Starting phenix.real_space_refine on Fri May 23 12:35:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e95_27956/05_2025/8e95_27956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e95_27956/05_2025/8e95_27956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e95_27956/05_2025/8e95_27956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e95_27956/05_2025/8e95_27956.map" model { file = "/net/cci-nas-00/data/ceres_data/8e95_27956/05_2025/8e95_27956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e95_27956/05_2025/8e95_27956.cif" } resolution = 2.9 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= 0.003 sd= 0.143 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 68 5.49 5 Mg 1 5.21 5 S 87 5.16 5 C 14792 2.51 5 N 4255 2.21 5 O 4738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.47s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23943 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 221} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8485 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1033} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 9916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9916 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1208} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 75} Chain: "P" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 666 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "Q" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12487 SG CYS D 60 109.325 75.054 111.808 1.00 59.49 S ATOM 12505 SG CYS D 62 111.304 75.898 112.270 1.00 67.74 S ATOM 12614 SG CYS D 75 110.872 72.803 114.866 1.00 67.04 S ATOM 12640 SG CYS D 78 109.341 75.116 114.388 1.00 66.98 S ATOM 19055 SG CYS D 891 70.397 22.954 88.079 1.00 31.73 S ATOM 19622 SG CYS D 968 69.866 26.822 89.590 1.00 9.65 S ATOM 19664 SG CYS D 975 70.676 25.954 86.115 1.00 14.23 S ATOM 19682 SG CYS D 978 67.693 25.179 86.622 1.00 17.04 S Time building chain proxies: 14.15, per 1000 atoms: 0.59 Number of scatterers: 23943 At special positions: 0 Unit cell: (127.735, 134.23, 198.097, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 87 16.00 P 68 15.00 Mg 1 11.99 O 4738 8.00 N 4255 7.00 C 14792 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: 6.69 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " Number of angles added : 12 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5346 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 38 sheets defined 39.2% alpha, 15.7% beta 29 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 10.24 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 203 through 219 Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.558A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 203 through 219 removed outlier: 3.690A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.662A pdb=" N ARG B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.900A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 62 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.616A pdb=" N GLU C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.073A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.520A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 262 " --> pdb=" O MET C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 300 Processing helix chain 'C' and resid 308 through 320 Processing helix chain 'C' and resid 334 through 349 removed outlier: 3.738A pdb=" N ILE C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 404 Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.514A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.675A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 533 through 537 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.715A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 631 through 639 removed outlier: 3.506A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 779 through 784 removed outlier: 4.561A pdb=" N ASP C 783 " --> pdb=" O VAL C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.681A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1079 removed outlier: 3.642A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.671A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1108 removed outlier: 3.780A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1131 removed outlier: 3.784A pdb=" N VAL C1123 " --> pdb=" O GLU C1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.541A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 141 through 186 removed outlier: 4.404A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 229 Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.664A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.627A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 4.069A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.582A pdb=" N LYS D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.858A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 447 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 removed outlier: 3.513A pdb=" N ALA D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 491 removed outlier: 4.271A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 4.146A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.634A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.654A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.846A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.766A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1008 No H-bonds generated for 'chain 'D' and resid 1006 through 1008' Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1126 removed outlier: 3.729A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 4.033A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1160 removed outlier: 4.311A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1196 removed outlier: 3.628A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.507A pdb=" N ALA D1224 " --> pdb=" O TRP D1220 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1254 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 74 removed outlier: 3.830A pdb=" N GLY E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.508A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.614A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 189 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA A 180 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.451A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.772A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 15 removed outlier: 6.138A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.010A pdb=" N VAL B 111 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 134 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.670A pdb=" N GLY B 103 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.552A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.535A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.764A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 3.912A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 505 through 506 removed outlier: 4.154A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 4.616A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 562 " --> pdb=" O VAL C 541 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL C 559 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.439A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.952A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC3, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC4, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 5.738A pdb=" N ILE C 735 " --> pdb=" O ILE C 895 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 