: chain 'B' and resid 865 through 867 removed outlier: 7.231A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD8, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.905A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.293A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 50 " --> pdb=" O PHE L 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.616A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 30 through 31 removed outlier: 6.750A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AE5, first strand: chain 'E' and resid 102 through 106 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 5.722A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.531A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AE9, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.707A pdb=" N VAL H 141 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY H 94 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.852A pdb=" N TYR I 37 " --> pdb=" O GLN I 46 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN I 46 " --> pdb=" O TYR I 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF4, first strand: chain 'M' and resid 24 through 26 removed outlier: 3.577A pdb=" N VAL M 124 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU M 64 " --> pdb=" O ILE M 87 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU M 89 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP M 66 " --> pdb=" O LEU M 89 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N CYS M 91 " --> pdb=" O ASP M 66 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR M 68 " --> pdb=" O CYS M 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 241 through 243 removed outlier: 4.261A pdb=" N VAL M 310 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE M 311 " --> pdb=" O LEU M 303 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU M 341 " --> pdb=" O ILE M 364 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE M 364 " --> pdb=" O LEU M 341 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASP M 343 " --> pdb=" O TYR M 362 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 271 through 275 removed outlier: 4.184A pdb=" N VAL M 274 " --> pdb=" O CYS M 453 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP M 455 " --> pdb=" O VAL M 274 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N ASP M 455 " --> pdb=" O PRO M 444 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU M 457 " --> pdb=" O PHE M 442 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 466 through 470 removed outlier: 4.091A pdb=" N VAL M 467 " --> pdb=" O CYS M 517 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU M 516 " --> pdb=" O MET M 527 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 472 through 476 removed outlier: 7.681A pdb=" N VAL M 491 " --> pdb=" O PRO M 497 " (cutoff:3.500A) 1445 hydrogen bonds defined for protein. 3951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 9.60 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6002 1.31 - 1.44: 9900 1.44 - 1.56: 21133 1.56 - 1.69: 169 1.69 - 1.81: 351 Bond restraints: 37555 Sorted by residual: bond pdb=" C GLN M 18 " pdb=" N PRO M 19 " ideal model delta sigma weight residual 1.333 1.733 -0.401 1.17e-02 7.31e+03 1.17e+03 bond pdb=" N LYS M 28 " pdb=" CA LYS M 28 " ideal model delta sigma weight residual 1.457 1.531 -0.074 1.29e-02 6.01e+03 3.29e+01 bond pdb=" C LEU M 31 " pdb=" O LEU M 31 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.26e-02 6.30e+03 1.53e+01 bond pdb=" N LEU M 27 " pdb=" CA LEU M 27 " ideal model delta sigma weight residual 1.451 1.511 -0.060 1.62e-02 3.81e+03 1.36e+01 bond pdb=" N ARG M 564 " pdb=" CA ARG M 564 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.25e+01 ... (remaining 37550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 50755 3.92 - 7.84: 319 7.84 - 11.76: 30 11.76 - 15.68: 4 15.68 - 19.60: 1 Bond angle restraints: 51109 Sorted by residual: angle pdb=" N MET M 30 " pdb=" CA MET M 30 " pdb=" C MET M 30 " ideal model delta sigma weight residual 110.35 129.95 -19.60 1.36e+00 5.41e-01 2.08e+02 angle pdb=" N PRO M 118 " pdb=" CA PRO M 118 " pdb=" C PRO M 118 " ideal model delta sigma weight residual 110.70 123.65 -12.95 1.22e+00 6.72e-01 1.13e+02 angle pdb=" N LYS M 28 " pdb=" CA LYS M 28 " pdb=" CB LYS M 28 " ideal model delta sigma weight residual 110.49 97.93 12.56 1.69e+00 3.50e-01 5.53e+01 angle pdb=" C ARG M 132 " pdb=" CA ARG M 132 " pdb=" CB ARG M 132 " ideal model delta sigma weight residual 109.83 117.14 -7.31 9.90e-01 1.02e+00 5.45e+01 angle pdb=" CA LEU M 27 " pdb=" C LEU M 27 " pdb=" O LEU M 27 " ideal model delta sigma weight residual 120.77 113.07 7.70 1.06e+00 8.90e-01 5.28e+01 ... (remaining 51104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 21934 33.25 - 66.49: 767 66.49 - 99.74: 50 99.74 - 132.98: 0 132.98 - 166.23: 3 Dihedral angle restraints: 22754 sinusoidal: 10050 harmonic: 12704 Sorted by residual: dihedral pdb=" C4' C P 43 " pdb=" C3' C P 43 " pdb=" C2' C P 43 " pdb=" C1' C P 43 " ideal model delta sinusoidal sigma weight residual 36.35 -40.39 76.74 1 3.10e+00 1.04e-01 7.70e+02 dihedral pdb=" C4' A P 37 " pdb=" C3' A P 37 " pdb=" C2' A P 37 " pdb=" C1' A P 37 " ideal model delta sinusoidal sigma weight residual 36.34 -27.52 63.86 1 3.10e+00 1.04e-01 5.59e+02 dihedral pdb=" O4' A P 37 " pdb=" C4' A P 37 " pdb=" C3' A P 37 " pdb=" C2' A P 37 " ideal model delta sinusoidal sigma weight residual -35.15 34.69 -69.84 1 4.00e+00 6.25e-02 3.93e+02 ... (remaining 22751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.941: 5705 0.941 - 1.882: 1 1.882 - 2.824: 0 2.824 - 3.765: 0 3.765 - 4.706: 1 Chirality restraints: 5707 Sorted by residual: chirality pdb=" CA MET M 30 " pdb=" N MET M 30 " pdb=" C MET M 30 " pdb=" CB MET M 30 " both_signs ideal model delta sigma weight residual False 2.51 -2.20 4.71 2.00e-01 2.50e+01 5.54e+02 chirality pdb=" CA CYS M 13 " pdb=" N CYS M 13 " pdb=" C CYS M 13 " pdb=" CB CYS M 13 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.15 2.00e-01 2.50e+01 3.28e+01 chirality pdb=" CA ARG M 132 " pdb=" N ARG M 132 " pdb=" C ARG M 132 " pdb=" CB ARG M 132 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.96e+01 ... (remaining 5704 not shown) Planarity restraints: 6328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN M 18 " 0.040 2.00e-02 2.50e+03 7.08e-02 5.02e+01 pdb=" C GLN M 18 " -0.122 2.00e-02 2.50e+03 pdb=" O GLN M 18 " 0.047 2.00e-02 2.50e+03 pdb=" N PRO M 19 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1102 " -0.029 2.00e-02 2.50e+03 5.74e-02 3.29e+01 pdb=" C MET A1102 " 0.099 2.00e-02 2.50e+03 pdb=" O MET A1102 " -0.038 2.00e-02 2.50e+03 pdb=" N THR A1103 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS M 28 " 0.027 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C LYS M 28 " -0.095 2.00e-02 2.50e+03 pdb=" O LYS M 28 " 0.036 2.00e-02 2.50e+03 pdb=" N THR M 29 " 0.032 2.00e-02 2.50e+03 ... (remaining 6325 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 294 2.55 - 3.14: 29611 3.14 - 3.72: 60513 3.72 - 4.31: 84191 4.31 - 4.90: 136185 Nonbonded interactions: 310794 Sorted by model distance: nonbonded pdb=" O LEU D 86 " pdb=" NZ LYS D 90 " model vdw 1.959 3.120 nonbonded pdb=" OP1 A P 44 " pdb=" O3' A P 44 " model vdw 2.058 3.040 nonbonded pdb=" OG1 THR F 58 " pdb=" OE1 GLU F 61 " model vdw 2.066 3.040 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.085 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2001 " model vdw 2.094 2.170 ... (remaining 310789 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.570 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: 0.410 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 37.960 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.006 0.427 37582 Z= 0.366 Angle : 0.933 66.442 51136 Z= 0.558 Chirality : 0.092 4.706 5707 Planarity : 0.005 0.101 6328 Dihedral : 15.208 166.227 14538 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.58 % Favored : 95.23 % Rotamer: