Starting phenix.real_space_refine on Tue Sep 15 15:39:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7emy_31198/09_2026/7emy_31198_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7emy_31198/09_2026/7emy_31198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7emy_31198/09_2026/7emy_31198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7emy_31198/09_2026/7emy_31198.map" model { file = "/net/cci-nas-00/data/ceres_data/7emy_31198/09_2026/7emy_31198_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7emy_31198/09_2026/7emy_31198_neut_trim.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 70 5.16 5 C 12924 2.51 5 N 3778 2.21 5 O 3740 1.98 5 H 20502 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41020 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 20444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 20444 Classifications: {'peptide': 1334} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 1248} Chain: "B" Number of atoms: 20444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 20444 Classifications: {'peptide': 1334} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 1248} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' MG': 1, 'AMP%rna2p': 1, 'PNS': 1, 'SAL': 1} Classifications: {'RNA_mixed': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'NH1NOTPRO': 1, 'rna2p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Planarities with less than four sites: {'SAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' MG': 1, 'AMP%rna2p': 1, 'PNS': 1, 'SAL': 1} Classifications: {'RNA_mixed': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'NH1NOTPRO': 1, 'rna2p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Planarities with less than four sites: {'SAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N PHE B 741 " occ=0.50 ... (18 atoms not shown) pdb=" HZ PHE B 741 " occ=0.50 residue: pdb=" C1 SAL A1502 " occ=0.00 ... (7 atoms not shown) pdb=" O2 SAL A1502 " occ=0.00 residue: pdb=" C1 SAL B1502 " occ=0.00 ... (7 atoms not shown) pdb=" O2 SAL B1502 " occ=0.00 Time building chain proxies: 5.66, per 1000 atoms: 0.14 Number of scatterers: 41020 At special positions: 0 Unit cell: (160, 129, 139, 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) S 70 16.00 P 4 15.00 Mg 2 11.99 O 3740 8.00 N 3778 7.00 C 12924 6.00 H 20502 1.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 24 sheets defined 47.7% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 7 through 24 Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 45 through 60 Processing helix chain 'A' and resid 64 through 71 removed outlier: 4.009A pdb=" N ARG A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 removed outlier: 4.194A pdb=" N ARG A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.654A pdb=" N ARG A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 240 through 257 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 268 through 295 removed outlier: 5.240A pdb=" N GLU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 343 through 360 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 403 through 422 removed outlier: 4.029A pdb=" N ASP A 420 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 457 through 464 removed outlier: 3.865A pdb=" N ALA A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 523 Processing helix chain 'A' and resid 534 through 546 Processing helix chain 'A' and resid 557 through 567 Processing helix chain 'A' and resid 582 through 599 Processing helix chain 'A' and resid 614 through 627 Processing helix chain 'A' and resid 639 through 651 Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 711 through 726 removed outlier: 3.869A pdb=" N LEU A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.810A pdb=" N PHE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 766 Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 787 through 796 removed outlier: 3.663A pdb=" N LEU A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 826 Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 906 through 914 Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 1008 through 1028 removed outlier: 3.966A pdb=" N ALA A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1033 removed outlier: 3.548A pdb=" N GLU A1032 " --> pdb=" O ALA A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1048 removed outlier: 4.008A pdb=" N ALA A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1064 removed outlier: 4.170A pdb=" N ARG A1061 " --> pdb=" O ASP A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 Processing helix chain 'A' and resid 1087 through 1093 Processing helix chain 'A' and resid 1097 through 1103 Processing helix chain 'A' and resid 1107 through 1117 Processing helix chain 'A' and resid 1120 through 1125 Processing helix chain 'A' and resid 1138 through 1149 removed outlier: 5.704A pdb=" N ALA A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER A1147 " --> pdb=" O GLN A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1172 removed outlier: 3.791A pdb=" N LEU A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1185 Processing helix chain 'A' and resid 1189 through 1191 No H-bonds generated for 'chain 'A' and resid 1189 through 1191' Processing helix chain 'A' and resid 1208 through 1219 removed outlier: 3.590A pdb=" N GLY