756 removed outlier: 3.555A pdb=" N VAL C 873 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 759 through 760 removed outlier: 6.897A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.653A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AC9, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD1, first strand: chain 'C' and resid 1136 through 1138 Processing sheet with id=AD2, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.645A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.591A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 328 through 330 removed outlier: 4.247A pdb=" N VAL D 328 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 632 through 637 Processing sheet with id=AD6, first strand: chain 'D' and resid 822 through 825 removed outlier: 9.311A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AD8, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.986A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1051 through 1053 removed outlier: 5.561A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 4.879A pdb=" N ARG D1164 " --> pdb=" O VAL D1206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D1206 " --> pdb=" O ARG D1164 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1271 through 1274 932 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 11.22 Time building geometry restraints manager: 7.60 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: 7802 1.34 - 1.46: 3305 1.46 - 1.58: 13099 1.58 - 1.70: 132 1.70 - 1.81: 153 Bond restraints: 24491 Sorted by residual: bond pdb=" N GLY D -1 " pdb=" CA GLY D -1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.18e+00 bond pdb=" P DG P 112 " pdb=" OP2 DG P 112 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" P DT P 115 " pdb=" OP2 DT P 115 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" P DG P 114 " pdb=" OP2 DG P 114 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" P DT P 117 " pdb=" OP2 DT P 117 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.43e+00 ... (remaining 24486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 33227 2.75 - 5.49: 235 5.49 - 8.24: 11 8.24 - 10.98: 1 10.98 - 13.73: 1 Bond angle restraints: 33475 Sorted by residual: angle pdb=" C3' DA P 116 " pdb=" O3' DA P 116 " pdb=" P DT P 117 " ideal model delta sigma weight residual 120.20 106.47 13.73 1.50e+00 4.44e-01 8.38e+01 angle pdb=" C3' DG P 112 " pdb=" O3' DG P 112 " pdb=" P DG P 113 " ideal model delta sigma weight residual 120.20 111.03 9.17 1.50e+00 4.44e-01 3.73e+01 angle pdb=" C3' DT P 115 " pdb=" O3' DT P 115 " pdb=" P DA P 116 " ideal model delta sigma weight residual 120.20 112.08 8.12 1.50e+00 4.44e-01 2.93e+01 angle pdb=" N VAL B 183 " pdb=" CA VAL B 183 " pdb=" C VAL B 183 " ideal model delta sigma weight residual 113.71 109.62 4.09 9.50e-01 1.11e+00 1.86e+01 angle pdb=" N ARG C 584 " pdb=" CA ARG C 584 " pdb=" C ARG C 584 " ideal model delta sigma weight residual 111.71 106.56 5.15 1.34e+00 5.57e-01 1.48e+01 ... (remaining 33470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 14350 33.36 - 66.72: 458 66.72 - 100.07: 5 100.07 - 133.43: 1 133.43 - 166.79: 1 Dihedral angle restraints: 14815 sinusoidal: 6497 harmonic: 8318 Sorted by residual: dihedral pdb=" O4' C R 11 " pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sinusoidal sigma weight residual 200.00 33.21 166.79 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" CA GLU E 77 " pdb=" C GLU E 77 " pdb=" N TYR E 78 " pdb=" CA TYR E 78 " ideal model delta harmonic sigma weight residual 180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASN D 5 " pdb=" C ASN D 5 " pdb=" N PHE D 6 " pdb=" CA PHE D 6 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 14812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3692 0.104 - 0.209: 127 0.209 - 0.313: 0 0.313 - 0.417: 0 0.417 - 0.522: 6 Chirality restraints: 3825 Sorted by residual: chirality pdb=" P DA P 116 " pdb=" OP1 DA P 116 " pdb=" OP2 DA P 116 " pdb=" O5' DA P 116 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" P DG P 112 " pdb=" OP1 DG P 112 " pdb=" OP2 DG P 112 " pdb=" O5' DG P 112 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" P DG P 114 " pdb=" OP1 DG P 114 " pdb=" OP2 DG P 114 " pdb=" O5' DG P 114 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.44e+00 ... (remaining 3822 not shown) Planarity restraints: 4169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT P 117 " -0.004 2.00e-02 2.50e+03 2.11e-02 1.11e+01 pdb=" N1 DT P 117 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DT P 117 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DT P 117 " -0.019 2.00e-02 2.50e+03 pdb=" N3 DT P 117 " 0.056 2.00e-02 2.50e+03 pdb=" C4 DT P 117 " -0.006 2.00e-02 2.50e+03 pdb=" O4 DT P 117 " -0.024 2.00e-02 2.50e+03 pdb=" C5 DT P 117 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT P 117 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT P 117 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT P 115 " 0.016 2.00e-02 2.50e+03 1.29e-02 4.17e+00 pdb=" N1 DT P 115 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT P 115 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT P 115 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DT P 115 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT P 115 " -0.012 2.00e-02 2.50e+03 pdb=" O4 DT P 115 " 0.025 2.00e-02 2.50e+03 pdb=" C5 DT P 115 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT P 115 " -0.017 2.00e-02 2.50e+03 pdb=" C6 DT P 115 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 413 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO C 414 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " -0.028 5.00e-02 4.00e+02 ... (remaining 4166 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 64 2.42 - 3.04: 15009 3.04 - 3.66: 33929 3.66 - 4.28: 52286 4.28 - 4.90: 88884 Nonbonded interactions: 190172 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 1.796 2.170 nonbonded pdb=" OE1 GLN C 150 " pdb=" OG1 THR C 413 " model vdw 1.992 3.040 nonbonded pdb=" O3' A R 20 " pdb="MG MG D2002 " model vdw 2.027 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.097 2.170 nonbonded pdb=" O SER B 45 " pdb=" NH1 ARG B 144 " model vdw 2.099 3.120 ... (remaining 190167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and resid 1 through 226) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.170 Set scattering table: 0.250 Process input model: 69.180 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.248 24499 Z= 0.169 Angle : 0.772 47.946 33487 Z= 0.357 Chirality : 0.045 0.522 3825 Planarity : 0.004 0.050 4169 Dihedral : 14.082 166.790 9469 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.70 % Favored : 95.02 % Rotamer: Outliers : 4.39 % Allowed : 6.56 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -0.81 (0.16), residues: 2893 helix: 0.83 (0.17), residues: 1011 sheet: -0.94 (0.29), residues: 316 loop : -1.40 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 938 HIS 0.003 0.001 HIS D 689 PHE 0.013 0.001 PHE C 439 TYR 0.010 0.001 TYR D 586 ARG 0.003 0.000 ARG C1067 Details of bonding type rmsd hydrogen bonds : bond 0.18172 ( 1007) hydrogen bonds : angle 6.74905 ( 2743) metal coordination : bond 0.14591 ( 8) metal coordination : angle 26.18530 ( 12) covalent geometry : bond 0.00276 (24491) covalent geometry : angle 0.59209 (33475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 496 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4486 (tpp) cc_final: 0.3594 (tmt) REVERT: A 221 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6877 (mt) REVERT: B 24 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6485 (mt-10) REVERT: B 55 ARG cc_start: 0.7583 (ptm160) cc_final: 0.7097 (ptp90) REVERT: C 160 MET cc_start: 0.9154 (ttm) cc_final: 0.8546 (ttp) REVERT: C 215 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6716 (m-30) REVERT: C 262 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5859 (pp) REVERT: C 302 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6295 (mmtt) REVERT: C 419 ASN cc_start: 0.7166 (t0) cc_final: 0.6905 (t160) REVERT: C 483 MET cc_start: 0.9033 (ttp) cc_final: 0.8796 (ttt) REVERT: C 528 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8287 (pt) REVERT: C 673 ARG cc_start: 0.8101 (ptm160) cc_final: 0.7604 (ptm-80) REVERT: C 805 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5803 (pttt) REVERT: C 901 VAL cc_start: 0.8765 (p) cc_final: 0.8466 (t) REVERT: C 952 VAL cc_start: 0.7953 (m) cc_final: 0.7715 (t) REVERT: C 1030 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8472 (mm) REVERT: C 1138 LEU cc_start: 0.8649 (mt) cc_final: 0.8382 (mt) REVERT: D 229 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6279 (tt) REVERT: D 403 SER cc_start: 0.8513 (t) cc_final: 0.8277 (m) REVERT: D 410 GLN cc_start: 0.8419 (mp10) cc_final: 0.8092 (mm-40) REVERT: D 423 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: D 496 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8133 (p) REVERT: D 672 MET cc_start: 0.8123 (mtt) cc_final: 0.7857 (mtt) REVERT: D 865 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7546 (mm) REVERT: D 1117 ASP cc_start: 0.7561 (p0) cc_final: 0.7325 (t0) REVERT: E 33 LEU cc_start: 0.8450 (pt) cc_final: 0.8159 (mt) REVERT: E 40 ILE cc_start: 0.8448 (tp) cc_final: 0.8076 (tp) REVERT: E 62 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7787 (mmt-90) outliers start: 107 outliers final: 32 residues processed: 575 average time/residue: 1.2941 time to fit residues: 858.8487 Evaluate side-chains 335 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 947 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 7.9990 chunk 222 optimal weight: 0.0040 chunk 123 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 overall best weight: 2.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 ASN ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 HIS C 685 ASN C 739 ASN C 751 HIS C 755 HIS C 889 HIS D 564 ASN D 693 GLN D 748 HIS D 810 ASN D1032 GLN D1125 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.197155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149521 restraints weight = 25916.403| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.68 r_work: 0.3381 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24499 Z= 0.262 Angle : 0.767 18.531 33487 Z= 0.394 Chirality : 0.050 0.207 3825 Planarity : 0.006 0.072 4169 Dihedral : 14.659 167.358 4018 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.19 % Favored : 93.50 % Rotamer: Outliers : 5.87 % Allowed : 13.54 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -1.04 (0.15), residues: 2893 helix: 0.62 (0.16), residues: 1016 sheet: -0.68 (0.27), residues: 357 loop : -1.65 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 938 HIS 0.008 0.002 HIS D 689 PHE 0.025 0.003 PHE C 906 TYR 0.018 0.002 TYR A 168 ARG 0.008 0.001 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.06724 ( 1007) hydrogen bonds : angle 5.32329 ( 2743) metal coordination : bond 0.02196 ( 8) metal coordination : angle 8.99881 ( 12) covalent geometry : bond 0.00645 (24491) covalent geometry : angle 0.74796 (33475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 295 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4701 (tpp) cc_final: 0.2903 (tmt) REVERT: A 193 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8169 (mt) REVERT: A 221 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.6984 (mt) REVERT: B 6 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7058 (tmt170) REVERT: B 24 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6724 (mt-10) REVERT: B 55 ARG cc_start: 0.8019 (ptm160) cc_final: 0.6412 (ptp90) REVERT: B 123 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7572 (ttt) REVERT: B 150 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7630 (t) REVERT: C 92 GLU cc_start: 0.7240 (tp30) cc_final: 0.5909 (tt0) REVERT: C 127 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7841 (ptp) REVERT: C 347 ARG cc_start: 0.6293 (mtt-85) cc_final: 0.6046 (tpt170) REVERT: C 505 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7582 (ptp-170) REVERT: C 570 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: C 584 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7981 (ttt180) REVERT: C 673 ARG cc_start: 0.8530 (ptm160) cc_final: 0.7534 (ptm-80) REVERT: C 767 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6212 (pm20) REVERT: C 805 LYS cc_start: 0.5462 (OUTLIER) cc_final: 0.5162 (pttt) REVERT: C 877 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8372 (mtm-85) REVERT: C 952 VAL cc_start: 0.7947 (m) cc_final: 0.7662 (t) REVERT: C 1028 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8385 (ttm) REVERT: C 1030 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8479 (mm) REVERT: C 1119 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: D 9 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: D 30 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7064 (tppp) REVERT: D 92 MET cc_start: 0.8653 (mtp) cc_final: 0.8044 (mtm) REVERT: D 126 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6806 (tt0) REVERT: D 266 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7258 (mp0) REVERT: D 410 GLN cc_start: 0.8368 (mp10) cc_final: 0.7786 (mm-40) REVERT: D 623 ASP cc_start: 0.7345 (m-30) cc_final: 0.6953 (m-30) REVERT: D 665 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7761 (pp20) REVERT: D 787 GLN cc_start: 0.7108 (tp40) cc_final: 0.6789 (tm-30) REVERT: D 824 VAL cc_start: 0.8323 (m) cc_final: 0.7723 (p) REVERT: D 865 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7201 (mm) REVERT: D 901 LEU cc_start: 0.7235 (tp) cc_final: 0.6963 (tt) REVERT: D 959 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7390 (pt0) REVERT: D 1117 ASP cc_start: 0.7554 (p0) cc_final: 0.7063 (t0) REVERT: D 1129 GLU cc_start: 0.8303 (mp0) cc_final: 0.7903 (mm-30) REVERT: D 1231 ARG cc_start: 0.8238 (ttp-170) cc_final: 0.8006 (ttm170) REVERT: E 31 THR cc_start: 0.7867 (t) cc_final: 0.7645 (m) REVERT: E 62 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7598 (mmt-90) outliers start: 143 outliers final: 67 residues processed: 399 average time/residue: 1.3122 time to fit residues: 603.2268 Evaluate side-chains 345 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 256 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 42 optimal weight: 0.0980 chunk 283 optimal weight: 6.9990 chunk 204 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS D1145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.201937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155513 restraints weight = 25797.363| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.83 r_work: 0.3448 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24499 Z= 0.123 Angle : 0.581 15.424 33487 Z= 0.298 Chirality : 0.042 0.168 3825 Planarity : 0.005 0.064 4169 Dihedral : 14.303 166.231 3996 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.36 % Favored : 95.37 % Rotamer: Outliers : 4.51 % Allowed : 16.74 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -0.65 (0.15), residues: 2893 helix: 1.00 (0.17), residues: 1030 sheet: -0.69 (0.27), residues: 363 loop : -1.43 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 656 HIS 0.006 0.001 