Outliers : 3.72 % Allowed : 1.59 % Favored : 94.69 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 4319 helix: 0.63 (0.14), residues: 1435 sheet: -1.29 (0.19), residues: 667 loop : -1.13 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 63 TYR 0.030 0.002 TYR M 177 PHE 0.056 0.002 PHE M 416 TRP 0.034 0.002 TRP M 10 HIS 0.010 0.001 HIS A 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.36 (37555) covalent geometry : angle 0.85421 / 0.55 (51109) hydrogen bonds : bond 0.20248 / 13.69 ( 1465) hydrogen bonds : angle 7.62776 / 5.36 ( 4063) metal coordination : bond 0.08295 / 6.51 ( 27) metal coordination : angle 16.33660 / 10.29 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 253 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.9427 (tmm) cc_final: 0.9079 (tmm) REVERT: A 467 MET cc_start: 0.9228 (mpp) cc_final: 0.8808 (mpp) REVERT: A 470 MET cc_start: 0.7877 (mmm) cc_final: 0.7241 (mmm) REVERT: A 535 MET cc_start: 0.8580 (mmm) cc_final: 0.8181 (mmp) REVERT: A 986 MET cc_start: 0.9144 (mtm) cc_final: 0.8629 (mtt) REVERT: A 1102 MET cc_start: 0.8790 (ppp) cc_final: 0.8511 (ppp) REVERT: A 1103 THR cc_start: 0.6337 (OUTLIER) cc_final: 0.6114 (m) REVERT: A 1109 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6970 (p90) REVERT: A 1128 ILE cc_start: 0.9701 (mm) cc_final: 0.9490 (mm) REVERT: A 1228 MET cc_start: 0.8983 (tpp) cc_final: 0.8630 (tpp) REVERT: A 1344 MET cc_start: 0.8204 (tmm) cc_final: 0.7610 (tmm) REVERT: B 239 MET cc_start: 0.9046 (ttt) cc_final: 0.8764 (tpp) REVERT: B 407 MET cc_start: 0.8675 (mtp) cc_final: 0.8399 (ttt) REVERT: B 908 MET cc_start: 0.8333 (tmm) cc_final: 0.8103 (tmm) REVERT: B 1081 ASP cc_start: 0.8896 (t0) cc_final: 0.8595 (t0) REVERT: B 1115 GLN cc_start: 0.9104 (pt0) cc_final: 0.8775 (pp30) REVERT: B 1172 MET cc_start: 0.8837 (mpp) cc_final: 0.8631 (mpp) REVERT: E 72 MET cc_start: 0.8176 (ptp) cc_final: 0.7617 (ptp) REVERT: E 110 MET cc_start: 0.7349 (tmm) cc_final: 0.7115 (tmm) REVERT: F 58 THR cc_start: 0.9204 (p) cc_final: 0.8997 (p) REVERT: F 91 LEU cc_start: 0.9764 (mt) cc_final: 0.9482 (mt) REVERT: F 94 MET cc_start: 0.9126 (tpt) cc_final: 0.8898 (tmm) REVERT: G 10 GLU cc_start: 0.9044 (mp0) cc_final: 0.8524 (mp0) REVERT: G 131 MET cc_start: 0.7535 (mpp) cc_final: 0.7171 (pmm) REVERT: I 82 GLU cc_start: 0.8508 (mp0) cc_final: 0.8096 (tp30) REVERT: I 92 LYS cc_start: 0.8871 (tptp) cc_final: 0.8578 (tptp) REVERT: L 15 MET cc_start: 0.7897 (mmp) cc_final: 0.7501 (tpp) REVERT: M 81 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7127 (tttt) REVERT: M 104 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: M 150 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7891 (mm-30) REVERT: M 182 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: M 346 MET cc_start: -0.0798 (tpt) cc_final: -0.1334 (tpt) REVERT: M 476 MET cc_start: 0.9405 (tmm) cc_final: 0.9145 (tmm) REVERT: M 524 TRP cc_start: 0.8636 (OUTLIER) cc_final: 0.8395 (m-10) outliers start: 143 outliers final: 53 residues processed: 391 average time/residue: 0.2309 time to fit residues: 143.7875 Evaluate side-chains 263 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1109 TYR Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain I residue 60 HIS Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain M residue 12 ASN Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 85 LYS Chi-restraints excluded: chain M residue 101 GLU Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 110 CYS Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 132 ARG Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 150 GLU Chi-restraints excluded: chain M residue 171 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 175 ARG Chi-restraints excluded: chain M residue 182 GLU Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 468 ASP Chi-restraints excluded: chain M residue 470 ARG Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 494 TYR Chi-restraints excluded: chain M residue 502 LYS Chi-restraints excluded: chain M residue 503 VAL Chi-restraints excluded: chain M residue 509 GLN Chi-restraints excluded: chain M residue 510 TYR Chi-restraints excluded: chain M residue 524 TRP Chi-restraints excluded: chain M residue 530 ARG Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 533 LYS Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 547 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN A 704 ASN A 791 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 HIS B 68 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN B 585 ASN B 649 ASN B 777 ASN B1094 GLN B1133 HIS C 66 HIS E 148 HIS I 46 GLN ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN M 114 ASN ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN M 255 GLN M 280 ASN M 537 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.050126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.033372 restraints weight = 244869.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.034477 restraints weight = 125957.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035191 restraints weight = 80755.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.035648 restraints weight = 60031.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.035905 restraints weight = 49312.086| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37582 Z= 0.252 Angle : 0.774 16.644 51136 Z= 0.391 Chirality : 0.050 0.716 5707 Planarity : 0.006 0.184 6328 Dihedral : 15.353 176.267 5899 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 1.98 % Allowed : 6.80 % Favored : 91.22 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 4319 helix: 0.82 (0.14), residues: 1445 sheet: -1.36 (0.19), residues: 639 loop : -0.90 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 530 TYR 0.038 0.002 TYR M 53 PHE 0.045 0.002 PHE M 416 TRP 0.038 0.002 TRP M 10 HIS 0.014 0.001 HIS M 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 (37555) covalent geometry : angle 0.76309 / 0.39 (51109) hydrogen bonds : bond 0.05197 / 3.37 ( 1465) hydrogen bonds : angle 5.84984 / 4.08 ( 4063) metal coordination : bond 0.01517 / 0.91 ( 27) metal coordination : angle 5.57217 / 4.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 214 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9226 (mtp) cc_final: 0.8609 (ttm) REVERT: A 467 MET cc_start: 0.9247 (mpp) cc_final: 0.8934 (mpp) REVERT: A 469 MET cc_start: 0.8944 (ttp) cc_final: 0.8418 (ttp) REVERT: A 535 MET cc_start: 0.8717 (mmm) cc_final: 0.7990 (mmm) REVERT: A 561 MET cc_start: 0.9294 (tpp) cc_final: 0.8870 (tpp) REVERT: A 565 MET cc_start: 0.9046 (ttm) cc_final: 0.8700 (mtt) REVERT: A 637 MET cc_start: 0.9079 (ppp) cc_final: 0.7978 (ppp) REVERT: A 986 MET cc_start: 0.9286 (mtm) cc_final: 0.8360 (mtt) REVERT: A 1102 MET cc_start: 0.8582 (ppp) cc_final: 0.8252 (ppp) REVERT: A 1103 THR cc_start: 0.6527 (OUTLIER) cc_final: 0.6231 (m) REVERT: A 1128 ILE cc_start: 0.9701 (mm) cc_final: 0.9449 (mm) REVERT: A 1166 LEU cc_start: 0.9480 (mt) cc_final: 0.9274 (tp) REVERT: A 1228 MET cc_start: 0.8996 (tpp) cc_final: 0.8503 (ttm) REVERT: A 1344 MET cc_start: 0.8353 (tmm) cc_final: 0.7739 (tpp) REVERT: A 1428 MET cc_start: 0.8969 (mmp) cc_final: 0.8754 (mmp) REVERT: B 297 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8777 (pmm) REVERT: B 908 MET cc_start: 0.8515 (tmm) cc_final: 0.8151 (tmm) REVERT: B 976 MET cc_start: 0.8692 (mpp) cc_final: 0.8080 (mpp) REVERT: B 1075 MET cc_start: 0.8467 (mmm) cc_final: 0.8261 (mmm) REVERT: B 1081 ASP cc_start: 0.9103 (t0) cc_final: 0.8670 (t0) REVERT: B 1115 GLN cc_start: 0.9297 (pt0) cc_final: 0.8818 (pp30) REVERT: B 1151 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8254 (tmm) REVERT: B 1171 MET cc_start: 0.9304 (mtm) cc_final: 0.8677 (mpp) REVERT: B 1172 MET cc_start: 0.9001 (mpp) cc_final: 0.8493 (mpp) REVERT: E 110 MET cc_start: 0.7438 (tmm) cc_final: 0.6921 (tmm) REVERT: F 88 ASP cc_start: 0.9320 (t0) cc_final: 0.8976 (t70) REVERT: F 91 LEU cc_start: 0.9753 (mt) cc_final: 