A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1246 removed outlier: 3.559A pdb=" N LEU A1240 " --> pdb=" O PRO A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1252 removed outlier: 3.848A pdb=" N ARG A1251 " --> pdb=" O ARG A1248 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1252 " --> pdb=" O PRO A1249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1248 through 1252' Processing helix chain 'A' and resid 1254 through 1265 Processing helix chain 'A' and resid 1291 through 1303 Processing helix chain 'A' and resid 1327 through 1340 removed outlier: 3.958A pdb=" N GLY A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 45 through 60 Processing helix chain 'B' and resid 64 through 71 removed outlier: 4.009A pdb=" N ARG B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 removed outlier: 4.194A pdb=" N ARG B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.687A pdb=" N ARG B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 240 through 257 Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 268 through 295 removed outlier: 5.240A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 343 through 360 Processing helix chain 'B' and resid 378 through 384 Processing helix chain 'B' and resid 403 through 422 removed outlier: 4.041A pdb=" N ASP B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 457 through 464 removed outlier: 3.866A pdb=" N ALA B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 523 removed outlier: 3.543A pdb=" N THR B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 546 Processing helix chain 'B' and resid 557 through 567 Processing helix chain 'B' and resid 582 through 599 Processing helix chain 'B' and resid 614 through 627 Processing helix chain 'B' and resid 639 through 651 Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 711 through 726 removed outlier: 3.862A pdb=" N LEU B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 754 removed outlier: 3.767A pdb=" N PHE B 746 " --> pdb=" O ASP B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 768 through 780 Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.647A pdb=" N LEU B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 826 Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 906 through 914 Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 1008 through 1028 removed outlier: 3.966A pdb=" N ALA B1012 " --> pdb=" O PHE B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1033 removed outlier: 3.548A pdb=" N GLU B1032 " --> pdb=" O ALA B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1048 removed outlier: 4.008A pdb=" N ALA B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1064 removed outlier: 4.170A pdb=" N ARG B1061 " --> pdb=" O ASP B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1083 Processing helix chain 'B' and resid 1087 through 1093 Processing helix chain 'B' and resid 1097 through 1103 Processing helix chain 'B' and resid 1107 through 1117 Processing helix chain 'B' and resid 1120 through 1125 Processing helix chain 'B' and resid 1138 through 1149 removed outlier: 5.704A pdb=" N ALA B1146 " --> pdb=" O ASP B1142 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER B1147 " --> pdb=" O GLN B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1172 removed outlier: 3.790A pdb=" N LEU B1165 " --> pdb=" O SER B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1181 through 1185 Processing helix chain 'B' and resid 1189 through 1191 No H-bonds generated for 'chain 'B' and resid 1189 through 1191' Processing helix chain 'B' and resid 1208 through 1219 removed outlier: 3.590A pdb=" N GLY B1212 " --> pdb=" O ALA B1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 1235 through 1246 removed outlier: 3.558A pdb=" N LEU B1240 " --> pdb=" O PRO B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1252 removed outlier: 3.848A pdb=" N ARG B1251 " --> pdb=" O ARG B1248 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B1252 " --> pdb=" O PRO B1249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1248 through 1252' Processing helix chain 'B' and resid 1254 through 1265 Processing helix chain 'B' and resid 1291 through 1303 Processing helix chain 'B' and resid 1327 through 1340 removed outlier: 3.957A pdb=" N GLY B1340 " --> pdb=" O THR B1336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 183 removed outlier: 3.686A pdb=" N VAL A 221 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 227 " --> pdb=" O MET A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 325 removed outlier: 5.888A pdb=" N VAL A 445 " --> pdb=" O HIS A 481 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU A 483 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 372 removed outlier: 3.562A pdb=" N LEU A 394 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.556A pdb=" N VAL A 580 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA A 572 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 733 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG A 732 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN A 785 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 734 " --> pdb=" O ASN A 785 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TRP A 784 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER A 813 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N