HIS D 748 PHE 0.022 0.001 PHE C 214 TYR 0.017 0.001 TYR C 344 ARG 0.006 0.000 ARG D 421 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 1007) hydrogen bonds : angle 4.85699 ( 2743) metal coordination : bond 0.01369 ( 8) metal coordination : angle 8.05138 ( 12) covalent geometry : bond 0.00265 (24491) covalent geometry : angle 0.56114 (33475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 292 time to evaluate : 2.620 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4374 (tpp) cc_final: 0.3110 (tmt) REVERT: A 22 VAL cc_start: 0.7733 (p) cc_final: 0.7500 (t) REVERT: A 177 LYS cc_start: 0.8185 (ptpp) cc_final: 0.7718 (ptmm) REVERT: A 221 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.6925 (mt) REVERT: B 24 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6337 (mt-10) REVERT: B 123 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7455 (ttt) REVERT: B 150 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7659 (t) REVERT: C 127 MET cc_start: 0.7910 (ptp) cc_final: 0.7654 (ptp) REVERT: C 163 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.6930 (mmpt) REVERT: C 225 ARG cc_start: 0.6864 (mtp180) cc_final: 0.6658 (ttt180) REVERT: C 347 ARG cc_start: 0.6169 (mtt-85) cc_final: 0.5823 (tpt170) REVERT: C 396 MET cc_start: 0.6568 (ttp) cc_final: 0.6328 (ttp) REVERT: C 505 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7388 (ptp-170) REVERT: C 584 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7784 (ttt180) REVERT: C 673 ARG cc_start: 0.8364 (ptm160) cc_final: 0.7447 (ptm-80) REVERT: C 952 VAL cc_start: 0.7853 (m) cc_final: 0.7593 (t) REVERT: C 1030 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8478 (mm) REVERT: C 1119 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: D 16 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7193 (p) REVERT: D 92 MET cc_start: 0.8460 (mtp) cc_final: 0.7863 (mtm) REVERT: D 323 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: D 350 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.7295 (mmt180) REVERT: D 410 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7723 (mm-40) REVERT: D 623 ASP cc_start: 0.7203 (m-30) cc_final: 0.6856 (m-30) REVERT: D 791 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7008 (pt0) REVERT: D 824 VAL cc_start: 0.7925 (m) cc_final: 0.7405 (p) REVERT: D 865 LEU cc_start: 0.7599 (tp) cc_final: 0.7178 (mm) REVERT: D 959 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7180 (pt0) REVERT: D 987 LYS cc_start: 0.8061 (mttp) cc_final: 0.7648 (mttp) REVERT: D 1117 ASP cc_start: 0.7435 (p0) cc_final: 0.6814 (t0) REVERT: E 62 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7679 (mmt-90) REVERT: E 66 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7185 (t0) REVERT: E 92 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7048 (tt) outliers start: 110 outliers final: 41 residues processed: 372 average time/residue: 1.3121 time to fit residues: 564.5230 Evaluate side-chains 304 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 248 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1096 THR Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 203 optimal weight: 0.2980 chunk 109 optimal weight: 8.9990 chunk 208 optimal weight: 0.0970 chunk 164 optimal weight: 0.0050 chunk 257 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 246 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS D 748 HIS D1145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.202218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155620 restraints weight = 25996.767| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.74 r_work: 0.3461 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24499 Z= 0.115 Angle : 0.559 12.731 33487 Z= 0.288 Chirality : 0.042 0.167 3825 Planarity : 0.005 0.063 4169 Dihedral : 14.098 165.110 3980 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.84 % Favored : 94.88 % Rotamer: Outliers : 4.35 % Allowed : 17.68 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -0.44 (0.15), residues: 2893 helix: 1.18 (0.17), residues: 1033 sheet: -0.55 (0.27), residues: 379 loop : -1.32 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 778 HIS 0.006 0.001 HIS D 748 PHE 0.023 0.001 PHE C 214 TYR 0.014 0.001 TYR D 61 ARG 0.006 0.000 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 1007) hydrogen bonds : angle 4.65598 ( 2743) metal coordination : bond 0.01113 ( 8) metal coordination : angle 6.68897 ( 12) covalent geometry : bond 0.00253 (24491) covalent geometry : angle 0.54443 (33475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 287 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4602 (tpp) cc_final: 0.3038 (tmt) REVERT: A 22 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7481 (t) REVERT: A 177 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7810 (ptmm) REVERT: A 221 LEU cc_start: 0.7730 (pt) cc_final: 0.6916 (mt) REVERT: B 24 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: B 150 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7659 (t) REVERT: C 127 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7712 (ptp) REVERT: C 163 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.6952 (mmpt) REVERT: C 347 ARG cc_start: 0.6188 (mtt-85) cc_final: 0.5803 (tpt170) REVERT: C 505 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7434 (ptp-170) REVERT: C 653 VAL cc_start: 0.8651 (p) cc_final: 0.8380 (t) REVERT: C 673 ARG cc_start: 0.8455 (ptm160) cc_final: 0.7451 (ptm-80) REVERT: C 767 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6105 (pm20) REVERT: C 877 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8310 (mtm-85) REVERT: C 952 VAL cc_start: 0.7818 (m) cc_final: 0.7576 (t) REVERT: C 1030 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8442 (mm) REVERT: C 1062 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7920 (pt0) REVERT: C 1119 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: D 16 THR cc_start: 0.7546 (OUTLIER) cc_final: 0.7270 (p) REVERT: D 92 MET cc_start: 0.8562 (mtp) cc_final: 0.7970 (mtm) REVERT: D 126 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: D 350 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7275 (mmt180) REVERT: D 376 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7107 (mt-10) REVERT: D 410 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7960 (mm-40) REVERT: D 623 ASP cc_start: 0.7360 (m-30) cc_final: 0.7005 (m-30) REVERT: D 791 GLU cc_start: 0.7774 (tm-30) cc_final: 0.6996 (pt0) REVERT: D 865 LEU cc_start: 0.7594 (tp) cc_final: 0.7177 (mm) REVERT: D 959 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7207 (pt0) REVERT: D 987 LYS cc_start: 0.8156 (mttp) cc_final: 0.7683 (mttt) REVERT: D 1117 ASP cc_start: 0.7555 (p0) cc_final: 0.7077 (p0) REVERT: D 1129 GLU cc_start: 0.8105 (mp0) cc_final: 0.7795 (mm-30) REVERT: E 62 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7641 (mmt-90) REVERT: E 92 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7034 (tt) outliers start: 106 outliers final: 45 residues processed: 368 average time/residue: 1.2341 time to fit residues: 527.4188 Evaluate side-chains 315 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 254 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 ASN D 748 HIS D1145 GLN D1153 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.194497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145584 restraints weight = 26014.508| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.15 r_work: 0.3318 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 24499 Z= 0.344 Angle : 0.803 13.189 33487 Z= 0.415 Chirality : 0.052 0.233 3825 Planarity : 0.007 0.066 