0.9411 (mt) REVERT: G 10 GLU cc_start: 0.8838 (mp0) cc_final: 0.8612 (mp0) REVERT: H 123 MET cc_start: 0.9143 (tmm) cc_final: 0.8884 (tmm) REVERT: I 82 GLU cc_start: 0.8644 (mp0) cc_final: 0.8167 (tp30) REVERT: I 92 LYS cc_start: 0.9045 (tptp) cc_final: 0.8664 (tptp) REVERT: K 38 GLU cc_start: 0.8668 (tp30) cc_final: 0.8124 (tp30) REVERT: L 44 MET cc_start: 0.8499 (tpp) cc_final: 0.8263 (tpp) REVERT: M 81 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7113 (tttt) REVERT: M 116 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8424 (mmm160) REVERT: M 150 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.7939 (mm-30) REVERT: M 179 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8802 (t0) REVERT: M 182 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7079 (tt0) REVERT: M 346 MET cc_start: -0.0979 (tpt) cc_final: -0.1192 (tpt) REVERT: M 476 MET cc_start: 0.9478 (tmm) cc_final: 0.8980 (ppp) REVERT: M 524 TRP cc_start: 0.8937 (OUTLIER) cc_final: 0.8496 (m-10) outliers start: 76 outliers final: 40 residues processed: 281 average time/residue: 0.2313 time to fit residues: 107.9578 Evaluate side-chains 251 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 110 CYS Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 132 ARG Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 150 GLU Chi-restraints excluded: chain M residue 171 LYS Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 182 GLU Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 470 ARG Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 494 TYR Chi-restraints excluded: chain M residue 502 LYS Chi-restraints excluded: chain M residue 503 VAL Chi-restraints excluded: chain M residue 509 GLN Chi-restraints excluded: chain M residue 510 TYR Chi-restraints excluded: chain M residue 511 ASP Chi-restraints excluded: chain M residue 524 TRP Chi-restraints excluded: chain M residue 525 VAL Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 533 LYS Chi-restraints excluded: chain M residue 547 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 289 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 327 optimal weight: 0.9980 chunk 375 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 356 optimal weight: 8.9990 chunk 373 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 350 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.049603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.032820 restraints weight = 244854.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033921 restraints weight = 125173.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.034635 restraints weight = 80346.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.035100 restraints weight = 59334.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.035395 restraints weight = 48626.767| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37582 Z= 0.227 Angle : 0.694 16.109 51136 Z= 0.352 Chirality : 0.046 0.491 5707 Planarity : 0.004 0.094 6328 Dihedral : 14.959 173.986 5834 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 1.75 % Allowed : 8.52 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.13), residues: 4319 helix: 0.95 (0.14), residues: 1457 sheet: -1.23 (0.19), residues: 673 loop : -0.86 (0.14), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 63 TYR 0.039 0.002 TYR A 187 PHE 0.038 0.002 PHE M 416 TRP 0.026 0.002 TRP M 10 HIS 0.016 0.001 HIS I 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 (37555) covalent geometry : angle 0.68184 / 0.35 (51109) hydrogen bonds : bond 0.04585 / 2.96 ( 1465) hydrogen bonds : angle 5.48356 / 3.82 ( 4063) metal coordination : bond 0.01432 / 0.81 ( 27) metal coordination : angle 5.76095 / 4.74 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 211 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9226 (tpt) cc_final: 0.8831 (tpp) REVERT: A 184 CYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8002 (m) REVERT: A 238 MET cc_start: 0.9072 (mpp) cc_final: 0.8716 (mpp) REVERT: A 317 MET cc_start: 0.9504 (tmm) cc_final: 0.9112 (tmm) REVERT: A 467 MET cc_start: 0.9245 (mpp) cc_final: 0.8936 (mmt) REVERT: A 469 MET cc_start: 0.8955 (ttp) cc_final: 0.8360 (ttp) REVERT: A 535 MET cc_start: 0.8768 (mmm) cc_final: 0.8091 (mmm) REVERT: A 637 MET cc_start: 0.9126 (ppp) cc_final: 0.8019 (ppp) REVERT: A 986 MET cc_start: 0.9271 (mtm) cc_final: 0.8327 (mtt) REVERT: A 1086 MET cc_start: 0.9204 (mmp) cc_final: 0.8905 (mmp) REVERT: A 1102 MET cc_start: 0.8675 (ppp) cc_final: 0.8215 (ppp) REVERT: A 1128 ILE cc_start: 0.9717 (mm) cc_final: 0.9448 (mm) REVERT: A 1228 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8680 (ttm) REVERT: A 1344 MET cc_start: 0.8477 (tmm) cc_final: 0.7849 (tpp) REVERT: B 298 MET cc_start: 0.8836 (mtt) cc_final: 0.8358 (mtt) REVERT: B 508 MET cc_start: 0.9123 (mmm) cc_final: 0.8837 (mmp) REVERT: B 674 MET cc_start: 0.8782 (tpt) cc_final: 0.8251 (tpp) REVERT: B 866 ILE cc_start: 0.9589 (OUTLIER) cc_final: 0.9386 (mp) REVERT: B 908 MET cc_start: 0.8524 (tmm) cc_final: 0.8135 (tmm) REVERT: B 976 MET cc_start: 0.8642 (mpp) cc_final: 0.8274 (mpp) REVERT: B 1075 MET cc_start: 0.8620 (mmm) cc_final: 0.8203 (mmm) REVERT: B 1081 ASP cc_start: 0.9159 (t0) cc_final: 0.8717 (t0) REVERT: B 1151 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7983 (tmm) REVERT: B 1171 MET cc_start: 0.9346 (mtm) cc_final: 0.8577 (mpp) REVERT: D 84 ARG cc_start: 0.9306 (mmm160) cc_final: 0.9003 (mmm160) REVERT: D 97 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8685 (pp) REVERT: E 110 MET cc_start: 0.7697 (tmm) cc_final: 0.6918 (tmm) REVERT: G 10 GLU cc_start: 0.8917 (mp0) cc_final: 0.8588 (mp0) REVERT: H 123 MET cc_start: 0.9210 (tmm) cc_final: 0.8916 (tmm) REVERT: I 82 GLU cc_start: 0.8700 (mp0) cc_final: 0.8290 (mm-30) REVERT: K 7 PHE cc_start: 0.9227 (p90) cc_final: 0.9018 (p90) REVERT: K 38 GLU cc_start: 0.8741 (tp30) cc_final: 0.8186 (tp30) REVERT: K 97 GLU cc_start: 0.8710 (tt0) cc_final: 0.8486 (tp30) REVERT: L 44 MET cc_start: 0.8457 (tpp) cc_final: 0.8201 (tpp) REVERT: M 81 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7106 (tttt) REVERT: M 116 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8443 (mmm160) REVERT: M 150 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: M 179 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8721 (t0) REVERT: M 182 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6773 (tt0) REVERT: M 346 MET cc_start: -0.1225 (tpt) cc_final: -0.1543 (tpt) REVERT: M 476 MET cc_start: 0.9487 (tmm) cc_final: 0.8960 (ppp) REVERT: M 558 LEU cc_start: 0.0459 (OUTLIER) cc_final: 0.0068 (pt) outliers start: 67 outliers final: 38 residues processed: 269 average time/residue: 0.2295 time to fit residues: 103.8945 Evaluate side-chains 246 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 150 GLU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 182 GLU Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 470 ARG Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 494 TYR Chi-restraints excluded: chain M residue 502 LYS Chi-restraints excluded: chain M residue 503 VAL Chi-restraints excluded: chain M residue 509 GLN Chi-restraints excluded: chain M residue 510 TYR Chi-restraints excluded: chain M residue 511 ASP Chi-restraints excluded: chain M residue 525 VAL Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 533 LYS Chi-restraints excluded: chain M residue 547 ASN Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 47 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 408 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 150 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN A1116 ASN B 725 GLN B1049 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN M 255 GLN M 412 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031355 restraints weight = 249277.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.032417 restraints weight = 125101.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.033106 restraints weight = 79707.