SER A 786 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL A 810 " --> pdb=" O HIS A 836 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A 838 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 812 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN A 849 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 867 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 630 through 633 removed outlier: 6.436A pdb=" N VAL A 607 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA A 606 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE A 656 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A 608 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 691 through 697 removed outlier: 3.681A pdb=" N GLY A 902 " --> pdb=" O GLU A 708 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 872 through 877 removed outlier: 4.945A pdb=" N ASP A 927 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ARG A 928 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 915 through 917 Processing sheet with id=AB1, first strand: chain 'A' and resid 946 through 949 Processing sheet with id=AB2, first strand: chain 'A' and resid 969 through 976 removed outlier: 6.679A pdb=" N VAL A 989 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 972 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 987 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA A 974 " --> pdb=" O GLY A 985 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY A 985 " --> pdb=" O ALA A 974 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 984 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N TRP A1313 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA A 986 " --> pdb=" O TRP A1313 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1176 through 1178 removed outlier: 7.974A pdb=" N VAL A1177 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A1155 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG A1129 " --> pdb=" O ARG A1196 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ILE A1198 " --> pdb=" O ARG A1129 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A1131 " --> pdb=" O ILE A1198 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE A1200 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR A1194 " --> pdb=" O ARG A1221 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLN A1223 " --> pdb=" O TYR A1194 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ARG A1196 " --> pdb=" O GLN A1223 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG A1225 " --> pdb=" O ARG A1196 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE A1198 " --> pdb=" O ARG A1225 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A1227 " --> pdb=" O ILE A1198 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N PHE A1200 " --> pdb=" O LEU A1227 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A1229 " --> pdb=" O PHE A1200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 105 through 106 Processing sheet with id=AB5, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.686A pdb=" N VAL B 221 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 227 " --> pdb=" O MET B 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 318 through 325 Processing sheet with id=AB7, first strand: chain 'B' and resid 364 through 372 removed outlier: 3.562A pdb=" N LEU B 394 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 579 through 581 removed outlier: 6.276A pdb=" N ARG B 732 " --> pdb=" O LEU B 783 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASN B 785 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 734 " --> pdb=" O ASN B 785 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TRP B 784 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N SER B 813 " --> pdb=" O TRP B 784 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N SER B 786 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 810 " --> pdb=" O HIS B 836 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU B 838 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 812 " --> pdb=" O LEU B 838 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 849 " --> pdb=" O GLY B 839 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 867 " --> pdb=" O LEU B 850 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.436A pdb=" N VAL B 607 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA B 606 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE B 656 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU B 608 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 691 through 697 removed outlier: 3.637A pdb=" N GLY B 902 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 872 through 877 removed outlier: 4.978A pdb=" N ASP B 927 " --> pdb=" O LEU B 892 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG B 928 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 915 through 917 Processing sheet with id=AC4, first strand: chain 'B' and resid 946 through 949 Processing sheet with id=AC5, first strand: chain 'B' and resid 969 through 976 removed outlier: 6.677A pdb=" N VAL B 989 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA B 972 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 987 " --> pdb=" O ALA B 972 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA B 974 " --> pdb=" O GLY B 985 