4169 Dihedral : 14.453 167.556 3971 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.71 % Favored : 93.02 % Rotamer: Outliers : 6.28 % Allowed : 17.51 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -1.03 (0.15), residues: 2893 helix: 0.54 (0.16), residues: 1026 sheet: -0.52 (0.26), residues: 380 loop : -1.64 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 938 HIS 0.011 0.002 HIS D 689 PHE 0.031 0.003 PHE C 214 TYR 0.022 0.003 TYR C1027 ARG 0.009 0.001 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.07440 ( 1007) hydrogen bonds : angle 5.09111 ( 2743) metal coordination : bond 0.01236 ( 8) metal coordination : angle 6.70731 ( 12) covalent geometry : bond 0.00862 (24491) covalent geometry : angle 0.79337 (33475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 269 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4848 (tpp) cc_final: 0.3181 (tmt) REVERT: A 177 LYS cc_start: 0.8346 (ptpp) cc_final: 0.7778 (ptmm) REVERT: A 202 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.7942 (tp) REVERT: A 221 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.6676 (mt) REVERT: B 6 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7154 (tmt170) REVERT: B 24 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: B 45 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7618 (p) REVERT: B 75 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: B 123 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7960 (ttt) REVERT: B 150 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7640 (t) REVERT: C 127 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7833 (ptp) REVERT: C 163 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.6915 (mmpt) REVERT: C 188 ASP cc_start: 0.8501 (p0) cc_final: 0.8119 (p0) REVERT: C 258 MET cc_start: 0.5514 (OUTLIER) cc_final: 0.5250 (tpt) REVERT: C 347 ARG cc_start: 0.6382 (mtt-85) cc_final: 0.6055 (tpt170) REVERT: C 505 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7612 (ptp-170) REVERT: C 570 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6905 (m-80) REVERT: C 584 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7897 (ttt180) REVERT: C 673 ARG cc_start: 0.8574 (ptm160) cc_final: 0.7528 (ptm-80) REVERT: C 756 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: C 767 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6215 (pm20) REVERT: C 791 ARG cc_start: 0.6887 (mtt90) cc_final: 0.6474 (mtp180) REVERT: C 797 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.5855 (ptp90) REVERT: C 877 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8393 (mtm-85) REVERT: C 1030 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8371 (mm) REVERT: C 1062 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: C 1119 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: C 1139 SER cc_start: 0.8371 (t) cc_final: 0.8137 (m) REVERT: D 16 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7309 (p) REVERT: D 92 MET cc_start: 0.8744 (mtp) cc_final: 0.8050 (mtm) REVERT: D 126 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: D 127 LYS cc_start: 0.7384 (mttt) cc_final: 0.7133 (mttm) REVERT: D 350 ARG cc_start: 0.7486 (tpp-160) cc_final: 0.7108 (tpp-160) REVERT: D 410 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7750 (mm-40) REVERT: D 420 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8897 (mttm) REVERT: D 791 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7284 (pt0) REVERT: D 865 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7147 (mm) REVERT: D 900 GLU cc_start: 0.7380 (tp30) cc_final: 0.6622 (mm-30) REVERT: D 917 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: D 959 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7418 (pt0) REVERT: D 987 LYS cc_start: 0.8193 (mttp) cc_final: 0.7633 (mttt) REVERT: E 62 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7606 (mmt-90) REVERT: E 92 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7281 (tt) outliers start: 153 outliers final: 78 residues processed: 381 average time/residue: 1.2700 time to fit residues: 561.9960 Evaluate side-chains 352 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 245 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 242 optimal weight: 0.9990 chunk 264 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 748 HIS D1145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.199530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152022 restraints weight = 25743.313| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.70 r_work: 0.3411 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24499 Z= 0.129 Angle : 0.593 12.553 33487 Z= 0.307 Chirality : 0.042 0.169 3825 Planarity : 0.005 0.062 4169 Dihedral : 14.206 167.426 3971 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.77 % Favored : 94.95 % Rotamer: Outliers : 4.84 % Allowed : 19.16 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -0.65 (0.15), residues: 2893 helix: 1.00 (0.17), residues: 1027 sheet: -0.51 (0.26), residues: 378 loop : -1.47 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 70 HIS 0.006 0.001 HIS D 748 PHE 0.024 0.001 PHE C 214 TYR 0.015 0.001 TYR D 61 ARG 0.007 0.000 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 1007) hydrogen bonds : angle 4.71460 ( 2743) metal coordination : bond 0.00986 ( 8) metal coordination : angle 6.04018 ( 12) covalent geometry : bond 0.00284 (24491) covalent geometry : angle 0.58152 (33475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 273 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4847 (tpp) cc_final: 0.3189 (tmt) REVERT: A 221 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.6697 (mt) REVERT: A 223 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6222 (ttm-80) REVERT: B 24 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: B 75 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: B 123 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8046 (ttt) REVERT: B 137 GLU cc_start: 0.6385 (mt-10) cc_final: 0.5852 (tt0) REVERT: B 150 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7634 (t) REVERT: C 116 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7141 (mtmt) REVERT: C 127 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7781 (ptp) REVERT: C 154 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6747 (tpt) REVERT: C 163 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7022 (mmpt) REVERT: C 188 ASP cc_start: 0.8332 (p0) cc_final: 0.8021 (p0) REVERT: C 347 ARG cc_start: 0.6281 (mtt-85) cc_final: 0.5926 (tpt170) REVERT: C 505 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7472 (ptp-170) REVERT: C 570 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6951 (m-80) REVERT: C 580 ASP cc_start: 0.8563 (m-30) cc_final: 0.8210 (m-30) REVERT: C 584 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7824 (ttt180) REVERT: C 673 ARG cc_start: 0.8539 (ptm160) cc_final: 0.7486 (ptm-80) REVERT: C 691 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: C 756 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: C 767 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: C 877 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8315 (mtm-85) REVERT: C 1030 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8380 (mm) REVERT: C 1062 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: C 1119 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: C 1139 SER cc_start: 0.8372 (t) cc_final: 0.8130 (m) REVERT: D 16 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7229 (p) REVERT: D 19 ASP cc_start: 0.8076 (m-30) cc_final: 0.7833 (m-30) REVERT: D 92 MET cc_start: 0.8661 (mtp) cc_final: 0.8039 (mtm) REVERT: D 117 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7909 (tp) REVERT: D 127 LYS cc_start: 0.7407 (mttt) cc_final: 0.7128 (mttm) REVERT: D 323 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: D 350 ARG cc_start: 0.7475 (tpp-160) cc_final: 0.7128 (mmt180) REVERT: D 376 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7104 (mt-10) REVERT: D 410 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8086 (mm-40) REVERT: D 496 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8116 (p) REVERT: D 791 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7054 (pt0) REVERT: D 865 LEU cc_start: 0.7490 (tp) cc_final: 0.7042 (mm) REVERT: D 900 GLU cc_start: 0.7344 (tp30) cc_final: 0.6588 (mm-30) REVERT: D 959 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7346 (pt0) REVERT: D 987 LYS cc_start: 0.8185 (mttp) cc_final: 0.7611 (mttt) REVERT: D 1129 GLU cc_start: 0.8066 (mp0) cc_final: 0.7677 (mm-30) REVERT: E 62 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7573 (mmt-90) REVERT: E 92 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7098 (tt) outliers start: 118 outliers final: 65 residues processed: 364 average time/residue: 1.3487 time to fit residues: 564.3918 Evaluate side-chains 354 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 262 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 691 ASP Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 714 ASP Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 189 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 281 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 269 optimal weight: 0.1980 chunk 176 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 227 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 GLN D 748 HIS D 759 GLN D1145 GLN D1246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.198664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152467 restraints weight = 25822.005| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.62 r_work: 0.3394 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24499 Z= 0.159 Angle : 0.605 11.370 33487 Z= 0.313 Chirality : 0.044 0.172 3825 Planarity : 0.005 0.065 4169 Dihedral : 14.152 166.261 3971 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.32 % Favored : 94.40 % Rotamer: Outliers : 5.09 % Allowed : 19.52 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -0.57 (0.15), residues: 2893 helix: 1.09 (0.17), residues: 1031 sheet: -0.47 (0.26), residues: 373 loop : -1.45 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 70 HIS 0.006 0.001 HIS D 748 PHE 0.017 0.002 PHE C 153 TYR 0.016 0.002 TYR C 344 ARG 0.007 0.000 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.04988 ( 1007) hydrogen bonds : angle 4.65035 ( 2743) metal coordination : bond 0.00956 ( 8) metal coordination : angle 5.55344 ( 12) covalent geometry : bond 0.00377 (24491) covalent geometry : angle 0.59570 (33475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 256 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4934 (tpp) cc_final: 0.3450 (tmt) REVERT: A 221 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.6712 (mt) REVERT: B 24 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6104 (mt-10) REVERT: B 75 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: B 123 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7983 (ttt) REVERT: B 150 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7683 (t) REVERT: C 116 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7091 (mtmt) REVERT: C 127 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7701 (ptp) REVERT: C 154 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6842 (tpt) REVERT: C 163 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7090 (mmpt) REVERT: C 188 ASP cc_start: 0.8083 (p0) cc_final: 0.7820 (p0) REVERT: C 347 ARG cc_start: 0.6284 (mtt-85) cc_final: 0.5871 (tpt170) REVERT: C 421 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6300 (mmp-170) REVERT: C 505 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7423 (ptp-170) REVERT: C 570 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6887 (m-80) REVERT: C 580 ASP cc_start: 0.8446 (m-30) cc_final: 0.8186 (m-30) REVERT: C 584 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7752 (ttt180) REVERT: C 673 ARG cc_start: 0.8438 (ptm160) cc_final: 0.7425 (ptm-80) REVERT: C 756 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: C 767 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: C 877 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8233 (mtm-85) REVERT: C 1030 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8380 (mm) REVERT: C 1062 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7901 (pt0) REVERT: C 1119 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: C 1139 SER cc_start: 0.8366 (t) cc_final: 0.8139 (m) REVERT: D 16 THR cc_start: 0.7434 (OUTLIER) cc_final: 0.7186 (p) REVERT: D 92 MET cc_start: 0.8574 (mtp) cc_final: 0.8008 (mtm) REVERT: D 117 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7752 (tp) REVERT: D 127 LYS cc_start: 0.7306 (mttt) cc_final: 0.7031 (mttm) REVERT: D 320 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7512 (tt) REVERT: D 323 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: D 350 ARG cc_start: 0.7477 (tpp-160) cc_final: 0.7117 (mmt180) REVERT: D 376 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7051 (mt-10) REVERT: D 410 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7738 (mm-40) REVERT: D 420 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8882 (mttm) REVERT: D 496 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8065 (p) REVERT: D 791 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7144 (pt0) REVERT: D 865 LEU cc_start: 0.7519 (tp) cc_final: 0.7076 (mm) REVERT: D 959 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7283 (pt0) REVERT: D 987 LYS cc_start: 0.8106 (mttp) cc_final: 0.7578 (mttt) REVERT: D 1112 MET cc_start: 0.7686 (tpp) cc_final: 0.7456 (mmm) REVERT: D 1129 GLU cc_start: 0.7988 (mp0) cc_final: 0.7642 (mm-30) REVERT: E 62 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7416 (mmt-90) REVERT: E 92 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6999 (tt) outliers start: 124 outliers final: 68 residues processed: 351 average time/residue: 1.3084 time to fit residues: 529.2274 Evaluate side-chains 342 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 246 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 177 optimal weight: 0.0170 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 291 optimal weight: 20.0000 chunk 263 optimal weight: 0.0050 overall best weight: 1.