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.033561 restraints weight = 58761.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.033803 restraints weight = 48055.804| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 37582 Z= 0.341 Angle : 0.788 18.961 51136 Z= 0.393 Chirality : 0.047 0.411 5707 Planarity : 0.005 0.064 6328 Dihedral : 14.800 175.461 5813 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 2.32 % Allowed : 9.90 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.13), residues: 4319 helix: 0.85 (0.14), residues: 1469 sheet: -1.24 (0.19), residues: 624 loop : -0.92 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 140 TYR 0.022 0.002 TYR A 187 PHE 0.035 0.002 PHE M 416 TRP 0.025 0.002 TRP M 10 HIS 0.010 0.002 HIS M 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.34 (37555) covalent geometry : angle 0.77445 / 0.39 (51109) hydrogen bonds : bond 0.04694 / 3.02 ( 1465) hydrogen bonds : angle 5.47855 / 3.83 ( 4063) metal coordination : bond 0.02082 / 1.19 ( 27) metal coordination : angle 6.48843 / 5.56 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 195 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9079 (ppp) cc_final: 0.8859 (ppp) REVERT: A 78 MET cc_start: 0.9201 (tpt) cc_final: 0.8868 (tpp) REVERT: A 238 MET cc_start: 0.9078 (mpp) cc_final: 0.8732 (mpp) REVERT: A 317 MET cc_start: 0.9575 (tmm) cc_final: 0.9348 (tmm) REVERT: A 467 MET cc_start: 0.9283 (mpp) cc_final: 0.8993 (mmt) REVERT: A 469 MET cc_start: 0.9047 (ttp) cc_final: 0.8390 (ttp) REVERT: A 501 MET cc_start: 0.8868 (tpt) cc_final: 0.7791 (mmm) REVERT: A 535 MET cc_start: 0.8918 (mmm) cc_final: 0.8312 (mmm) REVERT: A 637 MET cc_start: 0.9085 (ppp) cc_final: 0.7899 (ppp) REVERT: A 986 MET cc_start: 0.9292 (mtm) cc_final: 0.8332 (mtt) REVERT: A 1102 MET cc_start: 0.8752 (ppp) cc_final: 0.8154 (ppp) REVERT: A 1103 THR cc_start: 0.6784 (OUTLIER) cc_final: 0.6546 (m) REVERT: A 1228 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8712 (ttm) REVERT: B 298 MET cc_start: 0.8958 (mtt) cc_final: 0.8451 (mtt) REVERT: B 529 MET cc_start: 0.8887 (mtm) cc_final: 0.8548 (mtp) REVERT: B 823 PHE cc_start: 0.9286 (t80) cc_final: 0.8945 (t80) REVERT: B 897 ARG cc_start: 0.8858 (ttm110) cc_final: 0.8330 (ttm110) REVERT: B 908 MET cc_start: 0.8425 (tmm) cc_final: 0.7765 (tmm) REVERT: B 976 MET cc_start: 0.8770 (mpp) cc_final: 0.8338 (mpp) REVERT: B 1125 MET cc_start: 0.9355 (mtm) cc_final: 0.9060 (mtm) REVERT: B 1151 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8195 (tmm) REVERT: B 1163 MET cc_start: 0.9442 (mtt) cc_final: 0.9163 (mtp) REVERT: D 84 ARG cc_start: 0.9341 (mmm160) cc_final: 0.9060 (mmm160) REVERT: D 97 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8902 (pp) REVERT: E 110 MET cc_start: 0.8036 (tmm) cc_final: 0.7180 (tmm) REVERT: F 50 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8895 (pttm) REVERT: G 10 GLU cc_start: 0.8997 (mp0) cc_final: 0.8726 (mm-30) REVERT: H 123 MET cc_start: 0.9265 (tmm) cc_final: 0.8961 (tmm) REVERT: I 82 GLU cc_start: 0.8801 (mp0) cc_final: 0.8578 (tp30) REVERT: M 81 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7194 (tttt) REVERT: M 150 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: M 182 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6571 (tt0) REVERT: M 471 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8694 (tp) REVERT: M 476 MET cc_start: 0.9563 (tmm) cc_final: 0.9017 (ppp) REVERT: M 558 LEU cc_start: 0.0640 (OUTLIER) cc_final: 0.0141 (pt) outliers start: 89 outliers final: 52 residues processed: 273 average time/residue: 0.2061 time to fit residues: 95.4770 Evaluate side-chains 248 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 186 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 46 HIS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 150 GLU Chi-restraints excluded: chain M residue 182 GLU Chi-restraints excluded: chain M residue 416 PHE Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 470 ARG Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 494 TYR Chi-restraints excluded: chain M residue 502 LYS Chi-restraints excluded: chain M residue 509 GLN Chi-restraints excluded: chain M residue 510 TYR Chi-restraints excluded: chain M residue 511 ASP Chi-restraints excluded: chain M residue 525 VAL Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 533 LYS Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 228 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 138 optimal weight: 0.0010 chunk 174 optimal weight: 8.9990 chunk 326 optimal weight: 40.0000 chunk 220 optimal weight: 6.9990 chunk 330 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 363 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 404 optimal weight: 5.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.048377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.031764 restraints weight = 243777.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.032860 restraints weight = 122507.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.033566 restraints weight = 77528.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.033984 restraints weight = 57167.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.034301 restraints weight = 46823.773| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 37582 Z= 0.208 Angle : 0.677 16.842 51136 Z= 0.340 Chirality : 0.046 0.339 5707 Planarity : 0.004 0.044 6328 Dihedral : 14.709 177.208 5805 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 1.95 % Allowed : 11.07 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.13), residues: 4319 helix: 1.06 (0.14), residues: 1459 sheet: -1.19 (0.19), residues: 664 loop : -0.84 (0.14), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 84 TYR 0.019 0.001 TYR A 187 PHE 0.036 0.002 PHE M 416 TRP 0.020 0.002 TRP M 10 HIS 0.014 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (37555) covalent geometry : angle 0.66432 / 0.34 (51109) hydrogen bonds : bond 0.04113 / 2.66 ( 1465) hydrogen bonds : angle 5.25035 / 3.65 ( 4063) metal coordination : bond 0.01376 / 0.76 ( 27) metal coordination : angle 5.62956 / 4.81 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 200 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9121 (ppp) cc_final: 0.8897 (ppp) REVERT: A 78 MET cc_start: 0.9164 (tpt) cc_final: 0.8826 (tpp) REVERT: A 238 MET cc_start: 0.9090 (mpp) cc_final: 0.8747 (mpp) REVERT: A 317 MET cc_start: 0.9596 (tmm) cc_final: 0.9379 (tmm) REVERT: A 467 MET cc_start: 0.9240 (mpp) cc_final: 0.8990 (mmt) REVERT: A 469 MET cc_start: 0.9050 (ttp) cc_final: 0.8381 (ttp) REVERT: A 501 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8636 (mmt) REVERT: A 535 MET cc_start: 0.8931 (mmm) cc_final: 0.8265 (mmm) REVERT: A 637 MET cc_start: 0.9145 (ppp) cc_final: 0.7904 (ppp) REVERT: A 986 MET cc_start: 0.9291 (mtm) cc_final: 0.8298 (mtt) REVERT: A 1102 MET cc_start: 0.8869 (ppp) cc_final: 0.8476 (ppp) REVERT: A 1103 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6260 (m) REVERT: A 1228 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8501 (ttm) REVERT: A 1344 MET cc_start: 0.8493 (tmm) cc_final: 0.7768 (tmm) REVERT: B 298 MET cc_start: 0.8953 (mtt) cc_final: 0.8395 (mtt) REVERT: B 300 MET cc_start: 0.9471 (tpp) cc_final: 0.9247 (tpp) REVERT: B 550 MET cc_start: 0.9042 (tmm) cc_final: 0.8764 (tmm) REVERT: B 674 MET cc_start: 0.8736 (tpt) cc_final: 0.7648 (tpp) REVERT: B 733 MET cc_start: 0.8694 (ptm) cc_final: 0.8381 (ttp) REVERT: B 823 PHE cc_start: 0.9274 (t80) cc_final: 0.8918 (t80) REVERT: B 897 ARG cc_start: 0.8862 (ttm110) cc_final: 0.8455 (ttm110) REVERT: B 908 MET cc_start: 0.8470 (tmm) cc_final: 0.7926 (tmm) REVERT: B 976 MET cc_start: 0.8712 (mpp) cc_final: 0.8353 (mpp) REVERT: B 1125 MET cc_start: 0.9362 (mtm) cc_final: 0.9129 (mtm) REVERT: B 1151 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8408 (tmm) REVERT: B 1163 MET cc_start: 0.9406 (mtt) cc_final: 0.9111 (mtm) REVERT: C 83 GLN cc_start: 0.9321 (mm-40) cc_final: 0.9037 (tp-100) REVERT: D 84 ARG cc_start: 0.9312 (mmm160) cc_final: 0.8976 (mmm160) REVERT: D 97 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8804 (pp) REVERT: E 110 MET cc_start: 0.8052 (tmm) cc_final: 0.7264 (tmm) REVERT: G 10 GLU cc_start: 0.9005 (mp0) cc_final: 0.8690 (mm-30) REVERT: H 123 MET cc_start: 0.9282 (tmm) cc_final: 0.8915 (tmm) REVERT: I 82 GLU cc_start: 0.8819 (mp0) cc_final: 0.8524 (mm-30) REVERT: K 38 GLU cc_start: 0.8685 (tp30) cc_final: 0.7957 (tp30) REVERT: K 42 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9388 (mm) REVERT: L 44 MET cc_start: 0.8224 (tpp) cc_final: 0.7933 (tpp) REVERT: M 81 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7239 (tttt) REVERT: M 471 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8655 (tp) REVERT: M 476 MET cc_start: 0.9571 (tmm) cc_final: 0.9008 (ppp) REVERT: M 527 MET cc_start: 0.9382 (tpp) cc_final: 0.8978 (mtt) REVERT: M 543 MET cc_start: 0.8819 (tpp) cc_final: 0.8503 (mmp) REVERT: M 558 LEU cc_start: -0.0369 (OUTLIER) cc_final: -0.0816 (pt) outliers start: 75 outliers final: 47 residues processed: 266 average time/residue: 0.2227 time to fit residues: 100.5445 Evaluate side-chains 245 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 46 HIS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 182 GLU Chi-restraints excluded: chain M residue 416 PHE Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 470 ARG Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 494 TYR Chi-restraints excluded: chain M residue 502 LYS Chi-restraints excluded: chain M residue 509 GLN Chi-restraints excluded: chain M residue 510 TYR Chi-restraints excluded: chain M residue 511 ASP Chi-restraints excluded: chain M residue 525 VAL Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 533 LYS Chi-restraints excluded: chain M residue 541 THR Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 310 optimal weight: 1.9990 chunk 138 optimal weight: 0.0000 chunk 78 optimal weight: 3.9990 chunk 371 optimal weight: 5.9990 chunk 423 optimal weight: 7.9990 chunk 379 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 315 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.048328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.031667 restraints weight = 242518.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.032772 restraints weight = 122089.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.033477 restraints weight = 77294.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.033892 restraints weight = 56776.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.034213 restraints weight = 46558.768| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37582 Z= 0.195 Angle : 0.665 15.484 51136 Z= 0.334 Chirality : 0.045 0.300 5707 Planarity : 0.004 0.047 6328 Dihedral : 14.589 179.539 5801 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 2.63 % Allowed : 11.31 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 4319 helix: 1.18 (0.14), residues: 1447 sheet: -1.18 (0.19), residues: 684 loop : -0.76 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 84 TYR 0.018 0.001 TYR B 388 PHE 0.035 0.001 PHE M 416 TRP 0.019 0.002 TRP M 10 HIS 0.009 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (37555) covalent geometry : angle 0.65399 / 0.33 (51109) hydrogen bonds : bond 0.03890 / 2.50 ( 1465) hydrogen bonds : angle 5.12473 / 3.56 ( 4063) metal coordination : bond 0.01260 / 0.69 ( 27) metal coordination : angle 5.25835 / 4.45 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 198 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9151 (ppp) cc_final: 0.8928 (ppp) REVERT: A 78 MET cc_start: 0.9102 (tpt) cc_final: 0.8771 (tpp) REVERT: A 238 MET cc_start: 0.9047 (mpp) cc_final: 0.8758 (mpp) REVERT: A 317 MET cc_start: 0.9619 (tmm) cc_final: 0.9358 (tmm) REVERT: A 469 MET cc_start: 0.9069 (ttp) cc_final: 0.8400 (ttp) REVERT: A 470 MET cc_start: 0.8384 (mmm) cc_final: 0.7974 (mmm) REVERT: A 501 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8647 (mmt) REVERT: A 535 MET cc_start: 0.8929 (mmm) cc_final: 0.8288 (mmm) REVERT: A 637 MET cc_start: 0.9148 (ppp) cc_final: 0.7898 (ppp) REVERT: A 986 MET cc_start: 0.9292 (mtm) cc_final: 0.8311 (mtt) REVERT: A 1102 MET cc_start: 0.8888 (ppp) cc_final: 0.8446 (ppp) REVERT: A 1228 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8513 (ttm) REVERT: A 1344 MET cc_start: 0.8490 (tmm) cc_final: 0.7778 (tmm) REVERT: B 298 MET cc_start: 0.8984 (mtt) cc_final: 0.8433 (mtt) REVERT: B 300 MET cc_start: 0.9428 (tpp) cc_final: 0.9213 (tpp) REVERT: B 347 MET cc_start: 0.9402 (ppp) cc_final: 0.8906 (ppp) REVERT: B 550 MET cc_start: 0.9073 (tmm) cc_final: 0.8703 (tmm) REVERT: B 823 PHE cc_start: 0.9295 (t80) cc_final: 0.8942 (t80) REVERT: B 897 ARG cc_start: 0.8872 (ttm110) cc_final: 0.8444 (ttm110) REVERT: B 908 MET cc_start: 0.8522 (tmm) cc_final: 0.7954 (tmm) REVERT: B 976 MET cc_start: 0.8765 (mpp) cc_final: 0.8405 (mpp) REVERT: B 1075 MET cc_start: 0.8685 (mmm) cc_final: 0.8444 (mmm) REVERT: B 1125 MET cc_start: 0.9377 (mtm) cc_final: 0.9163 (mtm) REVERT: B 1151 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8464 (tmm) REVERT: B 1163 MET cc_start: 0.9403 (mtt) cc_final: 0.9113 (mtm) REVERT: C 83 GLN cc_start: 0.9316 (mm-40) cc_final: 0.9037 (tp-100) REVERT: D 84 ARG cc_start: 0.9323 (mmm160) cc_final: 0.8945 (mmm160) REVERT: D 97 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8828 (pp) REVERT: E 110 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7339 (tmm) REVERT: G 10 GLU cc_start: 0.9071 (mp0) cc_final: 0.8768 (mm-30) REVERT: H 123 MET cc_start: 0.9299 (tmm) cc_final: 0.8884 (tmm) REVERT: I 82 GLU cc_start: 0.8841 (mp0) cc_final: 0.8569 (tp30) REVERT: K 38 GLU cc_start: 0.8720 (tp30) cc_final: 0.8398 (tp30) REVERT: L 44 MET cc_start: 0.8299 (tpp) cc_final: 0.7946 (tpp) REVERT: M 31 LEU cc_start: 0.4851 (OUTLIER) cc_final: 0.4320 (tm) REVERT: M 63 LEU cc_start: 0.4336 (OUTLIER) cc_final: 0.4000 (mt) REVERT: M 145 MET cc_start: 0.8707 (mpp) cc_final: 0.8459 (mpp) REVERT: M 301 MET cc_start: -0.2963 (mtp) cc_final: -0.3290 (ttm) REVERT: M 471 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8676 (tp) REVERT: M 476 MET cc_start: 0.9586 (tmm) cc_final: 0.9031 (ppp) REVERT: M 527 MET cc_start: 0.9402 (tpp) cc_final: 0.9018 (mtt) REVERT: M 558 LEU cc_start: -0.0300 (OUTLIER) cc_final: -0.0772 (pt) outliers start: 101 outliers final: 53 residues processed: 286 average time/residue: 0.2029 time to fit residues: 98.8622 Evaluate side-chains 255 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 46 HIS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 416 PHE Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 494 TYR Chi-restraints excluded: chain M residue 502 LYS Chi-restraints excluded: chain M residue 509 GLN Chi-restraints excluded: chain M residue 510 TYR Chi-restraints excluded: chain M residue 525 VAL Chi-restraints excluded: chain M residue 532 ASP Chi-restraints excluded: chain M residue 533 LYS Chi-restraints excluded: chain M residue 541 THR Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 339 optimal weight: 0.6980 chunk 396 optimal weight: 0.9980 chunk 379 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 402 optimal weight: 20.0000 chunk 418 optimal weight: 50.0000 chunk 237 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 281 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS K 49 GLN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.048529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.031989 restraints weight = 239327.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.033073 restraints weight = 119956.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.033799 restraints weight = 75984.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.034252 restraints weight = 55403.