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY B 985 " --> pdb=" O ALA B 974 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU B 984 " --> pdb=" O ARG B1311 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N TRP B1313 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 986 " --> pdb=" O TRP B1313 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1176 through 1178 removed outlier: 7.975A pdb=" N VAL B1177 " --> pdb=" O LEU B1153 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B1155 " --> pdb=" O VAL B1177 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG B1129 " --> pdb=" O ARG B1196 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ILE B1198 " --> pdb=" O ARG B1129 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B1131 " --> pdb=" O ILE B1198 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE B1200 " --> pdb=" O ALA B1131 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR B1194 " --> pdb=" O ARG B1221 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLN B1223 " --> pdb=" O TYR B1194 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ARG B1196 " --> pdb=" O GLN B1223 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG B1225 " --> pdb=" O ARG B1196 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE B1198 " --> pdb=" O ARG B1225 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B1227 " --> pdb=" O ILE B1198 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N PHE B1200 " --> pdb=" O LEU B1227 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B1229 " --> pdb=" O PHE B1200 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.99 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10405 1.04 - 1.24: 13106 1.24 - 1.44: 8149 1.44 - 1.64: 9690 1.64 - 1.84: 94 Bond restraints: 41444 Sorted by residual: bond pdb=" CA ALA B 442 " pdb=" CB ALA B 442 " ideal model delta sigma weight residual 1.529 1.422 0.108 1.13e-02 7.83e+03 9.07e+01 bond pdb=" CA ALA A 442 " pdb=" CB ALA A 442 " ideal model delta sigma weight residual 1.529 1.422 0.107 1.13e-02 7.83e+03 8.95e+01 bond pdb=" ND1 HIS B 481 " pdb=" CE1 HIS B 481 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.92e+01 bond pdb=" ND1 HIS B 156 " pdb=" CE1 HIS B 156 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.92e+01 bond pdb=" ND1 HIS B 880 " pdb=" CE1 HIS B 880 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.91e+01 ... (remaining 41439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.29: 71393 6.29 - 12.58: 3578 12.58 - 18.87: 11 18.87 - 25.16: 6 25.16 - 31.45: 12 Bond angle restraints: 75000 Sorted by residual: angle pdb="HG11 VAL A1229 " pdb=" CG1 VAL A1229 " pdb="HG12 VAL A1229 " ideal model delta sigma weight residual 110.00 78.55 31.45 3.00e+00 1.11e-01 1.10e+02 angle pdb=" CA ALA A 996 " pdb=" CB ALA A 996 " pdb=" HB3 ALA A 996 " ideal model delta sigma weight residual 109.00 78.87 30.13 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CA ALA A1123 " pdb=" CB ALA A1123 " pdb=" HB3 ALA A1123 " ideal model delta sigma weight residual 109.00 79.08 29.92 3.00e+00 1.11e-01 9.94e+01 angle pdb=" CA ALA A 996 " pdb=" CB ALA A 996 " pdb=" HB1 ALA A 996 " ideal model delta sigma weight residual 109.00 79.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" CA ALA A1123 " pdb=" CB ALA A1123 " pdb=" HB2 ALA A1123 " ideal model delta sigma weight residual 109.00 79.52 29.48 3.00e+00 1.11e-01 9.66e+01 ... (remaining 74995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.85: 18139 22.85 - 45.69: 774 45.69 - 68.54: 381 68.54 - 91.38: 44 91.38 - 114.23: 2 Dihedral angle restraints: 19340 sinusoidal: 10750 harmonic: 8590 Sorted by residual: dihedral pdb=" C1' AMP A1504 " pdb=" C4' AMP A1504 " pdb=" O4' AMP A1504 " pdb=" C5' AMP A1504 " ideal model delta sinusoidal sigma weight residual -123.00 -79.69 -43.31 1 8.00e+00 1.56e-02 4.09e+01 dihedral pdb=" C1' AMP B1504 " pdb=" C4' AMP B1504 " pdb=" O4' AMP B1504 " pdb=" C5' AMP B1504 " ideal model delta sinusoidal sigma weight residual -123.00 -79.97 -43.03 1 8.00e+00 1.56e-02 4.04e+01 dihedral pdb=" CA SER A 786 " pdb=" C SER A 786 " pdb=" N ALA A 787 " pdb=" CA ALA A 787 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 19337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1811 0.152 - 0.305: 81 0.305 - 0.457: 165 0.457 - 0.609: 886 0.609 - 0.761: 259 Chirality restraints: 3202 Sorted by residual: chirality pdb=" CG LEU B 483 " pdb=" CB LEU B 483 " pdb=" CD1 LEU B 483 " pdb=" CD2 LEU B 483 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" CG LEU A 483 " pdb=" CB LEU A 483 " pdb=" CD1 LEU A 483 " pdb=" CD2 LEU A 483 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CG LEU A 574 " pdb=" CB LEU A 574 " pdb=" CD1 LEU A 574 " pdb=" CD2 LEU A 574 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.40e+01 ... (remaining 3199 not shown) Planarity restraints: 6292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AMP A1504 " -0.348 2.00e-02 2.50e+03 1.48e-01 6.06e+02 pdb=" C2 AMP A1504 " 0.053 2.00e-02 2.50e+03 pdb=" C4 AMP A1504 " 0.110 2.00e-02 2.50e+03 pdb=" C5 AMP A1504 " 0.082 2.00e-02 2.50e+03 pdb=" C6 AMP A1504 " -0.034 2.00e-02 2.50e+03 pdb=" C8 AMP A1504 " 0.104 2.00e-02 2.50e+03 pdb=" N1 AMP A1504 " -0.102 2.00e-02 2.50e+03 pdb=" N3 AMP A1504 " 0.174 2.00e-02 2.50e+03 pdb=" N6 AMP A1504 " -0.188 2.00e-02 2.50e+03 pdb=" N7 AMP A1504 " 