Starting phenix.real_space_refine on Thu May 29 18:56:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xy6_38767/05_2025/8xy6_38767.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xy6_38767/05_2025/8xy6_38767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xy6_38767/05_2025/8xy6_38767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xy6_38767/05_2025/8xy6_38767.map" model { file = "/net/cci-nas-00/data/ceres_data/8xy6_38767/05_2025/8xy6_38767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xy6_38767/05_2025/8xy6_38767.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 177 5.16 5 C 20654 2.51 5 N 5545 2.21 5 O 6024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32407 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 11216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11216 Classifications: {'peptide': 1410} Link IDs: {'PCIS': 2, 'PTRANS': 64, 'TRANS': 1343} Chain breaks: 3 Chain: "B" Number of atoms: 9492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1200, 9492 Classifications: {'peptide': 1200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1147} Chain breaks: 6 Chain: "C" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2907 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 338} Chain: "D" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1669 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "E" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 869 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain breaks: 1 Chain: "F" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 758 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain breaks: 1 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 816 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "I" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4042 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 467} Chain breaks: 3 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: "G" 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: "H" 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 450 SG CYS A 59 107.988 50.732 66.432 1.00 98.73 S ATOM 471 SG CYS A 62 106.537 49.610 63.110 1.00 86.50 S ATOM 531 SG CYS A 69 104.996 52.492 65.135 1.00 90.08 S ATOM 775 SG CYS A 99 93.781 30.036 105.401 1.00123.63 S ATOM 797 SG CYS A 102 94.321 26.983 103.205 1.00135.84 S ATOM 1049 SG CYS A 134 91.615 26.889 105.775 1.00138.43 S ATOM 1074 SG CYS A 137 95.202 26.826 106.920 1.00147.50 S ATOM 20227 SG CYS B1180 99.500 34.888 65.339 1.00 80.64 S ATOM 20252 SG CYS B1183 98.769 36.023 68.918 1.00 88.16 S ATOM 20368 SG CYS B1198 102.256 36.395 67.315 1.00 85.95 S ATOM 20390 SG CYS B1201 101.094 32.997 68.172 1.00 99.22 S ATOM 26942 SG CYS G 4 64.262 70.545 137.342 1.00 89.00 S ATOM 26962 SG CYS G 7 67.484 71.472 135.591 1.00 93.54 S ATOM 27096 SG CYS G 24 65.801 68.298 134.565 1.00104.39 S ATOM 27108 SG CYS G 26 67.201 68.420 138.035 1.00100.76 S ATOM 27478 SG CYS G 73 33.090 100.889 107.755 1.00 82.99 S ATOM 27499 SG CYS G 76 34.255 104.478 108.249 1.00 92.12 S ATOM 27656 SG CYS G 96 36.728 101.969 107.043 1.00 74.54 S ATOM 27673 SG CYS G 98 35.165 101.645 110.627 1.00 68.71 S ATOM 27778 SG CYS H 7 68.818 107.424 47.237 1.00 53.01 S ATOM 27802 SG CYS H 10 67.968 107.742 43.479 1.00 57.02 S ATOM 28221 SG CYS H 65 65.264 107.351 46.103 1.00 55.84 S ATOM 28227 SG CYS H 66 67.232 110.615 45.553 1.00 55.00 S Time building chain proxies: 18.57, per 1000 atoms: 0.57 Number of scatterers: 32407 At special positions: 0 Unit cell: (131.2, 143.5, 171.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 177 16.00 Mg 1 11.99 O 6024 8.00 N 5545 7.00 C 20654 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: 7.20 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 62 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 134 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 99 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 137 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 4 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 24 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 7 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 76 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 98 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 96 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " Number of angles added : 33 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 43 sheets defined 43.6% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 108 through 114 removed outlier: 4.101A pdb=" N TYR A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N HIS A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.573A pdb=" N ARG A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 177 removed outlier: 3.535A pdb=" N VAL A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.506A pdb=" N VAL A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.900A pdb=" N HIS A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.575A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.133A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 523 through 532 removed outlier: 3.572A pdb=" N PHE A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 648 Processing helix chain 'A' and resid 659 through 686 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 723 removed outlier: 3.895A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 removed outlier: 3.729A pdb=" N TYR A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.695A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 944 removed outlier: 3.551A pdb=" N ILE A 937 " --> pdb=" O ASN A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 971 Processing helix chain 'A' and resid 972 through 975 removed outlier: 3.539A pdb=" N PHE A 975 " --> pdb=" O PRO A 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 972 through 975' Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1007 through 1012 Processing helix chain 'A' and resid 1015 through 1033 Processing helix chain 'A' and resid 1040 through 1059 Proline residue: A1052 - end of helix removed outlier: 3.897A pdb=" N GLN A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1063 Processing helix chain 'A' and resid 1074 through 1082 Processing helix chain 'A' and resid 1085 through 1089 Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 3.715A pdb=" N ALA A1110 " --> pdb=" O ASN A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1125 No H-bonds generated for 'chain 'A' and resid 1122 through 1125' Processing helix chain 'A' and resid 1151 through 1162 Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1229 through 1233 Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1318 through 1327 Processing helix chain 'A' and resid 1327 through 1344 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.862A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.883A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.876A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.860A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 299 through 315 Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.123A pdb=" N SER B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 348 through 353' Processing helix chain 'B' and resid 353 through 372 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 382 through 402 Processing helix chain 'B' and resid 421 through 437 removed outlier: 4.117A pdb=" N ALA B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.756A pdb=" N LEU B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.306A pdb=" N ASP B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 565 removed outlier: 4.035A pdb=" N LYS B 564 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 565 " --> pdb=" O GLY B 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 561 through 565' Processing helix chain 'B' and resid 582 through 592 Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 627 through 642 Processing helix chain 'B' and resid 679 through 697 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 715 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 742 through 747 Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 removed outlier: 3.583A pdb=" N LEU B 779 " --> pdb=" O GLN B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 807 removed outlier: 3.860A pdb=" N ARG B 805 " --> pdb=" O THR B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 818 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 1030 through 1033 Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.967A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1162 through 1169 Processing helix chain 'B' and resid 1201 through 1205 Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.613A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 230 through 258 removed outlier: 3.717A pdb=" N ILE C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 Processing helix chain 'C' and resid 328 through 358 Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.844A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 removed outlier: 3.570A pdb=" N LEU D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.649A pdb=" N LEU D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 127 removed outlier: 3.603A pdb=" N CYS D 127 " --> pdb=" O HIS D 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 124 through 127' Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.767A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 35 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'H' and resid 14 through 33 removed outlier: 4.472A pdb=" N ALA H 19 " --> pdb=" O GLY H 15 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS H 23 " --> pdb=" O ALA H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 44 Proline residue: H 42 - end of helix Processing helix chain 'H' and resid 51 through 58 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.694A pdb=" N THR H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 removed outlier: 3.693A pdb=" N TYR H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 674 through 684 Processing helix chain 'I' and resid 684 through 697 removed outlier: 3.573A pdb=" N ASP I 688 " --> pdb=" O ASP I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 709 through 720 removed outlier: 3.784A pdb=" N TYR I 713 " --> pdb=" O LYS I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 722 through 729 Processing helix chain 'I' and resid 773 through 791 Processing helix chain 'I' and resid 794 through 816 removed outlier: 3.727A pdb=" N GLU I 798 " --> pdb=" O ASN I 794 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU I 816 " --> pdb=" O GLN I 812 " (cutoff:3.500A) Processing helix chain 'I' and resid 845 through 849 Processing helix chain 'I' and resid 882 through 887 Processing helix chain 'I' and resid 904 through 911 removed outlier: 3.547A pdb=" N VAL I 908 " --> pdb=" O GLN I 905 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY I 909 " --> pdb=" O HIS I 906 " (cutoff:3.500A) Processing helix chain 'I' and resid 912 through 933 Processing helix chain 'I' and resid 965 through 973 removed outlier: 4.001A pdb=" N LEU I 969 " --> pdb=" O SER I 965 " (cutoff:3.500A) Processing helix chain 'I' and resid 1016 through 1028 removed outlier: 4.398A pdb=" N ILE I1020 " --> pdb=" O ASP I1016 " (cutoff:3.500A) Processing helix chain 'I' and resid 1030 through 1036 removed outlier: 4.024A pdb=" N ILE I1034 " --> pdb=" O SER I1030 " (cutoff:3.500A) Processing helix chain 'I' and resid 1044 through 1051 Processing helix chain 'I' and resid 1063 through 1085 removed outlier: 3.937A pdb=" N MET I1067 " --> pdb=" O ASP I1063 " (cutoff:3.500A) Processing helix chain 'I' and resid 1093 through 1101 Processing helix chain 'I' and resid 1104 through 1115 Processing helix chain 'I' and resid 1121 through 1133 Processing helix chain 'I' and resid 1133 through 1154 Processing helix chain 'I' and resid 1158 through 1184 removed outlier: 4.080A pdb=" N ASN I1163 " --> pdb=" O SER I1159 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE I1164 " --> pdb=" O TRP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1209 through 1213 Processing helix chain 'I' and resid 1240 through 1247 removed outlier: 3.851A pdb=" N ASP I1244 " --> pdb=" O ASP I1241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.170A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 83 removed outlier: 10.048A pdb=" N MET A 78 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 10.457A pdb=" N GLN A 202 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.620A pdb=" N ALA A 139 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.788A pdb=" N VAL A 145 " --> pdb=" O TRP A 155 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 7.486A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 354 removed outlier: 3.824A pdb=" N ASP A 403 " --> pdb=" O VAL A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AA9, first strand: chain 'A' and resid 521 through 522 Processing sheet with id=AB1, first strand: chain 'A' and resid 567 through 569 Processing sheet with id=AB2, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB3, first strand: chain 'A' and resid 836 through 838 removed outlier: 3.514A pdb=" N ILE A 837 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB5, first strand: chain 'A' and resid 1267 through 1278 removed outlier: 6.438A pdb=" N ASN A1267 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR A1295 " --> pdb=" O ASN A1267 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN A1269 " --> pdb=" O ILE A1293 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A1293 " --> pdb=" O ASN A1269 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A1271 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR A1291 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU A1273 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASN A1289 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A1094 " --> pdb=" O THR A1295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 6.736A pdb=" N ILE A1120 " --> pdb=" O ILE A1259 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1206 through 1210 removed outlier: 6.618A pdb=" N ILE A1223 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A1176 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A1225 " --> pdb=" O TRP A1174 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TRP A1174 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU A1227 " --> pdb=" O ALA A1172 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER G 40 " --> pdb=" O LEU A1131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 4.057A pdb=" N ILE E 123 " --> pdb=" O ILE E 132 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE B1239 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE E 59 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 145 through 151 Processing sheet with id=AC1, first strand: chain 'B' and resid 145 through 151 removed outlier: 4.503A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC3, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC4, first strand: chain 'B' and resid 416 through 419 Processing sheet with id=AC5, first strand: chain 'B' and resid 213 through 216 removed outlier: 3.644A pdb=" N ARG B 229 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 228 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC7, first strand: chain 'B' and resid 710 through 712 Processing sheet with id=AC8, first strand: chain 'B' and resid 620 through 625 removed outlier: 5.379A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 826 Processing sheet with id=AD1, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD2, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 5.889A pdb=" N VAL B 867 " --> pdb=" O ALA B1007 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B1009 " --> pdb=" O VAL B 867 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 895 through 896 Processing sheet with id=AD4, first strand: chain 'B' and resid 932 through 933 removed outlier: 3.625A pdb=" N VAL B 955 " --> pdb=" O ILE B 933 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD6, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD7, first strand: chain 'C' and resid 5 through 12 removed outlier: 5.091A pdb=" N PHE C 5 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS C 48 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS C 216 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N HIS C 186 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG C 218 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C 184 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLY C 220 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 67 through 73 removed outlier: 4.089A pdb=" N ASP C 162 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE C 111 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 123 through 126 removed outlier: 3.543A pdb=" N ILE C 125 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY C 150 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 