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.034518 restraints weight = 45034.670| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37582 Z= 0.162 Angle : 0.665 18.718 51136 Z= 0.332 Chirality : 0.045 0.280 5707 Planarity : 0.004 0.050 6328 Dihedral : 14.463 178.615 5790 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 1.98 % Allowed : 12.37 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 4319 helix: 1.20 (0.14), residues: 1448 sheet: -1.14 (0.19), residues: 691 loop : -0.72 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 84 TYR 0.017 0.001 TYR B 388 PHE 0.035 0.001 PHE M 416 TRP 0.018 0.002 TRP M 10 HIS 0.030 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (37555) covalent geometry : angle 0.65490 / 0.33 (51109) hydrogen bonds : bond 0.03751 / 2.41 ( 1465) hydrogen bonds : angle 5.06369 / 3.51 ( 4063) metal coordination : bond 0.00973 / 0.54 ( 27) metal coordination : angle 4.99454 / 4.21 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 198 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9157 (ppp) cc_final: 0.8930 (ppp) REVERT: A 78 MET cc_start: 0.9073 (tpt) cc_final: 0.8765 (tpp) REVERT: A 184 CYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8036 (m) REVERT: A 238 MET cc_start: 0.9046 (mpp) cc_final: 0.8775 (mpp) REVERT: A 317 MET cc_start: 0.9616 (tmm) cc_final: 0.9388 (tmm) REVERT: A 355 MET cc_start: 0.9542 (mmm) cc_final: 0.9328 (mmm) REVERT: A 388 MET cc_start: 0.8873 (mmm) cc_final: 0.8447 (mmt) REVERT: A 469 MET cc_start: 0.9054 (ttp) cc_final: 0.8394 (ttp) REVERT: A 470 MET cc_start: 0.8344 (mmm) cc_final: 0.7962 (mmm) REVERT: A 501 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8620 (mmt) REVERT: A 535 MET cc_start: 0.8874 (mmm) cc_final: 0.8228 (mmm) REVERT: A 637 MET cc_start: 0.9159 (ppp) cc_final: 0.7896 (ppp) REVERT: A 986 MET cc_start: 0.9280 (mtm) cc_final: 0.8274 (mtt) REVERT: A 1102 MET cc_start: 0.8898 (ppp) cc_final: 0.8427 (ppp) REVERT: A 1211 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9155 (tt) REVERT: A 1228 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8507 (ttm) REVERT: A 1344 MET cc_start: 0.8485 (tmm) cc_final: 0.7908 (tmm) REVERT: B 155 MET cc_start: 0.8650 (ptt) cc_final: 0.8100 (ptt) REVERT: B 298 MET cc_start: 0.8984 (mtt) cc_final: 0.8408 (mtt) REVERT: B 300 MET cc_start: 0.9401 (tpp) cc_final: 0.9191 (tpp) REVERT: B 674 MET cc_start: 0.8787 (tpt) cc_final: 0.7627 (tpp) REVERT: B 733 MET cc_start: 0.8639 (ptm) cc_final: 0.8411 (ttp) REVERT: B 823 PHE cc_start: 0.9253 (t80) cc_final: 0.8894 (t80) REVERT: B 897 ARG cc_start: 0.8893 (ttm110) cc_final: 0.8600 (ttm110) REVERT: B 908 MET cc_start: 0.8526 (tmm) cc_final: 0.7949 (tmm) REVERT: B 976 MET cc_start: 0.8736 (mpp) cc_final: 0.8404 (mpp) REVERT: B 1075 MET cc_start: 0.8701 (mmm) cc_final: 0.8143 (mmm) REVERT: B 1151 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8458 (tmm) REVERT: B 1163 MET cc_start: 0.9399 (mtt) cc_final: 0.9107 (mtm) REVERT: C 15 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9030 (p) REVERT: C 83 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9061 (tp-100) REVERT: D 84 ARG cc_start: 0.9291 (mmm160) cc_final: 0.8901 (mmm160) REVERT: D 97 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8822 (pp) REVERT: E 72 MET cc_start: 0.8248 (ptp) cc_final: 0.7852 (ptp) REVERT: E 110 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7218 (tmm) REVERT: G 10 GLU cc_start: 0.9085 (mp0) cc_final: 0.8785 (mm-30) REVERT: H 123 MET cc_start: 0.9279 (tmm) cc_final: 0.8834 (tmm) REVERT: I 82 GLU cc_start: 0.8846 (mp0) cc_final: 0.8553 (tp30) REVERT: K 38 GLU cc_start: 0.8725 (tp30) cc_final: 0.8397 (tp30) REVERT: L 44 MET cc_start: 0.8274 (tpp) cc_final: 0.7939 (tpp) REVERT: M 31 LEU cc_start: 0.4947 (OUTLIER) cc_final: 0.4408 (tm) REVERT: M 63 LEU cc_start: 0.4362 (OUTLIER) cc_final: 0.4022 (mt) REVERT: M 145 MET cc_start: 0.8665 (mpp) cc_final: 0.8366 (mpp) REVERT: M 471 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8624 (tp) REVERT: M 476 MET cc_start: 0.9575 (tmm) cc_final: 0.9021 (ppp) outliers start: 76 outliers final: 47 residues processed: 265 average time/residue: 0.2158 time to fit residues: 96.2733 Evaluate side-chains 253 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 46 HIS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 131 ASN Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain M residue 416 PHE Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 494 TYR Chi-restraints excluded: chain M residue 502 LYS Chi-restraints excluded: chain M residue 509 GLN Chi-restraints excluded: chain M residue 510 TYR Chi-restraints excluded: chain M residue 511 ASP Chi-restraints excluded: chain M residue 525 VAL Chi-restraints excluded: chain M residue 533 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 149 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 427 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.048390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.031736 restraints weight = 242038.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.032835 restraints weight = 121497.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.033546 restraints weight = 76900.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.034008 restraints weight = 56572.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.034263 restraints weight = 45925.629| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37582 Z= 0.178 Angle : 0.680 20.069 51136 Z= 0.337 Chirality : 0.045 0.281 5707 Planarity : 0.004 0.050 6328 Dihedral : 14.384 176.795 5786 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 1.88 % Allowed : 12.63 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 4319 helix: 1.17 (0.14), residues: 1462 sheet: -1.13 (0.19), residues: 693 loop : -0.70 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 132 TYR 0.027 0.001 TYR G 3 PHE 0.034 0.001 PHE M 416 TRP 0.018 0.002 TRP M 10 HIS 0.012 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (37555) covalent geometry : angle 0.67140 / 0.34 (51109) hydrogen bonds : bond 0.03704 / 2.38 ( 1465) hydrogen bonds : angle 5.01431 / 3.48 ( 4063) metal coordination : bond 0.01085 / 0.60 ( 27) metal coordination : angle 4.75316 / 3.92 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 199 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9180 (ppp) cc_final: 0.8933 (ppp) REVERT: A 78 MET cc_start: 0.9045 (tpt) cc_final: 0.8748 (tpp) REVERT: A 238 MET cc_start: 0.9104 (mpp) cc_final: 0.8832 (mpp) REVERT: A 317 MET cc_start: 0.9625 (tmm) cc_final: 0.9390 (tmm) REVERT: A 355 MET cc_start: 0.9526 (mmm) cc_final: 0.9259 (mmm) REVERT: A 388 MET cc_start: 0.8960 (mmm) cc_final: 0.8552 (mmt) REVERT: A 469 MET cc_start: 0.9063 (ttp) cc_final: 0.8416 (ttp) REVERT: A 470 MET cc_start: 0.8421 (mmm) cc_final: 0.8044 (mmm) REVERT: A 501 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8652 (mmt) REVERT: A 535 MET cc_start: 0.8882 (mmm) cc_final: 0.8243 (mmm) REVERT: A 561 MET cc_start: 0.9219 (mmm) cc_final: 0.8988 (tpp) REVERT: A 637 MET cc_start: 0.9157 (ppp) cc_final: 0.7918 (ppp) REVERT: A 986 MET cc_start: 0.9280 (mtm) cc_final: 0.8292 (mtt) REVERT: A 1086 MET cc_start: 0.9013 (mmm) cc_final: 0.8649 (mmm) REVERT: A 1102 MET cc_start: 0.8914 (ppp) cc_final: 0.8434 (ppp) REVERT: A 1128 ILE cc_start: 0.9762 (mm) cc_final: 0.9492 (mm) REVERT: A 1166 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9353 (tt) REVERT: A 1211 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9147 (tt) REVERT: A 1228 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8520 (ttm) REVERT: A 1344 MET cc_start: 0.8531 (tmm) cc_final: 0.8293 (tmm) REVERT: B 155 MET cc_start: 0.8674 (ptt) cc_final: 0.8147 (ptt) REVERT: B 298 MET cc_start: 0.9030 (mtt) cc_final: 0.8436 (mtt) REVERT: B 300 MET cc_start: 0.9402 (tpp) cc_final: 0.9199 (tpp) REVERT: B 347 MET cc_start: 0.9412 (ppp) cc_final: 0.8941 (ppp) REVERT: B 407 MET cc_start: 0.8841 (mtp) cc_final: 0.8532 (ttt) REVERT: B 674 MET cc_start: 0.8837 (tpt) cc_final: 0.7644 (tpp) REVERT: B 733 MET cc_start: 0.8693 (ptm) cc_final: 0.8374 (ttp) REVERT: B 823 