0.095 2.00e-02 2.50e+03 pdb=" N9 AMP A1504 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AMP B1504 " 0.324 2.00e-02 2.50e+03 1.39e-01 5.31e+02 pdb=" C2 AMP B1504 " -0.054 2.00e-02 2.50e+03 pdb=" C4 AMP B1504 " -0.102 2.00e-02 2.50e+03 pdb=" C5 AMP B1504 " -0.074 2.00e-02 2.50e+03 pdb=" C6 AMP B1504 " 0.032 2.00e-02 2.50e+03 pdb=" C8 AMP B1504 " -0.100 2.00e-02 2.50e+03 pdb=" N1 AMP B1504 " 0.095 2.00e-02 2.50e+03 pdb=" N3 AMP B1504 " -0.162 2.00e-02 2.50e+03 pdb=" N6 AMP B1504 " 0.178 2.00e-02 2.50e+03 pdb=" N7 AMP B1504 " -0.091 2.00e-02 2.50e+03 pdb=" N9 AMP B1504 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 953 " -0.172 9.50e-02 1.11e+02 1.58e-01 4.89e+02 pdb=" NE ARG B 953 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 953 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG B 953 " 0.152 2.00e-02 2.50e+03 pdb=" NH2 ARG B 953 " 0.023 2.00e-02 2.50e+03 pdb="HH11 ARG B 953 " -0.309 2.00e-02 2.50e+03 pdb="HH12 ARG B 953 " 0.203 2.00e-02 2.50e+03 pdb="HH21 ARG B 953 " -0.054 2.00e-02 2.50e+03 pdb="HH22 ARG B 953 " -0.147 2.00e-02 2.50e+03 ... (remaining 6289 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 1642 2.10 - 2.73: 73788 2.73 - 3.35: 132238 3.35 - 3.98: 173029 3.98 - 4.60: 265290 Nonbonded interactions: 645987 Sorted by model distance: nonbonded pdb="HE22 GLN A 538 " pdb=" O GLN B 919 " model vdw 1.477 2.450 nonbonded pdb=" H LEU A 887 " pdb=" O TYR A 931 " model vdw 1.496 2.450 nonbonded pdb=" O ALA B 649 " pdb="HD21 ASN B 905 " model vdw 1.513 2.450 nonbonded pdb=" O ALA A 649 " pdb="HD21 ASN A 905 " model vdw 1.513 2.450 nonbonded pdb=" H ALA A 66 " pdb=" OD2 ASP A 420 " model vdw 1.514 2.450 ... (remaining 645982 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.260 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.080 Find NCS groups from input model: 0.290 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.037 0.156 20948 Z= 2.102 Angle : 2.793 17.993 28538 Z= 1.814 Chirality : 0.360 0.761 3202 Planarity : 0.012 0.148 3796 Dihedral : 12.083 114.229 7722 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.46 % Rotamer: Outliers : 0.88 % Allowed : 3.53 % Favored : 95.59 % Cbeta Deviations : 19.21 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.16), residues: 2664 helix: -0.18 (0.14), residues: 1088 sheet: -1.40 (0.23), residues: 478 loop : -0.15 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 953 TYR 0.194 0.025 TYR A 923 PHE 0.074 0.013 PHE B 372 TRP 0.176 0.013 TRP A 816 HIS 0.026 0.003 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.03717 / 2.09 (20942) covalent geometry : angle 2.79262 / 1.81 (28538) hydrogen bonds : bond 0.15574 / 10.30 ( 1004) hydrogen bonds : angle 7.39546 / 5.28 ( 2820) Misc. bond : bond 0.13768 / 7.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8936 (tpt) cc_final: 0.8726 (tpt) REVERT: A 1157 LEU cc_start: 0.9108 (mt) cc_final: 0.8852 (mt) REVERT: A 1185 LEU cc_start: 0.8147 (tp) cc_final: 0.7928 (mt) REVERT: B 346 SER cc_start: 0.8810 (m) cc_final: 0.8392 (p) REVERT: B 368 ASN cc_start: 0.7693 (m-40) cc_final: 0.7460 (m110) REVERT: B 665 LEU cc_start: 0.7695 (tp) cc_final: 0.7425 (tp) REVERT: B 1307 MET cc_start: 0.8504 (ptp) cc_final: 0.8277 (ptm) outliers start: 18 outliers final: 5 residues processed: 259 average time/residue: 1.5375 time to fit residues: 447.9441 Evaluate side-chains 130 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.109654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.074392 restraints weight = 138258.964| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.87 r_work: 0.3182 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20948 Z= 0.172 Angle : 0.668 8.819 28538 Z= 0.341 Chirality : 0.039 0.152 3202 Planarity : 0.006 0.056 3796 Dihedral : 7.391 104.023 3015 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.03 % Allowed : 8.33 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2664 helix: 1.02 (0.15), residues: 1118 sheet: -1.64 (0.22), residues: 502 loop : -0.23 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 726 TYR 0.017 0.002 TYR A 51 PHE 0.015 0.001 PHE A 560 TRP 0.014 0.001 TRP A 535 HIS 0.009 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (20942) covalent geometry : angle 0.66775 / 0.34 (28538) hydrogen bonds : bond 0.05239 / 3.47 ( 1004) hydrogen bonds : angle 5.98711 / 4.30 ( 2820) Misc. bond : bond 0.00085 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 989 VAL cc_start: 0.8516 (t) cc_final: 0.8082 (t) REVERT: A 1185 LEU cc_start: 0.7983 (tp) cc_final: 0.7776 (mt) REVERT: B 300 ASP cc_start: 0.8081 (t0) cc_final: 0.7776 (m-30) REVERT: B 346 SER cc_start: 0.8916 (m) cc_final: 0.8418 (p) REVERT: B 1307 MET cc_start: 0.9138 (ptp) cc_final: 0.8805 (ptm) outliers start: 21 outliers final: 6 residues processed: 150 average time/residue: 1.1189 time to fit residues: 196.7982 Evaluate side-chains 109 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 150 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 257 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.106680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.070824 restraints weight = 138494.919| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.83 r_work: 0.3103 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20948 Z= 0.243 Angle : 0.635 8.275 28538 Z= 0.320 