267 through 272 removed outlier: 4.391A pdb=" N GLU C 318 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL C 313 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 20 through 21 removed outlier: 6.639A pdb=" N ILE D 52 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE D 89 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER D 54 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE D 91 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE D 56 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU D 88 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR D 121 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU D 90 " --> pdb=" O TYR D 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 138 through 142 removed outlier: 3.628A pdb=" N LYS D 138 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 2 through 10 removed outlier: 6.566A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N SER F 79 " --> pdb=" O ASN F 47 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N ASN F 47 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AE6, first strand: chain 'I' and resid 876 through 879 Processing sheet with id=AE7, first strand: chain 'I' and resid 876 through 879 1436 hydrogen bonds defined for protein. 3990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.95 Time building geometry restraints manager: 8.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10621 1.34 - 1.46: 7029 1.46 - 1.58: 15114 1.58 - 1.70: 2 1.70 - 1.82: 290 Bond restraints: 33056 Sorted by residual: bond pdb=" CB PRO A1163 " pdb=" CG PRO A1163 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.92e+00 bond pdb=" CB PRO A1101 " pdb=" CG PRO A1101 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.93e+00 bond pdb=" CG1 ILE A 911 " pdb=" CD1 ILE A 911 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.08e+00 bond pdb=" CB GLN D 148 " pdb=" CG GLN D 148 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.75e+00 bond pdb=" N ILE C 149 " pdb=" CA ILE C 149 " ideal model delta sigma weight residual 1.459 1.439 0.020 1.25e-02 6.40e+03 2.64e+00 ... (remaining 33051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 44353 2.97 - 5.94: 355 5.94 - 8.92: 31 8.92 - 11.89: 8 11.89 - 14.86: 3 Bond angle restraints: 44750 Sorted by residual: angle pdb=" CA PRO A1101 " pdb=" N PRO A1101 " pdb=" CD PRO A1101 " ideal model delta sigma weight residual 112.00 101.13 10.87 1.40e+00 5.10e-01 6.03e+01 angle pdb=" CA PRO A1163 " pdb=" N PRO A1163 " pdb=" CD PRO A1163 " ideal model delta sigma weight residual 112.00 103.30 8.70 1.40e+00 5.10e-01 3.86e+01 angle pdb=" CA GLN D 148 " pdb=" CB GLN D 148 " pdb=" CG GLN D 148 " ideal model delta sigma weight residual 114.10 123.45 -9.35 2.00e+00 2.50e-01 2.19e+01 angle pdb=" CB MET A 70 " pdb=" CG MET A 70 " pdb=" SD MET A 70 " ideal model delta sigma weight residual 112.70 125.45 -12.75 3.00e+00 1.11e-01 1.81e+01 angle pdb=" CA GLU C 274 " pdb=" CB GLU C 274 " pdb=" CG GLU C 274 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 ... (remaining 44745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17408 17.95 - 35.90: 2032 35.90 - 53.85: 561 53.85 - 71.80: 85 71.80 - 89.75: 44 Dihedral angle restraints: 20130 sinusoidal: 8245 harmonic: 11885 Sorted by residual: dihedral pdb=" CA ILE A1422 " pdb=" C ILE A1422 " pdb=" N GLY A1423 " pdb=" CA GLY A1423 " ideal model delta harmonic sigma weight residual -180.00 -143.45 -36.55 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA ALA B1007 " pdb=" C ALA B1007 " pdb=" N LEU B1008 " pdb=" CA LEU B1008 " ideal model delta harmonic sigma weight residual 180.00 153.68 26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA THR B 92 " pdb=" C THR B 92 " pdb=" N ASP B 93 " pdb=" CA ASP B 93 " ideal model delta harmonic sigma weight residual 180.00 154.94 25.06 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 20127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4258 0.064 - 0.127: 754 0.127 - 0.191: 43 0.191 - 0.254: 2 0.254 - 0.318: 1 Chirality restraints: 5058 Sorted by residual: chirality pdb=" CB ILE A1074 " pdb=" CA ILE A1074 " pdb=" CG1 ILE A1074 " pdb=" CG2 ILE A1074 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA PRO A1101 " pdb=" N PRO A1101 " pdb=" C PRO A1101 " pdb=" CB PRO A1101 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB ILE C 358 " pdb=" CA ILE C 358 " pdb=" CG1 ILE C 358 " pdb=" CG2 ILE C 358 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 5055 not shown) Planarity restraints: 5761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1100 " -0.112 5.00e-02 4.00e+02 1.60e-01 4.11e+01 pdb=" N PRO A1101 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO A1101 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO A1101 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 707 " -0.089 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO I 708 " 0.231 5.00e-02 4.00e+02 pdb=" CA PRO I 708 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO I 708 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 126 " 0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO E 127 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO E 127 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 127 " 0.048 5.00e-02 4.00e+02 ... (remaining 5758 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 363 2.55 - 3.14: 26428 3.14 - 3.73: 52944 3.73 - 4.31: 75208 4.31 - 4.90: 125873 Nonbonded interactions: 280816 Sorted by model distance: nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A1503 " model vdw 1.966 2.170 nonbonded pdb=" OD1 ASP A 461 " pdb="MG MG A1503 " model vdw 2.002 2.170 nonbonded pdb=" O LYS C 79 " pdb=" OG SER C 83 " model vdw 2.018 3.040 nonbonded pdb=" NH2 ARG B 98 " pdb=" O ASN B 167 " model vdw 2.097 3.120 nonbonded pdb=" O MET B1161 " pdb=" N THR B1163 " model vdw 2.103 3.120 ... (remaining 280811 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.440 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: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 76.930 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.005 0.149 33080 Z= 0.209 Angle : 0.697 14.861 44783 Z= 0.363 Chirality : 0.047 0.318 5058 Planarity : 0.006 0.160 5761 Dihedral : 16.817 89.746 12450 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.73 % Favored : 93.89 % Rotamer: Outliers : 2.80 % Allowed : 22.55 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 4013 helix: 0.79 (0.13), residues: 1554 sheet: -0.30 (0.22), residues: 573 loop : -0.67 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 701 HIS 0.011 0.001 HIS B 173 PHE 0.053 0.002 PHE B 304 TYR 0.025 0.002 TYR F 69 ARG 0.011 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.16308 ( 1426) hydrogen bonds : angle 6.71661 ( 3990) metal coordination : bond 0.00700 ( 24) metal coordination : angle 3.40727 ( 33) covalent geometry : bond 0.00493 (33056) covalent geometry : angle 0.69134 (44750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 304 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8952 (p) cc_final: 0.8628 (t) REVERT: D 98 SER cc_start: 0.7038 (m) cc_final: 0.6785 (t) REVERT: D 109 GLN cc_start: 0.8361 (tp40) cc_final: 0.8092 (tp40) REVERT: E 127 PRO cc_start: 0.8097 (Cg_exo) cc_final: 0.7706 (Cg_endo) outliers start: 101 outliers final: 81 residues processed: 396 average time/residue: 1.1232 time to fit residues: 550.2132 Evaluate side-chains 365 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 284 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 789 CYS Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain A residue 1439 ASN Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain B residue 997 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 717 THR Chi-restraints excluded: chain I residue 722 THR Chi-restraints excluded: chain I residue 733 TYR Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain I residue 783 GLU Chi-restraints excluded: chain I residue 837 ARG Chi-restraints excluded: chain I residue 869 SER Chi-restraints excluded: chain I residue 970 VAL Chi-restraints excluded: chain I residue 1059 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 0.9990 chunk 304 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 162 optimal weight: 0.0670 chunk 315 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 234 optimal weight: 8.9990 chunk 365 optimal weight: 3.