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 759 GLN D1145 GLN D1246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.199131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152000 restraints weight = 25743.748| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.59 r_work: 0.3408 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24499 Z= 0.150 Angle : 0.595 10.941 33487 Z= 0.308 Chirality : 0.043 0.164 3825 Planarity : 0.005 0.063 4169 Dihedral : 14.114 165.220 3970 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.08 % Favored : 94.64 % Rotamer: Outliers : 5.13 % Allowed : 19.61 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -0.50 (0.15), residues: 2893 helix: 1.14 (0.17), residues: 1034 sheet: -0.46 (0.27), residues: 371 loop : -1.40 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 70 HIS 0.005 0.001 HIS D 94 PHE 0.016 0.002 PHE C 906 TYR 0.013 0.001 TYR D 749 ARG 0.007 0.000 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 1007) hydrogen bonds : angle 4.59861 ( 2743) metal coordination : bond 0.00928 ( 8) metal coordination : angle 5.35724 ( 12) covalent geometry : bond 0.00354 (24491) covalent geometry : angle 0.58601 (33475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 253 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4996 (tpp) cc_final: 0.3321 (tmt) REVERT: A 221 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.6685 (mt) REVERT: B 24 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6249 (mt-10) REVERT: B 75 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: B 123 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8055 (ttt) REVERT: B 137 GLU cc_start: 0.6222 (mt-10) cc_final: 0.5778 (tt0) REVERT: B 150 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7625 (t) REVERT: C 116 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.7073 (mtmt) REVERT: C 127 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7738 (ptp) REVERT: C 154 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6905 (tpt) REVERT: C 163 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7134 (mmpt) REVERT: C 188 ASP cc_start: 0.8203 (p0) cc_final: 0.7936 (p0) REVERT: C 225 ARG cc_start: 0.6999 (ttt180) cc_final: 0.6748 (ttt-90) REVERT: C 347 ARG cc_start: 0.6353 (mtt-85) cc_final: 0.5928 (tpt170) REVERT: C 396 MET cc_start: 0.6657 (ttp) cc_final: 0.6391 (ttp) REVERT: C 421 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6433 (mmp-170) REVERT: C 505 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7528 (ptp-170) REVERT: C 570 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: C 580 ASP cc_start: 0.8524 (m-30) cc_final: 0.8154 (m-30) REVERT: C 584 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7821 (ttt180) REVERT: C 673 ARG cc_start: 0.8568 (ptm160) cc_final: 0.7474 (ptm-80) REVERT: C 756 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: C 767 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6414 (pm20) REVERT: C 877 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8342 (mtm-85) REVERT: C 1030 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8406 (mm) REVERT: C 1062 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: C 1119 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: C 1139 SER cc_start: 0.8379 (t) cc_final: 0.8132 (m) REVERT: D 16 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7225 (p) REVERT: D 19 ASP cc_start: 0.8082 (m-30) cc_final: 0.7876 (m-30) REVERT: D 92 MET cc_start: 0.8679 (mtp) cc_final: 0.8056 (mtm) REVERT: D 117 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7878 (tp) REVERT: D 127 LYS cc_start: 0.7448 (mttt) cc_final: 0.7142 (mttm) REVERT: D 320 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7609 (tt) REVERT: D 323 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: D 350 ARG cc_start: 0.7507 (tpp-160) cc_final: 0.7137 (mmt180) REVERT: D 376 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7125 (mt-10) REVERT: D 410 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7830 (mm-40) REVERT: D 496 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8125 (p) REVERT: D 791 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7189 (pt0) REVERT: D 865 LEU cc_start: 0.7482 (tp) cc_final: 0.7036 (mm) REVERT: D 917 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: D 959 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: D 987 LYS cc_start: 0.8196 (mttp) cc_final: 0.7665 (mttt) REVERT: D 1129 GLU cc_start: 0.8147 (mp0) cc_final: 0.7729 (mm-30) REVERT: D 1246 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8337 (p0) REVERT: E 62 ARG cc_start: 0.8065 (mtt180) cc_final: 0.7514 (mmt-90) REVERT: E 92 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6988 (tt) outliers start: 125 outliers final: 71 residues processed: 347 average time/residue: 1.4118 time to fit residues: 564.0154 Evaluate side-chains 347 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 247 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 714 ASP Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1166 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1246 ASN Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 237 optimal weight: 0.0030 chunk 129 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 GLN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 759 GLN D1139 GLN D1145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.201458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153702 restraints weight = 25824.046| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.76 r_work: 0.3443 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24499 Z= 0.114 Angle : 0.552 10.079 33487 Z= 0.287 Chirality : 0.042 0.187 3825 Planarity : 0.005 0.069 4169 Dihedral : 14.004 164.144 3969 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.46 % Favored : 95.26 % Rotamer: Outliers : 3.94 % Allowed : 21.00 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -0.28 (0.16), residues: 2893 helix: 1.33 (0.17), residues: 1036 sheet: -0.46 (0.27), residues: 377 loop : -1.25 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 656 HIS 0.005 0.001 HIS D 94 PHE 0.024 0.001 PHE C 214 TYR 0.016 0.001 TYR C 344 ARG 0.006 0.000 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 1007) hydrogen bonds : angle 4.48559 ( 2743) metal coordination : bond 0.00855 ( 8) metal coordination : angle 5.03909 ( 12) covalent geometry : bond 0.00250 (24491) covalent geometry : angle 0.54413 (33475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 257 time to evaluate : 2.608 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4984 (tpp) cc_final: 0.3302 (tmt) REVERT: A 177 LYS cc_start: 0.8191 (ptpp) cc_final: 0.7733 (ptmm) REVERT: A 221 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.6651 (mt) REVERT: B 24 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6325 (mt-10) REVERT: B 75 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: B 123 MET cc_start: 0.8425 (ttt) cc_final: 0.8006 (ttt) REVERT: B 137 GLU cc_start: 0.6143 (mt-10) cc_final: 0.5740 (tt0) REVERT: B 150 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7638 (t) REVERT: C 127 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7661 (ptp) REVERT: C 163 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7087 (mmpt) REVERT: C 225 ARG cc_start: 0.6848 (ttt180) cc_final: 0.6601 (ttt-90) REVERT: C 347 ARG cc_start: 0.6297 (mtt-85) cc_final: 0.5867 (tpt170) REVERT: C 396 MET cc_start: 0.6534 (ttp) cc_final: 0.6328 (ttp) REVERT: C 421 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6415 (mmp-170) REVERT: C 490 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: C 505 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7418 (ptp-170) REVERT: C 584 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7741 (ttt180) REVERT: C 653 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8382 (t) REVERT: C 673 ARG cc_start: 0.8511 (ptm160) cc_final: 0.7419 (ptm-80) REVERT: C 767 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6379 (pm20) REVERT: C 787 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7280 (ttp-170) REVERT: C 877 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8317 (mtm-85) REVERT: C 952 VAL cc_start: 0.7715 (m) cc_final: 0.7412 (t) REVERT: C 1030 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8349 (mm) REVERT: C 1062 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: C 1139 SER cc_start: 0.8359 (t) cc_final: 0.8078 (m) REVERT: D 16 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7174 (p) REVERT: D 19 ASP cc_start: 0.8048 (m-30) cc_final: 0.7842 (m-30) REVERT: D 92 MET cc_start: 0.8602 (mtp) cc_final: 0.8046 (mtm) REVERT: D 127 LYS