Chirality : 0.039 0.135 3202 Planarity : 0.005 0.068 3796 Dihedral : 7.007 101.056 3012 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.98 % Allowed : 9.85 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2664 helix: 1.24 (0.16), residues: 1104 sheet: -1.93 (0.21), residues: 518 loop : -0.25 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 826 TYR 0.018 0.002 TYR B 696 PHE 0.024 0.002 PHE B 372 TRP 0.012 0.001 TRP B 535 HIS 0.006 0.001 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 (20942) covalent geometry : angle 0.63456 / 0.32 (28538) hydrogen bonds : bond 0.04643 / 3.09 ( 1004) hydrogen bonds : angle 5.69555 / 4.09 ( 2820) Misc. bond : bond 0.00149 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9321 (tpt) cc_final: 0.8948 (tpt) REVERT: A 854 ASP cc_start: 0.8572 (p0) cc_final: 0.8118 (p0) REVERT: A 1335 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8261 (mtp) REVERT: B 300 ASP cc_start: 0.8193 (t0) cc_final: 0.7936 (m-30) REVERT: B 368 ASN cc_start: 0.8651 (m-40) cc_final: 0.8308 (m110) REVERT: B 503 GLU cc_start: 0.7622 (tp30) cc_final: 0.7164 (tp30) REVERT: B 715 ILE cc_start: 0.9030 (tp) cc_final: 0.8757 (tp) REVERT: B 1307 MET cc_start: 0.9172 (ptp) cc_final: 0.8812 (ptm) outliers start: 20 outliers final: 7 residues processed: 125 average time/residue: 1.1843 time to fit residues: 173.5975 Evaluate side-chains 107 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 95 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 214 optimal weight: 0.6980 chunk 231 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.106772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.071009 restraints weight = 138202.592| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.81 r_work: 0.3106 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20948 Z= 0.206 Angle : 0.602 7.426 28538 Z= 0.302 Chirality : 0.038 0.138 3202 Planarity : 0.005 0.046 3796 Dihedral : 6.773 102.209 3010 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.23 % Allowed : 10.44 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.17), residues: 2664 helix: 1.27 (0.16), residues: 1110 sheet: -1.98 (0.22), residues: 492 loop : -0.21 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 541 TYR 0.015 0.002 TYR B 696 PHE 0.015 0.001 PHE B 372 TRP 0.012 0.001 TRP B1140 HIS 0.006 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (20942) covalent geometry : angle 0.60198 / 0.30 (28538) hydrogen bonds : bond 0.04250 / 2.83 ( 1004) hydrogen bonds : angle 5.54042 / 3.99 ( 2820) Misc. bond : bond 0.00141 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9366 (tpt) cc_final: 0.8972 (tpt) REVERT: A 1185 LEU cc_start: 0.8099 (tp) cc_final: 0.7844 (mm) REVERT: A 1335 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8119 (mtp) REVERT: B 503 GLU cc_start: 0.7634 (tp30) cc_final: 0.7186 (tp30) REVERT: B 715 ILE cc_start: 0.9047 (tp) cc_final: 0.8773 (tp) REVERT: B 1307 MET cc_start: 0.9161 (ptp) cc_final: 0.8784 (ptm) outliers start: 25 outliers final: 12 residues processed: 122 average time/residue: 1.2941 time to fit residues: 185.1249 Evaluate side-chains 103 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 124 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 80 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.107748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.072196 restraints weight = 138023.799| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.83 r_work: 0.3129 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20948 Z= 0.143 Angle : 0.578 7.060 28538 Z= 0.286 Chirality : 0.037 0.143 3202 Planarity : 0.005 0.047 3796 Dihedral : 6.592 101.878 3010 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.13 % Allowed : 10.88 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2664 helix: 1.37 (0.16), residues: 1112 sheet: -1.97 (0.22), residues: 492 loop : -0.14 (0.21), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 31 TYR 0.013 0.002 TYR B 696 PHE 0.015 0.001 PHE B 372 TRP 0.013 0.001 TRP B1140 HIS 0.005 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (20942) covalent geometry : angle 0.57795 / 0.29 (28538) hydrogen bonds : bond 0.03919 / 2.60 ( 1004) hydrogen bonds : angle 5.42370 / 3.92 ( 2820) Misc. bond : bond 0.00084 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8513 (tm) REVERT: A 158 MET cc_start: 0.9328 (tpt) cc_final: 0.8952 (tpt) REVERT: A 854 ASP cc_start: 0.8534 (p0) cc_final: 0.8098 (p0) REVERT: A 1185 LEU cc_start: 0.8121 (tp) cc_final: 0.7807 (mm) REVERT: A 1237 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8150 (mt) REVERT: B 346 SER cc_start: 0.9044 (m) cc_final: 0.8430 (p) REVERT: B 503 GLU cc_start: 0.7595 (tp30) cc_final: 0.7160 (tp30) REVERT: B 715 ILE cc_start: 0.9035 (tp) cc_final: 0.8765 (tp) REVERT: B 1307 MET cc_start: 0.9144 (ptp) cc_final: 0.8760 (ptm) outliers start: 23 outliers final: 11 residues processed: 122 average time/residue: 1.2989 time to fit residues: 187.3037 Evaluate side-chains 102 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1142 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 109 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 241 optimal weight: 0.0970 chunk 207 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 262 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.106707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.071004 