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 68 GLN A 168 GLN A 646 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN D 148 GLN F 47 ASN H 69 HIS I 703 HIS ** I 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.109870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088186 restraints weight = 66349.402| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.05 r_work: 0.3267 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33080 Z= 0.160 Angle : 0.622 17.936 44783 Z= 0.322 Chirality : 0.046 0.302 5058 Planarity : 0.005 0.084 5761 Dihedral : 7.103 78.652 4548 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.18 % Favored : 94.47 % Rotamer: Outliers : 5.05 % Allowed : 19.61 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 4013 helix: 0.93 (0.13), residues: 1557 sheet: -0.44 (0.22), residues: 575 loop : -0.56 (0.15), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 701 HIS 0.014 0.001 HIS B 173 PHE 0.044 0.002 PHE I1219 TYR 0.020 0.001 TYR F 69 ARG 0.007 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 1426) hydrogen bonds : angle 5.37501 ( 3990) metal coordination : bond 0.00523 ( 24) metal coordination : angle 3.00752 ( 33) covalent geometry : bond 0.00363 (33056) covalent geometry : angle 0.61689 (44750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 321 time to evaluate : 3.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.9037 (p) cc_final: 0.8829 (t) REVERT: A 123 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: A 476 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: A 880 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8932 (tp) REVERT: A 1096 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8337 (mt) REVERT: A 1185 MET cc_start: 0.8311 (ptm) cc_final: 0.8109 (ptm) REVERT: B 401 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8197 (tp) REVERT: B 1113 LYS cc_start: 0.8578 (mptt) cc_final: 0.8063 (mttp) REVERT: C 272 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6595 (ppp) REVERT: C 357 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6463 (mm) REVERT: D 4 GLN cc_start: 0.8297 (tt0) cc_final: 0.8095 (pm20) REVERT: E 127 PRO cc_start: 0.8182 (Cg_exo) cc_final: 0.7844 (Cg_endo) REVERT: F 33 ASN cc_start: 0.6984 (m-40) cc_final: 0.6775 (m-40) REVERT: I 801 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6140 (pp20) REVERT: I 933 TYR cc_start: 0.5649 (m-80) cc_final: 0.5321 (m-80) outliers start: 182 outliers final: 60 residues processed: 464 average time/residue: 1.0687 time to fit residues: 618.4025 Evaluate side-chains 361 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 293 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 997 SER Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 722 THR Chi-restraints excluded: chain I residue 733 TYR Chi-restraints excluded: chain I residue 801 GLU Chi-restraints excluded: chain I residue 869 SER Chi-restraints excluded: chain I residue 970 VAL Chi-restraints excluded: chain I residue 973 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 260 optimal weight: 4.9990 chunk 368 optimal weight: 7.9990 chunk 355 optimal weight: 8.9990 chunk 299 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 342 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 193 optimal weight: 0.6980 chunk 315 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 68 GLN A 462 GLN A 497 ASN A 532 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 108 ASN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN D 157 GLN F 47 ASN G 59 ASN I 703 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.106972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085092 restraints weight = 67123.909| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.08 r_work: 0.3209 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 33080 Z= 0.299 Angle : 0.699 18.423 44783 Z= 0.357 Chirality : 0.049 0.220 5058 Planarity : 0.005 0.070 5761 Dihedral : 6.632 73.023 4487 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.41 % Favored : 94.24 % Rotamer: Outliers : 5.61 % Allowed : 19.88 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 4013 helix: 0.80 (0.13), residues: 1552 sheet: -0.47 (0.22), residues: 556 loop : -0.68 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1154 HIS 0.006 0.001 HIS B 173 PHE 0.040 0.002 PHE I1219 TYR 0.028 0.002 TYR F 69 ARG 0.008 0.001 ARG A1177 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 1426) hydrogen bonds : angle 5.40086 ( 3990) metal coordination : bond 0.01062 ( 24) metal coordination : angle 4.07135 ( 33) covalent geometry : bond 0.00711 (33056) covalent geometry : angle 0.69056 (44750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 306 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8263 (pp-130) REVERT: A 97 VAL cc_start: 0.9151 (p) cc_final: 0.8914 (t) REVERT: A 171 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7452 (ttt-90) REVERT: A 745 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.9050 (mtp) REVERT: A 880 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8909 (tp) REVERT: A 1096 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 1131 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8393 (tm) REVERT: A 1323 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.7518 (tpt) REVERT: B 637 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8247 (mpp) REVERT: B 658 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: B 718 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8078 (mtt) REVERT: B 1113 LYS cc_start: 0.8642 (mptt) cc_final: 0.8166 (mttp) REVERT: C 272 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6550 (ppp) REVERT: C 284 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8065 (mttp) REVERT: C 357 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6453 (mm) REVERT: E 96 LYS cc_start: 0.7303 (mmtp) cc_final: 0.7098 (mmtm) REVERT: F 33 ASN cc_start: 0.7112 (m-40) cc_final: 0.6901 (m-40) REVERT: F 141 TYR cc_start: 0.5283 (m-80) cc_final: 0.4933 (m-80) REVERT: G 31 GLN cc_start: 0.7239 (mm-40) cc_final: 0.7031 (mm-40) REVERT: G 101 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7358 (tpp) REVERT: I 683 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8414 (tt) REVERT: I 783 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: I 801 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6283 (pp20) REVERT: I 933 TYR cc_start: 0.5656 (m-80) cc_final: 0.5279 (m-80) outliers start: 202 outliers final: 80 residues processed: 463 average time/residue: 1.1613 time to fit residues: 663.8551 Evaluate side-chains 383 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 286 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1173 ASN Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1323 MET Chi-restraints excluded: chain A residue 1425 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 997 SER Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1223 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 683 LEU Chi-restraints excluded: chain I residue 722 THR Chi-restraints excluded: chain I residue 733 TYR Chi-restraints excluded: chain I residue 783 GLU Chi-restraints excluded: chain I residue 801 GLU Chi-restraints excluded: chain I residue 837 ARG Chi-restraints excluded: chain I residue 860 THR Chi-restraints excluded: chain I residue 970 VAL Chi-restraints excluded: chain I residue 973 TYR Chi-restraints excluded: chain I residue 1147 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 191 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 210 optimal weight: 2.9990 chunk 296 optimal weight: 9.9990 chunk 297 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 354 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 279 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 370 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 68 GLN A 462 GLN A 497 ASN A 646 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN B 86 GLN B 108 ASN B 218 HIS B 598 GLN C 91 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN F 47 ASN I 703 HIS ** I 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.109984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088400 restraints weight = 66406.039| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.05 r_work: 0.3279 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33080 Z= 0.144 Angle : 0.603 17.668 44783 Z= 0.307 Chirality : 0.046 0.183 5058 Planarity : 0.004 0.062 5761 Dihedral : 6.126 81.182 4473 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.78 % Favored : 94.89 % Rotamer: Outliers : 4.80 % Allowed : 21.49 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 4013 helix: 1.00 (0.13), residues: 1562 sheet: -0.52 (0.22), residues: 544 loop : -0.55 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1154 HIS 0.011 0.001 HIS B 218 PHE 0.023 0.001 PHE I1219 TYR 0.021 0.001 TYR A1109 ARG 0.006 0.000 ARG A1177 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 1426) hydrogen bonds : angle 5.07204 ( 3990) metal coordination : bond 0.00589 ( 24) metal coordination : angle 3.32043 ( 33) covalent geometry : bond 0.00328 (33056) covalent geometry : angle 0.59642 (44750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 338 time to evaluate : 3.