PHE cc_start: 0.9262 (t80) cc_final: 0.8907 (t80) REVERT: B 897 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8580 (ttm110) REVERT: B 908 MET cc_start: 0.8582 (tmm) cc_final: 0.8001 (tmm) REVERT: B 976 MET cc_start: 0.8755 (mpp) cc_final: 0.8442 (mpp) REVERT: B 1075 MET cc_start: 0.8801 (mmm) cc_final: 0.8232 (mmm) REVERT: B 1151 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8480 (tmm) REVERT: B 1163 MET cc_start: 0.9419 (mtt) cc_final: 0.9120 (mtm) REVERT: C 15 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9042 (p) REVERT: D 84 ARG cc_start: 0.9294 (mmm160) cc_final: 0.8903 (mmm160) REVERT: D 97 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8874 (pp) REVERT: E 110 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7239 (tmm) REVERT: G 1 MET cc_start: 0.8559 (tpt) cc_final: 0.8314 (tmm) REVERT: G 10 GLU cc_start: 0.9110 (mp0) cc_final: 0.8803 (mm-30) REVERT: H 123 MET cc_start: 0.9293 (tmm) cc_final: 0.8823 (tmm) REVERT: I 75 ASP cc_start: 0.9532 (t0) cc_final: 0.9292 (t0) REVERT: I 82 GLU cc_start: 0.8839 (mp0) cc_final: 0.8540 (tp30) REVERT: K 38 GLU cc_start: 0.8751 (tp30) cc_final: 0.8409 (tp30) REVERT: L 44 MET cc_start: 0.8198 (tpp) cc_final: 0.7875 (tpp) REVERT: M 31 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4457 (tm) REVERT: M 63 LEU cc_start: 0.4545 (OUTLIER) cc_final: 0.4192 (mt) REVERT: M 145 MET cc_start: 0.8620 (mpp) cc_final: 0.8282 (mpp) REVERT: M 471 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8599 (tp) REVERT: M 476 MET cc_start: 0.9579 (tmm) cc_final: 0.9036 (ppp) REVERT: M 543 MET cc_start: 0.8724 (tpp) cc_final: 0.8508 (mmp) outliers start: 72 outliers final: 46 residues processed: 261 average time/residue: 0.2231 time to fit residues: 98.5970 Evaluate side-chains 253 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 46 HIS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 416 PHE Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 494 TYR Chi-restraints excluded: chain M residue 502 LYS Chi-restraints excluded: chain M residue 509 GLN Chi-restraints excluded: chain M residue 510 TYR Chi-restraints excluded: chain M residue 511 ASP Chi-restraints excluded: chain M residue 525 VAL Chi-restraints excluded: chain M residue 533 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 62 optimal weight: 5.9990 chunk 375 optimal weight: 0.9990 chunk 234 optimal weight: 9.9990 chunk 299 optimal weight: 0.9980 chunk 324 optimal weight: 20.0000 chunk 259 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 377 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.048775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.032249 restraints weight = 238756.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.033350 restraints weight = 118702.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.034069 restraints weight = 74926.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.034485 restraints weight = 54489.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.034813 restraints weight = 44489.130| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37582 Z= 0.137 Angle : 0.663 17.831 51136 Z= 0.328 Chirality : 0.045 0.302 5707 Planarity : 0.004 0.052 6328 Dihedral : 14.303 173.476 5786 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 1.69 % Allowed : 12.74 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 4319 helix: 1.21 (0.14), residues: 1464 sheet: -1.02 (0.19), residues: 691 loop : -0.66 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 132 TYR 0.022 0.001 TYR G 3 PHE 0.035 0.001 PHE M 416 TRP 0.017 0.002 TRP M 10 HIS 0.009 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (37555) covalent geometry : angle 0.65481 / 0.33 (51109) hydrogen bonds : bond 0.03513 / 2.27 ( 1465) hydrogen bonds : angle 4.90864 / 3.40 ( 4063) metal coordination : bond 0.00701 / 0.40 ( 27) metal coordination : angle 4.47252 / 3.65 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9196 (ppp) cc_final: 0.8932 (ppp) REVERT: A 78 MET cc_start: 0.9000 (tpt) cc_final: 0.8734 (tpp) REVERT: A 238 MET cc_start: 0.9075 (mpp) cc_final: 0.8826 (mpp) REVERT: A 317 MET cc_start: 0.9607 (tmm) cc_final: 0.9378 (tmm) REVERT: A 388 MET cc_start: 0.8975 (mmm) cc_final: 0.8615 (mmt) REVERT: A 469 MET cc_start: 0.9067 (ttp) cc_final: 0.8524 (ttp) REVERT: A 470 MET cc_start: 0.8463 (mmm) cc_final: 0.8073 (mmm) REVERT: A 501 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8612 (mmt) REVERT: A 535 MET cc_start: 0.8816 (mmm) cc_final: 0.8069 (mmm) REVERT: A 637 MET cc_start: 0.9183 (ppp) cc_final: 0.7948 (ppp) REVERT: A 660 MET cc_start: 0.9041 (mmt) cc_final: 0.8828 (mmm) REVERT: A 872 MET cc_start: 0.8181 (mmm) cc_final: 0.7497 (tpt) REVERT: A 959 MET cc_start: 0.9468 (mmt) cc_final: 0.9193 (mmm) REVERT: A 986 MET cc_start: 0.9271 (mtm) cc_final: 0.8286 (mtt) REVERT: A 1085 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7892 (mt-10) REVERT: A 1102 MET cc_start: 0.8945 (ppp) cc_final: 0.8446 (ppp) REVERT: A 1124 LEU cc_start: 0.9777 (tp) cc_final: 0.9522 (tp) REVERT: A 1128 ILE cc_start: 0.9740 (mm) cc_final: 0.9397 (mm) REVERT: A 1211 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9155 (tt) REVERT: A 1344 MET cc_start: 0.8484 (tmm) cc_final: 0.7984 (tmm) REVERT: A 1440 MET cc_start: 0.8856 (ppp) cc_final: 0.8526 (ppp) REVERT: B 155 MET cc_start: 0.8636 (ptt) cc_final: 0.8062 (ptt) REVERT: B 298 MET cc_start: 0.8999 (mtt) cc_final: 0.8403 (mtt) REVERT: B 407 MET cc_start: 0.8806 (mtp) cc_final: 0.8534 (ttt) REVERT: B 550 MET cc_start: 0.9052 (tmm) cc_final: 0.8602 (tmm) REVERT: B 674 MET cc_start: 0.8828 (tpt) cc_final: 0.7595 (tpp) REVERT: B 733 MET cc_start: 0.8670 (ptm) cc_final: 0.8387 (ttp) REVERT: B 823 PHE cc_start: 0.9218 (t80) cc_final: 0.8846 (t80) REVERT: B 897 ARG cc_start: 0.8849 (ttm110) cc_final: 0.8341 (ttm-80) REVERT: B 908 MET cc_start: 0.8636 (tmm) cc_final: 0.8166 (tmm) REVERT: B 976 MET cc_start: 0.8806 (mpp) cc_final: 0.8573 (mpp) REVERT: B 1075 MET cc_start: 0.8807 (mmm) cc_final: 0.8203 (mmm) REVERT: B 1151 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8466 (tmm) REVERT: B 1163 MET cc_start: 0.9429 (mtt) cc_final: 0.9156 (mtm) REVERT: C 15 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9058 (p) REVERT: D 84 ARG cc_start: 0.9293 (mmm160) cc_final: 0.9075 (mmm160) REVERT: E 72 MET cc_start: 0.8161 (ptp) cc_final: 0.7949 (ptp) REVERT: E 110 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7214 (tmm) REVERT: G 1 MET cc_start: 0.8562 (tpt) cc_final: 0.8087 (tmm) REVERT: G 3 TYR cc_start: 0.8852 (m-80) cc_final: 0.8582 (m-80) REVERT: G 8 GLU cc_start: 0.7415 (tp30) cc_final: 0.6326 (tp30) REVERT: G 10 GLU cc_start: 0.9135 (mp0) cc_final: 0.8723 (mm-30) REVERT: H 123 MET cc_start: 0.9277 (tmm) cc_final: 0.8864 (tmm) REVERT: I 75 ASP cc_start: 0.9517 (t0) cc_final: 0.9271 (t70) REVERT: I 82 GLU cc_start: 0.8832 (mp0) cc_final: 0.8532 (tp30) REVERT: I 103 ARG cc_start: 0.6716 (ttt90) cc_final: 0.6354 (ptm160) REVERT: K 38 GLU cc_start: 0.8728 (tp30) cc_final: 0.8431 (tp30) REVERT: L 44 MET cc_start: 0.8201 (tpp) cc_final: 0.7887 (tpp) REVERT: M 31 LEU cc_start: 0.5094 (OUTLIER) cc_final: 0.4488 (tm) REVERT: M 63 LEU cc_start: 0.4687 (OUTLIER) cc_final: 0.4433 (mt) REVERT: M 471 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8679 (tp) REVERT: M 476 MET cc_start: 0.9573 (tmm) cc_final: 0.9066 (ppp) REVERT: M 543 MET cc_start: 0.8769 (tpp) cc_final: 0.8567 (mmp) REVERT: M 557 MET cc_start: 0.4061 (tmm) cc_final: 0.3519 (ptt) outliers start: 65 outliers final: 48 residues processed: 262 average time/residue: 0.2237 time to fit residues: 98.9629 Evaluate side-chains 258 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 46 HIS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 131 ASN Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 416 PHE Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 473 ILE Chi-restraints excluded: chain M residue 494 TYR Chi-restraints excluded: chain M residue 509 GLN Chi-restraints excluded: chain M residue 510 TYR Chi-restraints excluded: chain M residue 511 ASP Chi-restraints excluded: chain M residue 527 MET Chi-restraints excluded: chain M residue 533 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 344 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 270 optimal weight: 0.0970 chunk 333 optimal weight: 40.0000 chunk 325 optimal weight: 50.0000 chunk 253 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 chunk 148 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 377 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 321 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.048719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.032273 restraints weight = 240430.