restraints weight = 138193.708| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.84 r_work: 0.3099 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20948 Z= 0.195 Angle : 0.585 7.084 28538 Z= 0.290 Chirality : 0.038 0.141 3202 Planarity : 0.005 0.079 3796 Dihedral : 6.522 99.844 3010 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.32 % Allowed : 11.18 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2664 helix: 1.47 (0.16), residues: 1098 sheet: -2.02 (0.22), residues: 496 loop : -0.16 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 31 TYR 0.025 0.002 TYR A1194 PHE 0.012 0.001 PHE B 372 TRP 0.018 0.001 TRP B1140 HIS 0.006 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (20942) covalent geometry : angle 0.58462 / 0.29 (28538) hydrogen bonds : bond 0.03955 / 2.64 ( 1004) hydrogen bonds : angle 5.35328 / 3.87 ( 2820) Misc. bond : bond 0.00116 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8532 (tm) REVERT: A 158 MET cc_start: 0.9377 (tpt) cc_final: 0.9004 (tpt) REVERT: A 1185 LEU cc_start: 0.8117 (tp) cc_final: 0.7873 (mm) REVERT: A 1237 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8189 (mt) REVERT: A 1335 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.7815 (mtp) REVERT: B 368 ASN cc_start: 0.8590 (m-40) cc_final: 0.8352 (m-40) REVERT: B 503 GLU cc_start: 0.7687 (tp30) cc_final: 0.7240 (tp30) REVERT: B 715 ILE cc_start: 0.9048 (tp) cc_final: 0.8763 (tp) REVERT: B 747 ASP cc_start: 0.8905 (m-30) cc_final: 0.8546 (m-30) REVERT: B 1307 MET cc_start: 0.9153 (ptp) cc_final: 0.8799 (ptm) outliers start: 27 outliers final: 12 residues processed: 116 average time/residue: 1.1047 time to fit residues: 154.5774 Evaluate side-chains 102 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 107 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.105662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.069566 restraints weight = 138558.485| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.80 r_work: 0.3065 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20948 Z= 0.254 Angle : 0.611 7.128 28538 Z= 0.304 Chirality : 0.038 0.182 3202 Planarity : 0.005 0.050 3796 Dihedral : 6.478 96.245 3008 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.18 % Allowed : 11.23 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2664 helix: 1.48 (0.16), residues: 1098 sheet: -2.02 (0.22), residues: 508 loop : -0.16 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 31 TYR 0.017 0.002 TYR B 696 PHE 0.012 0.002 PHE B 372 TRP 0.023 0.001 TRP B1140 HIS 0.006 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 (20942) covalent geometry : angle 0.61095 / 0.30 (28538) hydrogen bonds : bond 0.04092 / 2.75 ( 1004) hydrogen bonds : angle 5.37512 / 3.89 ( 2820) Misc. bond : bond 0.00151 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8525 (tm) REVERT: A 158 MET cc_start: 0.9380 (tpt) cc_final: 0.9015 (tpt) REVERT: A 854 ASP cc_start: 0.8596 (p0) cc_final: 0.8182 (p0) REVERT: A 1185 LEU cc_start: 0.8113 (tp) cc_final: 0.7877 (mm) REVERT: A 1237 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8188 (mt) REVERT: A 1335 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.7785 (mtp) REVERT: B 368 ASN cc_start: 0.8620 (m-40) cc_final: 0.8372 (m-40) REVERT: B 503 GLU cc_start: 0.7764 (tp30) cc_final: 0.7298 (tp30) REVERT: B 715 ILE cc_start: 0.9075 (tp) cc_final: 0.8790 (tp) REVERT: B 747 ASP cc_start: 0.8913 (m-30) cc_final: 0.8593 (m-30) REVERT: B 1307 MET cc_start: 0.9181 (ptp) cc_final: 0.8828 (ptm) outliers start: 24 outliers final: 11 residues processed: 110 average time/residue: 1.1164 time to fit residues: 147.7230 Evaluate side-chains 100 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 58 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.106612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.070784 restraints weight = 138375.078| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.82 r_work: 0.3096 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20948 Z= 0.175 Angle : 0.581 6.597 28538 Z= 0.287 Chirality : 0.038 0.217 3202 Planarity : 0.005 0.051 3796 Dihedral : 6.458 99.625 3008 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.03 % Allowed : 11.37 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2664 helix: 1.46 (0.16), residues: 1112 sheet: -2.12 (0.23), residues: 496 loop : -0.09 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.021 0.002 TYR A1194 PHE 0.015 0.001 PHE B 372 TRP 0.032 0.001 TRP B1140 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (20942) covalent geometry : angle 0.58051 / 0.29 (28538) hydrogen bonds : bond 0.03843 / 2.57 ( 1004) hydrogen bonds : angle 5.31976 / 3.85 ( 2820) Misc. bond : bond 0.00115 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8519 (tm) REVERT: A 158 MET cc_start: 0.9348 (tpt) cc_final: 0.8992 (tpt) REVERT: A 854 ASP cc_start: 0.8556 (p0) cc_final: 0.8112 (p0) REVERT: A 1185 LEU cc_start: 0.8149 (tp) cc_final: 0.7905 (mm) REVERT: A 1237 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8183 (mt) REVERT: A 1335 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.7708 (mtp) REVERT: B 368 ASN cc_start: 0.8550 (m-40) cc_final: 0.8281 (m-40) REVERT: B 503 GLU cc_start: 0.7769 (tp30) cc_final: 0.7342 (tp30) REVERT: B 715 ILE