Starting phenix.real_space_refine on Tue Jul 7 00:48:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7emy_31198/07_2026/7emy_31198_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7emy_31198/07_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_31198/07_2026/7emy_31198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7emy_31198/07_2026/7emy_31198.map" model { file = "/net/cci-nas-00/data/ceres_data/7emy_31198/07_2026/7emy_31198_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7emy_31198/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 6.67, per 1000 atoms: 0.16 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: 4.08 Conformation dependent library (CDL) restraints added in 1.5 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: 1.20 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: 14.51 Time building geometry restraints manager: 5.55 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: 71385 6.29 - 12.58: 3586 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 - 20.85: 17987 20.85 - 41.69: 842 41.69 - 62.54: 431 62.54 - 83.38: 77 83.38 - 104.23: 3 Dihedral angle restraints: 19340 sinusoidal: 10750 harmonic: 8590 Sorted by residual: 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 dihedral pdb=" CA SER B 786 " pdb=" C SER B 786 " pdb=" N ALA B 787 " pdb=" CA ALA B 787 " ideal model delta harmonic sigma weight residual 180.00 151.74 28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA LEU A 371 " pdb=" C LEU A 371 " pdb=" N PHE A 372 " pdb=" CA PHE A 372 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 19337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1809 0.152 - 0.305: 83 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: 1.130 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: 0.280 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 44.860 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 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:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- 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 : 2.797 17.993 28538 Z= 1.814 Chirality : 0.360 0.761 3202 Planarity : 0.012 0.148 3796 Dihedral : 12.091 104.229 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 2.79706 / 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 : 1.254 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: 1.5562 time to fit residues: 453.7236 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 : 1.078 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.109593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.074345 restraints weight = 138205.962| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.86 r_work: 0.3178 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 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 = 0.3044 r_free = 0.3044 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: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20948 Z= 0.174 Angle : 0.672 7.582 28538 Z= 0.341 Chirality : 0.040 0.153 3202 Planarity : 0.006 0.056 3796 Dihedral : 7.346 87.100 3015 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.03 % Allowed : 8.28 % Favored : 90.69 % 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: 1.06 (0.15), residues: 1104 sheet: -1.65 (0.22), residues: 502 loop : -0.22 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 726 TYR 0.018 0.002 TYR A 51 PHE 0.016 0.001 PHE A 560 TRP 0.015 0.001 TRP A 535 HIS 0.011 0.002 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (20942) covalent geometry : angle 0.67190 / 0.34 (28538) hydrogen bonds : bond 0.05215 / 3.45 ( 1004) hydrogen bonds : angle 5.98024 / 4.30 ( 2820) Misc. bond : bond 0.00057 / 0.03 ( 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 161 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.111 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: A 480 ASP cc_start: 0.8080 (t0) cc_final: 0.7791 (t0) REVERT: A 989 VAL cc_start: 0.8516 (t) cc_final: 0.8085 (t) REVERT: A 1185 LEU cc_start: 0.7983 (tp) cc_final: 0.7774 (mt) REVERT: B 300 ASP cc_start: 0.8076 (t0) cc_final: 0.7776 (m-30) REVERT: B 346 SER cc_start: 0.8914 (m) cc_final: 0.8416 (p) REVERT: B 1307 MET cc_start: 0.9136 (ptp) cc_final: 0.8805 (ptm) outliers start: 21 outliers final: 7 residues processed: 151 average time/residue: 1.2077 time to fit residues: 213.3760 Evaluate side-chains 110 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1145 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 954 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 150 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1179 GLN ** 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 = 0.3966 r_free = 0.3966 target = 0.108708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.073644 restraints weight = 138373.953| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.85 r_work: 0.3168 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20948 Z= 0.151 Angle : 0.607 7.962 28538 Z= 0.302 Chirality : 0.038 0.142 3202 Planarity : 0.005 0.063 3796 Dihedral : 6.809 82.751 3012 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.88 % Allowed : 9.95 % 