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8545 (ptm160) cc_final: 0.8055 (ttp80) REVERT: A 97 VAL cc_start: 0.9075 (p) cc_final: 0.8863 (t) REVERT: A 123 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 581 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: A 880 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8877 (tp) REVERT: A 911 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8191 (mp) REVERT: A 1057 MET cc_start: 0.8834 (tpp) cc_final: 0.8553 (mmt) REVERT: A 1096 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8307 (mt) REVERT: A 1131 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8366 (tm) REVERT: A 1274 MET cc_start: 0.8364 (mtm) cc_final: 0.7875 (mpt) REVERT: A 1323 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.7527 (tpt) REVERT: A 1422 ILE cc_start: 0.8702 (pp) cc_final: 0.8499 (pt) REVERT: B 62 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7749 (mtt) REVERT: B 637 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8172 (mpp) REVERT: B 700 ASP cc_start: 0.7021 (p0) cc_final: 0.6572 (OUTLIER) REVERT: B 1113 LYS cc_start: 0.8539 (mptt) cc_final: 0.8035 (mttp) REVERT: C 45 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8305 (mtp) REVERT: C 284 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7971 (mttp) REVERT: D 71 MET cc_start: 0.8977 (tpp) cc_final: 0.8696 (tpp) REVERT: D 157 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7818 (mp-120) REVERT: E 96 LYS cc_start: 0.7274 (mmtp) cc_final: 0.7060 (mmtm) REVERT: E 127 PRO cc_start: 0.8143 (Cg_exo) cc_final: 0.7870 (Cg_endo) REVERT: F 141 TYR cc_start: 0.5226 (m-80) cc_final: 0.4870 (m-80) REVERT: G 1 MET cc_start: 0.6839 (tpt) cc_final: 0.6360 (tpt) REVERT: G 31 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6894 (mm-40) REVERT: I 683 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8428 (tt) REVERT: I 783 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: I 801 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6156 (pp20) REVERT: I 933 TYR cc_start: 0.5595 (m-80) cc_final: 0.5205 (m-80) REVERT: I 1219 PHE cc_start: 0.6103 (t80) cc_final: 0.5757 (t80) outliers start: 173 outliers final: 69 residues processed: 465 average time/residue: 1.1627 time to fit residues: 669.0194 Evaluate side-chains 375 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 293 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 MET Chi-restraints excluded: chain A residue 1425 MET Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 997 SER Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 683 LEU Chi-restraints excluded: chain I residue 722 THR Chi-restraints excluded: chain I residue 733 TYR Chi-restraints excluded: chain I residue 783 GLU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 801 GLU Chi-restraints excluded: chain I residue 958 TYR Chi-restraints excluded: chain I residue 970 VAL Chi-restraints excluded: chain I residue 973 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 328 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 340 optimal weight: 7.9990 chunk 123 optimal weight: 0.2980 chunk 148 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 462 GLN A 497 ASN A 642 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN B 86 GLN B 108 ASN B 507 GLN F 47 ASN G 59 ASN I 703 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.109448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.087102 restraints weight = 65801.021| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.11 r_work: 0.3234 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33080 Z= 0.189 Angle : 0.620 18.452 44783 Z= 0.314 Chirality : 0.046 0.191 5058 Planarity : 0.005 0.061 5761 Dihedral : 6.093 79.141 4471 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.26 % Favored : 94.42 % Rotamer: Outliers : 4.80 % Allowed : 22.27 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 4013 helix: 1.01 (0.13), residues: 1562 sheet: -0.55 (0.22), residues: 551 loop : -0.52 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1154 HIS 0.008 0.001 HIS D 193 PHE 0.024 0.002 PHE B 304 TYR 0.024 0.001 TYR A1109 ARG 0.005 0.000 ARG A1177 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 1426) hydrogen bonds : angle 5.06244 ( 3990) metal coordination : bond 0.00702 ( 24) metal coordination : angle 3.36311 ( 33) covalent geometry : bond 0.00444 (33056) covalent geometry : angle 0.61325 (44750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 306 time to evaluate : 4.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8585 (ptm160) cc_final: 0.8092 (ttp80) REVERT: A 123 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: A 581 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: A 880 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8882 (tp) REVERT: A 911 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8199 (mp) REVERT: A 1057 MET cc_start: 0.8838 (tpp) cc_final: 0.8637 (mmt) REVERT: A 1131 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8388 (tm) REVERT: A 1274 MET cc_start: 0.8273 (mtm) cc_final: 0.7882 (mpt) REVERT: A 1323 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7665 (tpt) REVERT: A 1440 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.6218 (m-80) REVERT: B 538 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7385 (tpm-80) REVERT: B 658 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: B 700 ASP cc_start: 0.6947 (p0) cc_final: 0.6539 (t70) REVERT: B 1113 LYS cc_start: 0.8560 (mptt) cc_final: 0.8068 (mttm) REVERT: C 45 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8304 (mtp) REVERT: C 272 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6667 (ppp) REVERT: C 274 GLU cc_start: 0.6970 (pp20) cc_final: 0.6759 (pp20) REVERT: C 284 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7992 (mttp) REVERT: C 357 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6285 (mm) REVERT: D 71 MET cc_start: 0.9013 (tpp) cc_final: 0.8717 (tpp) REVERT: E 96 LYS cc_start: 0.7295 (mmtp) cc_final: 0.7077 (mmtm) REVERT: F 33 ASN cc_start: 0.7063 (m-40) cc_final: 0.6834 (m-40) REVERT: F 141 TYR cc_start: 0.5294 (m-80) cc_final: 0.4955 (m-80) REVERT: G 1 MET cc_start: 0.6848 (tpt) cc_final: 0.6589 (tpt) REVERT: I 679 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7738 (p) REVERT: I 683 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8422 (tt) REVERT: I 783 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: I 801 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6167 (pp20) REVERT: I 933 TYR cc_start: 0.5618 (m-80) cc_final: 0.5215 (m-80) outliers start: 173 outliers final: 76 residues processed: 442 average time/residue: 1.1324 time to fit residues: 620.7354 Evaluate side-chains 381 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 288 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 MET Chi-restraints excluded: chain A residue 1425 MET Chi-restraints excluded: chain A residue 1440 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 997 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1223 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 679 THR Chi-restraints excluded: chain I residue 683 LEU Chi-restraints excluded: chain I residue 722 THR Chi-restraints excluded: chain I residue 733 TYR Chi-restraints excluded: chain I residue 738 THR Chi-restraints excluded: chain I residue 783 GLU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 801 GLU Chi-restraints excluded: chain I residue 837 ARG Chi-restraints excluded: chain I residue 860 THR Chi-restraints excluded: chain I residue 970 VAL Chi-restraints excluded: chain I residue 973 TYR Chi-restraints excluded: chain I residue 1161 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 384 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 361 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 137 optimal weight: 0.4980 chunk 268 