cc_start: 0.7428 (mttt) cc_final: 0.7119 (mttm) REVERT: D 320 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7721 (tt) REVERT: D 323 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: D 350 ARG cc_start: 0.7508 (tpp-160) cc_final: 0.7107 (mmt180) REVERT: D 376 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7111 (mt-10) REVERT: D 410 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8118 (mm-40) REVERT: D 791 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7082 (pt0) REVERT: D 820 MET cc_start: 0.7982 (ttt) cc_final: 0.7773 (ttm) REVERT: D 917 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: D 987 LYS cc_start: 0.8222 (mttp) cc_final: 0.7716 (mttt) REVERT: D 1129 GLU cc_start: 0.8147 (mp0) cc_final: 0.7698 (mm-30) REVERT: E 62 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7545 (mmt-90) REVERT: E 92 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6762 (tt) outliers start: 96 outliers final: 54 residues processed: 329 average time/residue: 1.3424 time to fit residues: 507.3605 Evaluate side-chains 324 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 248 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 714 ASP Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1166 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 211 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 292 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 759 GLN D1145 GLN D1246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.198652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151004 restraints weight = 25857.017| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.60 r_work: 0.3400 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24499 Z= 0.167 Angle : 0.618 9.800 33487 Z= 0.319 Chirality : 0.044 0.170 3825 Planarity : 0.005 0.066 4169 Dihedral : 14.069 162.773 3969 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.08 % Favored : 94.64 % Rotamer: Outliers : 3.86 % Allowed : 21.16 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -0.44 (0.16), residues: 2893 helix: 1.15 (0.16), residues: 1041 sheet: -0.52 (0.26), residues: 374 loop : -1.31 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 938 HIS 0.005 0.001 HIS D 689 PHE 0.020 0.002 PHE C 906 TYR 0.016 0.002 TYR C1027 ARG 0.008 0.000 ARG D 834 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 1007) hydrogen bonds : angle 4.56828 ( 2743) metal coordination : bond 0.00873 ( 8) metal coordination : angle 4.97150 ( 12) covalent geometry : bond 0.00399 (24491) covalent geometry : angle 0.61064 (33475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 251 time to evaluate : 2.816 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5056 (tpp) cc_final: 0.3377 (tmt) REVERT: A 221 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.6682 (mt) REVERT: B 24 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6425 (mt-10) REVERT: B 75 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: B 137 GLU cc_start: 0.6181 (mt-10) cc_final: 0.5781 (tt0) REVERT: B 150 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7600 (t) REVERT: C 127 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7726 (ptp) REVERT: C 163 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7069 (mmpt) REVERT: C 225 ARG cc_start: 0.7006 (ttt180) cc_final: 0.6776 (ttt-90) REVERT: C 258 MET cc_start: 0.5337 (OUTLIER) cc_final: 0.5118 (tpt) REVERT: C 347 ARG cc_start: 0.6349 (mtt-85) cc_final: 0.5880 (tpt170) REVERT: C 350 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6240 (tt0) REVERT: C 421 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6511 (mmp-170) REVERT: C 505 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7619 (ptp-170) REVERT: C 584 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7824 (ttt180) REVERT: C 673 ARG cc_start: 0.8577 (ptm160) cc_final: 0.7460 (ptm-80) REVERT: C 767 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6307 (pm20) REVERT: C 787 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7427 (ttp-170) REVERT: C 866 ASN cc_start: 0.5397 (p0) cc_final: 0.5174 (m110) REVERT: C 877 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8393 (mtm-85) REVERT: C 1030 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8413 (mm) REVERT: C 1062 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: C 1102 VAL cc_start: 0.6884 (t) cc_final: 0.6657 (t) REVERT: C 1139 SER cc_start: 0.8365 (t) cc_final: 0.8097 (m) REVERT: D 16 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7210 (p) REVERT: D 19 ASP cc_start: 0.8083 (m-30) cc_final: 0.7880 (m-30) REVERT: D 92 MET cc_start: 0.8657 (mtp) cc_final: 0.8056 (mtm) REVERT: D 127 LYS cc_start: 0.7368 (mttt) cc_final: 0.7066 (mttm) REVERT: D 320 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7611 (tt) REVERT: D 323 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: D 350 ARG cc_start: 0.7483 (tpp-160) cc_final: 0.7065 (mmt180) REVERT: D 376 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7150 (mt-10) REVERT: D 410 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7826 (mm-40) REVERT: D 791 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7213 (pt0) REVERT: D 865 LEU cc_start: 0.7334 (tp) cc_final: 0.6998 (mm) REVERT: D 917 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: D 987 LYS cc_start: 0.8217 (mttp) cc_final: 0.7692 (mttt) REVERT: D 1129 GLU cc_start: 0.8134 (mp0) cc_final: 0.7672 (mm-30) REVERT: D 1246 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8361 (p0) REVERT: E 62 ARG cc_start: 0.8061 (mtt180) cc_final: 0.7501 (mmt-90) REVERT: E 92 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6970 (tt) outliers start: 94 outliers final: 60 residues processed: 318 average time/residue: 1.3740 time to fit residues: 503.7227 Evaluate side-chains 329 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 246 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 714 ASP Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1166 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1246 ASN Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 67 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 245 optimal weight: 0.0570 chunk 147 optimal weight: 3.9990 chunk 136 optimal weight: 0.0020 overall best weight: 0.4506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 GLN D 759 GLN D1145 GLN D1246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.202197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155520 restraints weight = 25664.376| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.70 r_work: 0.3455 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24499 Z= 0.111 Angle : 0.557 9.931 33487 Z= 0.290 Chirality : 0.041 0.161 3825 Planarity : 0.005 0.065 4169 Dihedral : 13.967 162.457 3969 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.53 % Favored : 95.20 % Rotamer: Outliers : 3.28 % Allowed : 21.86 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % 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: -0.21 (0.16), residues: 2893 helix: 1.40 (0.17), residues: 1037 sheet: -0.43 (0.27), residues: 363 loop : -1.20 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 656 HIS 0.005 0.001 HIS D 94 PHE 0.024 0.001 PHE C 214 TYR 0.015 0.001 TYR C 344 ARG 0.006 0.000 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 1007) hydrogen bonds : angle 4.43488 ( 2743) metal coordination : bond 0.00823 ( 8) metal coordination : angle 4.83995 ( 12) covalent geometry : bond 0.00239 (24491) covalent geometry : angle 0.54955 (33475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18697.12 seconds wall clock time: 321 minutes 17.46 seconds (19277.46 seconds total)