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: 1.31 (0.16), residues: 1106 sheet: -1.83 (0.21), residues: 506 loop : -0.18 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 31 TYR 0.015 0.002 TYR B 696 PHE 0.024 0.001 PHE B 372 TRP 0.012 0.001 TRP B 535 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (20942) covalent geometry : angle 0.60705 / 0.30 (28538) hydrogen bonds : bond 0.04419 / 2.93 ( 1004) hydrogen bonds : angle 5.66897 / 4.08 ( 2820) Misc. bond : bond 0.00083 / 0.04 ( 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 135 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.051 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 158 MET cc_start: 0.9312 (tpt) cc_final: 0.8984 (tpt) REVERT: A 854 ASP cc_start: 0.8573 (p0) cc_final: 0.8078 (p0) REVERT: A 1335 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8183 (mtp) REVERT: B 300 ASP cc_start: 0.8143 (t0) cc_final: 0.7803 (m-30) REVERT: B 368 ASN cc_start: 0.8592 (m-40) cc_final: 0.8269 (m110) REVERT: B 1307 MET cc_start: 0.9151 (ptp) cc_final: 0.8794 (ptm) outliers start: 18 outliers final: 8 residues processed: 125 average time/residue: 1.0279 time to fit residues: 153.2504 Evaluate side-chains 107 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ILE 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 1219 LEU 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: 3.9990 chunk 211 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 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 = 0.3912 r_free = 0.3912 target = 0.105586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.069307 restraints weight = 138421.389| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.81 r_work: 0.3068 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 20948 Z= 0.299 Angle : 0.654 8.717 28538 Z= 0.326 Chirality : 0.040 0.156 3202 Planarity : 0.005 0.045 3796 Dihedral : 6.719 77.340 3010 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.18 % Allowed : 10.64 % Favored : 88.19 % 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: -0.04 (0.17), residues: 2664 helix: 1.29 (0.16), residues: 1110 sheet: -2.00 (0.22), residues: 514 loop : -0.24 (0.21), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 541 TYR 0.018 0.003 TYR B 696 PHE 0.017 0.002 PHE B1200 TRP 0.012 0.001 TRP B1140 HIS 0.008 0.002 HIS A1190 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.30 (20942) covalent geometry : angle 0.65358 / 0.33 (28538) hydrogen bonds : bond 0.04531 / 3.03 ( 1004) hydrogen bonds : angle 5.59351 / 4.03 ( 2820) Misc. bond : bond 0.00170 / 0.09 ( 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: 24 poor density : 107 time to evaluate : 1.076 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: A 392 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8862 (tp) REVERT: A 854 ASP cc_start: 0.8550 (p0) cc_final: 0.8092 (p0) REVERT: A 1185 LEU cc_start: 0.8121 (tp) cc_final: 0.7840 (mm) REVERT: A 1237 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8131 (mt) REVERT: A 1335 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8215 (mtp) REVERT: B 503 GLU cc_start: 0.7699 (tp30) cc_final: 0.7225 (tp30) REVERT: B 715 ILE cc_start: 0.9090 (tp) cc_final: 0.8809 (tp) REVERT: B 1307 MET cc_start: 0.9182 (ptp) cc_final: 0.8807 (ptm) outliers start: 24 outliers final: 10 residues processed: 124 average time/residue: 1.1817 time to fit residues: 171.3960 Evaluate side-chains 101 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 757 SER 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 1219 LEU Chi-restraints excluded: chain A residue 1237 LEU 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 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: 30.0000 chunk 142 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 chunk 239 optimal weight: 30.0000 chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3939 r_free = 0.3939 target = 0.107233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071596 restraints weight = 137867.898| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.82 r_work: 0.3112 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20948 Z= 0.159 Angle : 0.593 7.627 28538 Z= 0.293 Chirality : 0.038 0.147 3202 Planarity : 0.005 0.047 3796 Dihedral : 6.420 75.992 3010 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.18 % Allowed : 10.98 % Favored : 87.84 % 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: 1.34 (0.16), residues: 1110 sheet: -1.96 (0.22), residues: 490 loop : -0.17 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 12 TYR 0.012 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 A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (20942) covalent geometry : angle 0.59250 / 0.29 (28538) hydrogen bonds : bond 0.04014 / 2.68 ( 1004) hydrogen bonds : angle 5.46573 / 3.95 ( 2820) Misc. bond : bond 0.00095 / 0.05 ( 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 127 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.966 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: A 27 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8571 (tm) REVERT: A 392 