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 386 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 462 GLN A 497 ASN A 646 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 108 ASN B 325 HIS D 148 GLN D 157 GLN F 47 ASN I 703 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.109252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.086966 restraints weight = 66125.890| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.10 r_work: 0.3225 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33080 Z= 0.202 Angle : 0.631 18.394 44783 Z= 0.319 Chirality : 0.047 0.208 5058 Planarity : 0.005 0.059 5761 Dihedral : 6.060 78.822 4464 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.43 % Favored : 94.24 % Rotamer: Outliers : 5.08 % Allowed : 22.22 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 4013 helix: 0.97 (0.13), residues: 1567 sheet: -0.55 (0.22), residues: 545 loop : -0.56 (0.15), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1154 HIS 0.008 0.001 HIS D 193 PHE 0.036 0.002 PHE I1219 TYR 0.023 0.001 TYR F 69 ARG 0.005 0.000 ARG A1177 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 1426) hydrogen bonds : angle 5.06831 ( 3990) metal coordination : bond 0.00757 ( 24) metal coordination : angle 3.59021 ( 33) covalent geometry : bond 0.00477 (33056) covalent geometry : angle 0.62362 (44750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 300 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8603 (ptm160) cc_final: 0.8098 (ttp80) REVERT: A 119 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6864 (mppt) REVERT: A 581 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: A 880 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8863 (tp) REVERT: A 911 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 1131 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8391 (tm) REVERT: A 1274 MET cc_start: 0.8325 (mtm) cc_final: 0.7891 (mpt) REVERT: A 1323 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7631 (tpt) REVERT: A 1440 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: B 538 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7463 (tpm-80) REVERT: B 700 ASP cc_start: 0.7042 (p0) cc_final: 0.6641 (t70) REVERT: B 1113 LYS cc_start: 0.8548 (mptt) cc_final: 0.7954 (mttm) REVERT: B 1202 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.5984 (t0) REVERT: C 45 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8299 (mtp) REVERT: C 272 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6638 (ppp) REVERT: C 284 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7966 (mttp) REVERT: C 357 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6288 (mm) REVERT: D 70 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6316 (p0) REVERT: D 71 MET cc_start: 0.9015 (tpp) cc_final: 0.8727 (tpp) REVERT: D 157 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7697 (mp-120) REVERT: E 96 LYS cc_start: 0.7285 (mmtp) cc_final: 0.7063 (mmtm) REVERT: F 61 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7786 (mtp-110) REVERT: F 141 TYR cc_start: 0.5253 (m-80) cc_final: 0.4957 (m-80) REVERT: G 1 MET cc_start: 0.6855 (tpt) cc_final: 0.6436 (tpt) REVERT: I 679 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7742 (p) REVERT: I 683 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8457 (tt) REVERT: I 783 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: I 801 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6171 (pp20) REVERT: I 915 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8120 (mttp) REVERT: I 933 TYR cc_start: 0.5577 (m-80) cc_final: 0.5167 (m-80) REVERT: I 1129 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8758 (mm) outliers start: 183 outliers final: 82 residues processed: 443 average time/residue: 1.1503 time to fit residues: 632.1117 Evaluate side-chains 388 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 285 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 MET Chi-restraints excluded: chain A residue 1425 MET Chi-restraints excluded: chain A residue 1440 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 997 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1223 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 679 THR Chi-restraints excluded: chain I residue 683 LEU Chi-restraints excluded: chain I residue 722 THR Chi-restraints excluded: chain I residue 733 TYR Chi-restraints excluded: chain I residue 738 THR Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain I residue 783 GLU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 801 GLU Chi-restraints excluded: chain I residue 837 ARG Chi-restraints excluded: chain I residue 860 THR Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 958 TYR Chi-restraints excluded: chain I residue 970 VAL Chi-restraints excluded: chain I residue 973 TYR Chi-restraints excluded: chain I residue 1129 LEU Chi-restraints excluded: chain I residue 1161 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 240 optimal weight: 0.9990 chunk 329 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 346 optimal weight: 0.8980 chunk 339 optimal weight: 0.4980 chunk 304 optimal weight: 4.9990 chunk 306 optimal weight: 0.5980 chunk 335 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 159 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 592 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 325 HIS ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN D 148 GLN F 47 ASN G 59 ASN I 703 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.111888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.089661 restraints weight = 65477.255| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.12 r_work: 0.3274 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33080 Z= 0.119 Angle : 0.599 17.956 44783 Z= 0.301 Chirality : 0.045 0.220 5058 Planarity : 0.004 0.057 5761 Dihedral : 5.816 84.119 4463 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.98 % Favored : 94.69 % Rotamer: Outliers : 3.83 % Allowed : 23.58 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 4013 helix: 1.12 (0.13), residues: 1565 sheet: -0.62 (0.22), residues: 555 loop : -0.44 (0.15), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1154 HIS 0.008 0.001 HIS D 193 PHE 0.033 0.001 PHE B 304 TYR 0.020 0.001 TYR A1109 ARG 0.006 0.000 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1426) hydrogen bonds : angle 4.91500 ( 3990) metal coordination : bond 0.00470 ( 24) metal coordination : angle 3.08782 ( 33) covalent geometry : bond 0.00262 (33056) covalent geometry : angle 0.59341 (44750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 345 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8070 (ttp80) REVERT: A 100 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7464 (tp) REVERT: A 119 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6666 (mppt) REVERT: A 599 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7370 (pp) REVERT: A 880 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8843 (tp) REVERT: A 911 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 1057 MET cc_start: 0.8834 (tpp) cc_final: 0.8545 (mmt) REVERT: A 1131 LEU cc_start: 0.8545 (tt) cc_final: 0.8325 (tm) REVERT: A 1274 MET cc_start: 0.8298 (mtm) cc_final: 0.7855 (mpt) REVERT: A 1440 TYR cc_start: 0.6555 (OUTLIER) cc_final: 0.6121 (m-80) REVERT: B 62 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7754 (mtt) REVERT: B 538 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7276 (tpm-80) REVERT: B 700 ASP cc_start: 0.6926 (p0) cc_final: 0.6527 (t70) REVERT: B 703 LYS cc_start: 0.8784 (tppt) cc_final: 0.8450 (tmmm) REVERT: B 1113 LYS cc_start: 0.8483 (mptt) cc_final: 0.7926 (mttm) REVERT: B 1202 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.5967 (t0) REVERT: C 45 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8302 (mtp) REVERT: C 272 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6575 (ppp) REVERT: C 284 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7983 (mttp) REVERT: D 70 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6428 (p0) REVERT: D 71 MET cc_start: 0.9019 (tpp) cc_final: 0.8776 (tpp) REVERT: E 96 LYS cc_start: 0.7294 (mmtp) cc_final: 0.7070 (mmtm) REVERT: E 127 PRO cc_start: 0.8168 (Cg_exo) cc_final: 0.7931 (Cg_endo) REVERT: F 141 TYR cc_start: 0.5262 (m-80) cc_final: 0.5008 (m-80) REVERT: I 683 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8443 (tt) REVERT: I 783 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: I 915 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8154 (mttp) REVERT: I 933 TYR cc_start: 0.5581 (m-80) cc_final: 0.5216 (m-80) REVERT: I 1129 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8658 (mm) outliers start: 138 outliers final: 62 residues processed: 455 average time/residue: 1.1079 time to fit residues: 627.7938 Evaluate side-chains 385 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 305 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1440 TYR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1223 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 673 ASP Chi-restraints excluded: chain I residue 683 LEU Chi-restraints excluded: chain I residue 722 THR Chi-restraints excluded: chain I residue 733 TYR Chi-restraints excluded: chain I residue 783 GLU Chi-restraints excluded: chain I residue 860 THR Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 958 TYR Chi-restraints excluded: chain I residue 973 TYR Chi-restraints excluded: chain I residue 1129 LEU Chi-restraints excluded: chain I residue 1161 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 69 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 179 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 373 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 646 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS B 748 ASN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN D 157 GLN F 47 ASN I 703 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.112803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.089165 restraints weight = 64574.842| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.35 r_work: 0.3253 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33080 Z= 0.127 Angle : 0.611 18.264 44783 Z= 0.305 Chirality : 0.045 0.229 5058 Planarity : 0.004 0.054 5761 Dihedral : 5.539 84.490 4456 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.08 % Favored : 94.62 % Rotamer: Outliers : 3.80 % Allowed : 24.24 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 4013 helix: 1.18 (0.13), residues: 1571 sheet: -0.60 (0.22), residues: 556 loop : -0.41 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 701 HIS 0.009 0.001 HIS D 193 PHE 0.036 0.001 PHE B 304 TYR 0.018 0.001 TYR B 104 ARG 0.014 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 1426) hydrogen bonds : angle 4.88035 ( 3990) metal coordination : bond 0.00445 ( 24) metal coordination : angle 2.87492 ( 33) covalent geometry : bond 0.00289 (33056) covalent geometry : angle 0.60615 (44750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 324 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7787 (ttp80) REVERT: A 100 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7326 (tp) REVERT: A 119 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6428 (tppt) REVERT: A 123 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: A 599 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7392 (pp) REVERT: A 911 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 1057 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8671 (mmt) REVERT: A 1131 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7909 (tm) REVERT: A 1209 MET cc_start: 0.7622 (mpt) cc_final: 0.7223 (mmm) REVERT: A 1274 MET cc_start: 0.8296 (mtm) cc_final: 0.7611 (mpt) REVERT: A 1440 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.6005 (m-80) REVERT: B 289 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7797 (pm20) REVERT: B 538 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6713 (tpm-80) REVERT: B 696 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7823 (tmmm) REVERT: B 700 ASP cc_start: 0.6887 (p0) cc_final: 0.6401 (t70) REVERT: B 704 HIS cc_start: 0.8580 (m-70) cc_final: 0.8350 (m-70) REVERT: B 1087 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8829 (ttpp) REVERT: B 1113 LYS cc_start: 0.8619 (mptt) cc_final: 0.7888 (mttm) REVERT: B 1202 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.5822 (t0) REVERT: C 45 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7814 (mtp) REVERT: C 272 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6166 (ppp) REVERT: C 284 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7713 (mttp) REVERT: D 70 ASP cc_start: 0.6600 (OUTLIER) cc_final: 0.6202 (p0) REVERT: D 71 MET cc_start: 0.8980 (tpp) cc_final: 0.8714 (tpp) REVERT: D 157 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7435 (mp10) REVERT: E 96 LYS cc_start: 0.7134 (mmtp) cc_final: 0.6845 (mmtm) REVERT: E 127 PRO cc_start: 0.8253 (Cg_exo) cc_final: 0.8033 (Cg_endo) REVERT: F 141 TYR cc_start: 0.5051 (m-80) cc_final: 0.4720 (m-80) REVERT: G 1 MET cc_start: 0.6910 (tpt) cc_final: 0.6692 (tpt) REVERT: G 31 GLN cc_start: 0.7061 (mm-40) cc_final: 0.6769 (mm-40) REVERT: I 783 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: I 915 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8000 (mttp) REVERT: I 933 TYR cc_start: 0.5364 (m-80) cc_final: 0.5070 (m-80) REVERT: I 1129 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8205 (mm) REVERT: I 1219 PHE cc_start: 0.5360 (t80) cc_final: 0.5039 (t80) outliers start: 137 outliers final: 59 residues processed: 434 average time/residue: 1.1204 time to fit residues: 600.2233 Evaluate side-chains 383 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 304 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1394 VAL Chi-restraints excluded: chain A residue 1440 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1087 LYS Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1223 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 673 ASP Chi-restraints excluded: chain I residue 722 THR Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain I residue 776 LEU Chi-restraints excluded: chain I residue 783 GLU Chi-restraints excluded: chain I residue 860 THR Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 958 TYR Chi-restraints excluded: chain I residue 973 TYR Chi-restraints excluded: chain I residue 1129 LEU Chi-restraints excluded: chain I residue 1161 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 137 optimal weight: 4.9990 chunk 269 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 353 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 197 optimal weight: 0.0970 chunk 7 optimal weight: 20.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 646 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 325 HIS ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN F 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.113077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090751 restraints weight = 64960.215| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.12 r_work: 0.3291 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33080 Z= 0.121 Angle : 0.617 18.242 44783 Z= 0.305 Chirality : 0.045 0.242 5058 Planarity : 0.004 0.056 5761 Dihedral : 5.401 85.940 4450 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.06 % Favored : 94.67 % Rotamer: Outliers : 3.30 % Allowed : 25.19 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 4013 helix: 1.27 (0.13), residues: 1566 sheet: -0.54 (0.22), residues: 568 loop : -0.35 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 701 HIS 0.009 0.001 HIS D 193 PHE 0.047 0.001 PHE B 304 TYR 0.027 0.001 TYR A 961 ARG 0.016 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1426) hydrogen bonds : angle 4.84061 ( 3990) metal coordination : bond 0.00404 ( 24) metal coordination : angle 2.74515 ( 33) covalent geometry : bond 0.00272 (33056) covalent geometry : angle 0.61272 (44750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 328 time to evaluate : 4.135 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8117 (ttp80) REVERT: A 100 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7331 (tp) REVERT: A 119 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.7000 (mmtm) REVERT: A 478 GLU cc_start: 0.8329 (pt0) cc_final: 0.7990 (tm-30) REVERT: A 599 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7066 (pp) REVERT: A 911 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8046 (mp) REVERT: A 954 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: A 1057 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8552 (mmt) REVERT: A 1274 MET cc_start: 0.8293 (mtm) cc_final: 0.7830 (mpt) REVERT: A 1304 MET cc_start: 0.7981 (ttm) cc_final: 0.7726 (mtp) REVERT: A 1440 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.6140 (m-80) REVERT: B 538 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7326 (tpm-80) REVERT: B 700 ASP cc_start: 0.6608 (p0) cc_final: 0.6274 (t70) REVERT: B 701 TRP cc_start: 0.8586 (p-90) cc_final: 0.7768 (p-90) REVERT: B 1113 LYS cc_start: 0.8512 (mptt) cc_final: 0.7954 (mttm) REVERT: B 1181 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6918 (tpp-160) REVERT: B 1202 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6043 (t0) REVERT: C 45 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: C 272 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.6618 (ppp) REVERT: C 284 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7986 (mttp) REVERT: D 71 MET cc_start: 0.9001 (tpp) cc_final: 0.8776 (tpp) REVERT: E 96 LYS cc_start: 0.7225 (mmtp) cc_final: 0.7004 (mmtm) REVERT: E 127 PRO cc_start: 0.8093 (Cg_exo) cc_final: 0.7887 (Cg_endo) REVERT: F 141 TYR cc_start: 0.5201 (m-80) cc_final: 0.4890 (m-80) REVERT: I 683 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8371 (tm) REVERT: I 783 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: I 915 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8147 (mttp) REVERT: I 933 TYR cc_start: 0.5618 (m-80) cc_final: 0.5282 (m-80) REVERT: I 1129 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8646 (mm) outliers start: 119 outliers final: 54 residues processed: 424 average time/residue: 1.2490 time to fit residues: 652.1989 Evaluate side-chains 378 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 306 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1440 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1181 ARG Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1223 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 673 ASP Chi-restraints excluded: chain I residue 683 LEU Chi-restraints excluded: chain I residue 703 HIS Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain I residue 776 LEU Chi-restraints excluded: chain I residue 783 GLU Chi-restraints excluded: chain I residue 860 THR Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 958 TYR Chi-restraints excluded: chain I residue 973 TYR Chi-restraints excluded: chain I residue 1129 LEU Chi-restraints excluded: chain I residue 1161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 146 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 371 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 393 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 281 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 231 GLN A 497 ASN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1276 HIS B 86 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 341 GLN D 148 GLN F 47 ASN I 703 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.111435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089168 restraints weight = 65374.676| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.10 r_work: 0.3260 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 33080 Z= 0.172 Angle : 0.657 23.003 44783 Z= 0.325 Chirality : 0.047 0.251 5058 Planarity : 0.004 0.059 5761 Dihedral : 5.340 82.998 4441 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.43 % Favored : 94.27 % Rotamer: Outliers : 2.75 % Allowed : 25.77 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 4013 helix: 1.17 (0.13), residues: 1578 sheet: -0.48 (0.22), residues: 556 loop : -0.40 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 701 HIS 0.007 0.001 HIS D 193 PHE 0.050 0.002 PHE B 304 TYR 0.020 0.001 TYR A 961 ARG 0.019 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 1426) hydrogen bonds : angle 4.92378 ( 3990) metal coordination : bond 0.00561 ( 24) metal coordination : angle 3.00058 ( 33) covalent geometry : bond 0.00407 (33056) covalent geometry : angle 0.65238 (44750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8026 Ramachandran restraints generated. 4013 Oldfield, 0 Emsley, 4013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 309 time to evaluate : 3.734 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: A 92 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8099 (ttp80) REVERT: A 100 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7379 (tp) REVERT: A 119 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6706 (tppt) REVERT: A 123 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 599 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7167 (pp) REVERT: A 954 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: A 1057 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8568 (mmt) REVERT: A 1274 MET cc_start: 0.8270 (mtm) cc_final: 0.7823 (mpt) REVERT: A 1304 MET cc_start: 0.7991 (ttm) cc_final: 0.7718 (mtp) REVERT: A 1440 TYR cc_start: 0.6540 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: B 538 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7307 (tpm-80) REVERT: B 700 ASP cc_start: 0.6637 (p0) cc_final: 0.6248 (t70) REVERT: B 701 TRP cc_start: 0.8626 (p-90) cc_final: 0.7797 (p-90) REVERT: B 703 LYS cc_start: 0.8731 (tppt) cc_final: 0.8489 (tmmm) REVERT: B 1113 LYS cc_start: 0.8538 (mptt) cc_final: 0.8008 (mttm) REVERT: B 1202 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6049 (t0) REVERT: C 272 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.6655 (ppp) REVERT: C 357 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6228 (mm) REVERT: D 64 TYR cc_start: 0.7918 (m-80) cc_final: 0.7706 (m-80) REVERT: D 71 MET cc_start: 0.9030 (tpp) cc_final: 0.8731 (tpp) REVERT: F 141 TYR cc_start: 0.5294 (m-80) cc_final: 0.4975 (m-80) REVERT: G 1 MET cc_start: 0.6806 (tpt) cc_final: 0.6315 (tpt) REVERT: G 101 MET cc_start: 0.7645 (ppp) cc_final: 0.7425 (tpp) REVERT: I 683 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8365 (tm) REVERT: I 783 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: I 915 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8142 (mttp) REVERT: I 933 TYR cc_start: 0.5552 (m-80) cc_final: 0.5244 (m-80) REVERT: I 958 TYR cc_start: 0.2065 (OUTLIER) cc_final: 0.1842 (p90) outliers start: 99 outliers final: 58 residues processed: 388 average time/residue: 1.1414 time to fit residues: 546.5070 Evaluate side-chains 373 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 298 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1440 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 888 GLU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1223 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1238 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 673 ASP Chi-restraints excluded: chain I residue 683 LEU Chi-restraints excluded: chain I residue 733 TYR Chi-restraints excluded: chain I residue 738 THR Chi-restraints excluded: chain I residue 746 THR Chi-restraints excluded: chain I residue 783 GLU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 860 THR Chi-restraints excluded: chain I residue 915 LYS Chi-restraints excluded: chain I residue 958 TYR Chi-restraints excluded: chain I residue 973 TYR Chi-restraints excluded: chain I residue 1161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 383 optimal weight: 0.0670 chunk 78 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 173 optimal weight: 0.1980 chunk 354 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 283 optimal weight: 0.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 325 HIS ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN D 157 GLN F 47 ASN I 703 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.113205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090398 restraints weight = 63966.530| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.32 r_work: 0.3286 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 33080 Z= 0.122 Angle : 0.638 21.743 44783 Z= 0.315 Chirality : 0.045 0.351 5058 Planarity : 0.004 0.056 5761 Dihedral : 5.246 86.062 4441 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.01 % Favored : 94.69 % Rotamer: Outliers : 2.55 % Allowed : 25.88 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 4013 helix: 1.25 (0.13), residues: 1567 sheet: -0.48 (0.22), residues: 560 loop : -0.34 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A1154 HIS 0.007 0.001 HIS D 193 PHE 0.029 0.001 PHE F 40 TYR 0.021 0.001 TYR A 961 ARG 0.019 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 1426) hydrogen bonds : angle 4.84827 ( 3990) metal coordination : bond 0.00382 ( 24) metal coordination : angle 2.73784 ( 33) covalent geometry : bond 0.00280 (33056) covalent geometry : angle 0.63430 (44750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20281.86 seconds wall clock time: 351 minutes 33.91 seconds (21093.91 seconds total)