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.033367 restraints weight = 119880.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034093 restraints weight = 75632.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.034520 restraints weight = 54834.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.034831 restraints weight = 44697.741| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37582 Z= 0.146 Angle : 0.670 16.422 51136 Z= 0.331 Chirality : 0.045 0.264 5707 Planarity : 0.004 0.049 6328 Dihedral : 14.240 170.861 5782 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.18 % Rotamer: Outliers : 1.62 % Allowed : 12.97 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4319 helix: 1.24 (0.14), residues: 1463 sheet: -1.06 (0.19), residues: 679 loop : -0.64 (0.14), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 132 TYR 0.018 0.001 TYR M 53 PHE 0.034 0.001 PHE M 416 TRP 0.017 0.002 TRP M 10 HIS 0.009 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (37555) covalent geometry : angle 0.66198 / 0.33 (51109) hydrogen bonds : bond 0.03499 / 2.26 ( 1465) hydrogen bonds : angle 4.87061 / 3.37 ( 4063) metal coordination : bond 0.00786 / 0.44 ( 27) metal coordination : angle 4.43011 / 3.65 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8638 Ramachandran restraints generated. 4319 Oldfield, 0 Emsley, 4319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9196 (ppp) cc_final: 0.8934 (ppp) REVERT: A 78 MET cc_start: 0.8993 (tpt) cc_final: 0.8725 (tpp) REVERT: A 238 MET cc_start: 0.9076 (mpp) cc_final: 0.8827 (mpp) REVERT: A 317 MET cc_start: 0.9620 (tmm) cc_final: 0.9374 (tmm) REVERT: A 388 MET cc_start: 0.8989 (mmm) cc_final: 0.8635 (mmt) REVERT: A 469 MET cc_start: 0.9068 (ttp) cc_final: 0.8496 (ttp) REVERT: A 470 MET cc_start: 0.8485 (mmm) cc_final: 0.8100 (mmm) REVERT: A 501 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8600 (mmt) REVERT: A 535 MET cc_start: 0.8804 (mmm) cc_final: 0.8073 (mmm) REVERT: A 637 MET cc_start: 0.9166 (ppp) cc_final: 0.7932 (ppp) REVERT: A 872 MET cc_start: 0.8181 (mmm) cc_final: 0.7478 (tpt) REVERT: A 959 MET cc_start: 0.9464 (mmt) cc_final: 0.9197 (mmm) REVERT: A 986 MET cc_start: 0.9260 (mtm) cc_final: 0.8289 (mtt) REVERT: A 1102 MET cc_start: 0.8915 (ppp) cc_final: 0.8407 (ppp) REVERT: A 1124 LEU cc_start: 0.9787 (tp) cc_final: 0.9537 (tp) REVERT: A 1128 ILE cc_start: 0.9735 (mm) cc_final: 0.9399 (mm) REVERT: A 1211 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9154 (tt) REVERT: A 1344 MET cc_start: 0.8473 (tmm) cc_final: 0.7963 (tmm) REVERT: A 1440 MET cc_start: 0.8861 (ppp) cc_final: 0.8517 (ppp) REVERT: B 155 MET cc_start: 0.8659 (ptt) cc_final: 0.8085 (ptt) REVERT: B 298 MET cc_start: 0.9016 (mtt) cc_final: 0.8390 (mtt) REVERT: B 347 MET cc_start: 0.9420 (ppp) cc_final: 0.8949 (ppp) REVERT: B 407 MET cc_start: 0.8805 (mtp) cc_final: 0.8531 (ttt) REVERT: B 550 MET cc_start: 0.9048 (tmm) cc_final: 0.8550 (tmm) REVERT: B 674 MET cc_start: 0.8844 (tpt) cc_final: 0.7693 (tpp) REVERT: B 733 MET cc_start: 0.8672 (ptm) cc_final: 0.8438 (ttp) REVERT: B 823 PHE cc_start: 0.9218 (t80) cc_final: 0.8850 (t80) REVERT: B 897 ARG cc_start: 0.8858 (ttm110) cc_final: 0.8449 (ttm110) REVERT: B 908 MET cc_start: 0.8637 (tmm) cc_final: 0.8169 (tmm) REVERT: B 1075 MET cc_start: 0.8833 (mmm) cc_final: 0.8242 (mmm) REVERT: B 1151 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8480 (tmm) REVERT: B 1163 MET cc_start: 0.9437 (mtt) cc_final: 0.9172 (mtm) REVERT: C 15 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9056 (p) REVERT: D 84 ARG cc_start: 0.9299 (mmm160) cc_final: 0.9017 (mmm160) REVERT: E 110 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7220 (tmm) REVERT: G 1 MET cc_start: 0.8605 (tpt) cc_final: 0.8154 (tmm) REVERT: G 3 TYR cc_start: 0.8860 (m-80) cc_final: 0.8657 (m-80) REVERT: G 8 GLU cc_start: 0.7426 (tp30) cc_final: 0.6409 (tp30) REVERT: G 10 GLU cc_start: 0.9148 (mp0) cc_final: 0.8725 (mm-30) REVERT: H 123 MET cc_start: 0.9278 (tmm) cc_final: 0.8865 (tmm) REVERT: I 75 ASP cc_start: 0.9512 (t0) cc_final: 0.9266 (t70) REVERT: I 82 GLU cc_start: 0.8814 (mp0) cc_final: 0.8524 (tp30) REVERT: I 103 ARG cc_start: 0.6702 (ttt90) cc_final: 0.6345 (ptm160) REVERT: K 38 GLU cc_start: 0.8729 (tp30) cc_final: 0.8386 (tp30) REVERT: L 44 MET cc_start: 0.8203 (tpp) cc_final: 0.7890 (tpp) REVERT: M 31 LEU cc_start: 0.5113 (OUTLIER) cc_final: 0.4501 (tm) REVERT: M 63 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.4528 (tp) REVERT: M 302 MET cc_start: 0.4496 (tmm) cc_final: 0.1855 (mtt) REVERT: M 471 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8668 (tp) REVERT: M 476 MET cc_start: 0.9564 (tmm) cc_final: 0.9054 (ppp) REVERT: M 557 MET cc_start: 0.4264 (tmm) cc_final: 0.3701 (ptt) outliers start: 62 outliers final: 49 residues processed: 254 average time/residue: 0.2201 time to fit residues: 94.9396 Evaluate side-chains 256 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 199 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 46 HIS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 416 PHE Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 473 ILE Chi-restraints excluded: chain M residue 494 TYR Chi-restraints excluded: chain M residue 509 GLN Chi-restraints excluded: chain M residue 510 TYR Chi-restraints excluded: chain M residue 511 ASP Chi-restraints excluded: chain M residue 527 MET Chi-restraints excluded: chain M residue 533 LYS Chi-restraints excluded: chain M residue 541 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 49 optimal weight: 8.9990 chunk 421 optimal weight: 7.9990 chunk 279 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 412 optimal weight: 50.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN M 547 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.048420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.032034 restraints weight = 239248.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.033117 restraints weight = 119360.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.033814 restraints weight = 75383.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.034305 restraints weight = 55023.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.034573 restraints weight = 44230.645| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37582 Z= 0.171 Angle : 0.670 14.351 51136 Z= 0.332 Chirality : 0.045 0.253 5707 Planarity : 0.004 0.049 6328 Dihedral : 14.176 165.747 5782 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 1.64 % Allowed : 13.00 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4319 helix: 1.27 (0.14), residues: 1465 sheet: -1.02 (0.19), residues: 684 loop : -0.63 (0.14), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.018 0.001 TYR B 388 PHE 0.034 0.001 PHE M 416 TRP 0.017 0.002 TRP M 10 HIS 0.029 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (37555) covalent geometry : angle 0.66175 / 0.33 (51109) hydrogen bonds : bond 0.03562 / 2.28 ( 1465) hydrogen bonds : angle 4.86095 / 3.37 ( 4063) metal coordination : bond 0.00987 / 0.55 ( 27) metal coordination : angle 4.72669 / 4.03 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6631.20 seconds wall clock time: 115 minutes 36.10 seconds (6936.10 seconds total)