cc_start: 0.9042 (tp) cc_final: 0.8762 (tp) REVERT: B 747 ASP cc_start: 0.8864 (m-30) cc_final: 0.8537 (m-30) REVERT: B 1307 MET cc_start: 0.9130 (ptp) cc_final: 0.8772 (ptm) outliers start: 21 outliers final: 11 residues processed: 110 average time/residue: 1.0331 time to fit residues: 138.9817 Evaluate side-chains 100 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1142 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 200 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.104822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068534 restraints weight = 139221.956| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.79 r_work: 0.3040 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20948 Z= 0.293 Angle : 0.634 7.047 28538 Z= 0.316 Chirality : 0.039 0.214 3202 Planarity : 0.005 0.051 3796 Dihedral : 6.499 96.398 3008 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.78 % Allowed : 11.72 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2664 helix: 1.45 (0.16), residues: 1114 sheet: -2.16 (0.22), residues: 506 loop : -0.12 (0.21), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 31 TYR 0.019 0.002 TYR B 696 PHE 0.016 0.002 PHE B 464 TRP 0.034 0.001 TRP B1140 HIS 0.006 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.29 (20942) covalent geometry : angle 0.63375 / 0.32 (28538) hydrogen bonds : bond 0.04169 / 2.81 ( 1004) hydrogen bonds : angle 5.39131 / 3.91 ( 2820) Misc. bond : bond 0.00158 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1185 LEU cc_start: 0.8201 (tp) cc_final: 0.7968 (mm) REVERT: A 1210 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7521 (tpp80) REVERT: A 1237 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8285 (mt) REVERT: A 1335 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.7774 (mtp) REVERT: B 503 GLU cc_start: 0.7927 (tp30) cc_final: 0.7488 (tp30) REVERT: B 715 ILE cc_start: 0.9099 (tp) cc_final: 0.8810 (tp) REVERT: B 747 ASP cc_start: 0.8919 (m-30) cc_final: 0.8579 (m-30) REVERT: B 1307 MET cc_start: 0.9143 (ptp) cc_final: 0.8789 (ptm) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 1.1063 time to fit residues: 141.8952 Evaluate side-chains 95 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 258 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.104705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068631 restraints weight = 138075.493| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.77 r_work: 0.3044 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20948 Z= 0.280 Angle : 0.628 6.735 28538 Z= 0.313 Chirality : 0.039 0.202 3202 Planarity : 0.005 0.096 3796 Dihedral : 6.516 95.751 3008 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.74 % Allowed : 12.11 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2664 helix: 1.40 (0.16), residues: 1118 sheet: -2.20 (0.22), residues: 506 loop : -0.09 (0.21), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 991 TYR 0.018 0.002 TYR B 696 PHE 0.017 0.002 PHE B 372 TRP 0.043 0.001 TRP B1140 HIS 0.006 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.28 (20942) covalent geometry : angle 0.62815 / 0.31 (28538) hydrogen bonds : bond 0.04146 / 2.80 ( 1004) hydrogen bonds : angle 5.41135 / 3.92 ( 2820) Misc. bond : bond 0.00166 / 0.08 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8905 (tp) REVERT: A 1185 LEU cc_start: 0.8195 (tp) cc_final: 0.7974 (mm) REVERT: A 1210 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7591 (tpp80) REVERT: A 1237 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8347 (mt) REVERT: A 1335 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.7676 (mtp) REVERT: B 503 GLU cc_start: 0.8011 (tp30) cc_final: 0.7566 (tp30) REVERT: B 747 ASP cc_start: 0.8896 (m-30) cc_final: 0.8574 (m-30) REVERT: B 1109 ARG cc_start: 0.7775 (tpt170) cc_final: 0.7418 (tpm170) REVERT: B 1307 MET cc_start: 0.9149 (ptp) cc_final: 0.8788 (ptm) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 1.0501 time to fit residues: 126.6576 Evaluate side-chains 96 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 100 optimal weight: 20.0000 chunk 205 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 219 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.106594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070650 restraints weight = 138451.280| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.82 r_work: 0.3087 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20948 Z= 0.150 Angle : 0.589 6.616 28538 Z= 0.291 Chirality : 0.038 0.186 3202 Planarity : 0.005 0.075 3796 Dihedral : 6.450 97.584 3008 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.98 % Allowed : 12.06 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.17), residues: 2664 helix: 1.48 (0.16), residues: 1118 sheet: -2.24 (0.22), residues: 504 loop : 0.01 (0.21), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 991 TYR 0.014 0.002 TYR B 696 PHE 0.015 0.002 PHE B 560 TRP 0.043 0.001 TRP B1140 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (20942) covalent geometry : angle 0.58850 / 0.29 (28538) hydrogen bonds : bond 0.03781 / 2.54 ( 1004) hydrogen bonds : angle 5.32026 / 3.86 ( 2820) Misc. bond : bond 0.00082 / 0.04 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13249.61 seconds wall clock time: 224 minutes 56.47 seconds (13496.47 seconds total)