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8880 (tp) REVERT: A 854 ASP cc_start: 0.8498 (p0) cc_final: 0.8025 (p0) REVERT: A 1185 LEU cc_start: 0.8129 (tp) cc_final: 0.7889 (mm) REVERT: A 1237 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8152 (mt) REVERT: B 503 GLU cc_start: 0.7643 (tp30) cc_final: 0.7203 (tp30) REVERT: B 715 ILE cc_start: 0.9044 (tp) cc_final: 0.8770 (tp) REVERT: B 1307 MET cc_start: 0.9163 (ptp) cc_final: 0.8779 (ptm) outliers start: 24 outliers final: 12 residues processed: 118 average time/residue: 0.9719 time to fit residues: 137.3150 Evaluate side-chains 105 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 392 LEU 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 267 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 109 optimal weight: 8.9990 chunk 176 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3931 r_free = 0.3931 target = 0.106811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.070961 restraints weight = 138326.323| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.82 r_work: 0.3103 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20948 Z= 0.186 Angle : 0.591 8.137 28538 Z= 0.291 Chirality : 0.038 0.139 3202 Planarity : 0.005 0.047 3796 Dihedral : 6.225 70.745 3010 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.93 % Allowed : 11.32 % Favored : 87.75 % 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: 1.47 (0.16), residues: 1096 sheet: -1.99 (0.23), residues: 496 loop : -0.19 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 320 TYR 0.015 0.002 TYR B 696 PHE 0.015 0.001 PHE B 372 TRP 0.015 0.001 TRP B1140 HIS 0.006 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (20942) covalent geometry : angle 0.59119 / 0.29 (28538) hydrogen bonds : bond 0.03936 / 2.63 ( 1004) hydrogen bonds : angle 5.37008 / 3.88 ( 2820) Misc. bond : bond 0.00112 / 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 116 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.000 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: A 27 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8595 (tm) REVERT: A 392 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8885 (tp) REVERT: A 854 ASP cc_start: 0.8523 (p0) cc_final: 0.8008 (p0) REVERT: A 1185 LEU cc_start: 0.8127 (tp) cc_final: 0.7801 (mm) REVERT: A 1237 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8216 (mt) REVERT: A 1335 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.7715 (mtp) REVERT: B 368 ASN cc_start: 0.8586 (m-40) cc_final: 0.8348 (m-40) REVERT: B 503 GLU cc_start: 0.7718 (tp30) cc_final: 0.7273 (tp30) REVERT: B 715 ILE cc_start: 0.9046 (tp) cc_final: 0.8762 (tp) REVERT: B 1307 MET cc_start: 0.9153 (ptp) cc_final: 0.8803 (ptm) outliers start: 19 outliers final: 7 residues processed: 110 average time/residue: 1.0091 time to fit residues: 133.4760 Evaluate side-chains 101 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 392 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1219 LEU 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 954 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 chunk 179 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** ** 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 = 0.3902 r_free = 0.3902 target = 0.105092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.068771 restraints weight = 138726.201| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.79 r_work: 0.3049 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20948 Z= 0.288 Angle : 0.634 8.373 28538 Z= 0.314 Chirality : 0.039 0.183 3202 Planarity : 0.005 0.047 3796 Dihedral : 6.189 70.365 3008 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.32 % Allowed : 10.93 % Favored : 87.75 % 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: 1.44 (0.16), residues: 1098 sheet: -2.01 (0.22), residues: 508 loop : -0.21 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 541 TYR 0.019 0.002 TYR B 696 PHE 0.012 0.002 PHE B 372 TRP 0.021 0.001 TRP B1140 HIS 0.006 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.29 (20942) covalent geometry : angle 0.63422 / 0.31 (28538) hydrogen bonds : bond 0.04207 / 2.82 ( 1004) hydrogen bonds : angle 5.41921 / 3.92 ( 2820) Misc. bond : bond 0.00162 / 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 124 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.090 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: 0.8800 (OUTLIER) cc_final: 0.8582 (tm) REVERT: A 64 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8363 (t0) REVERT: A 392 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8901 (tp) REVERT: A 1185 LEU cc_start: 0.8119 (tp) cc_final: 0.7865 (mm) REVERT: A 1237 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8294 (mt) REVERT: A 1335 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.7787 (mtp) REVERT: B 368 ASN cc_start: 0.8667 (m-40) cc_final: 0.8426 (m-40) REVERT: B 503 GLU cc_start: 0.7897 (tp30) cc_final: 0.7424 (tp30) REVERT: B 715 ILE cc_start: 0.9106 (tp) cc_final: 0.8823 (tp) REVERT: B 747 ASP cc_start: 0.8935 (m-30) cc_final: 0.8604 (m-30) REVERT: B 1307 MET cc_start: 0.9176 (ptp) cc_final: 0.8829 (ptm) outliers start: 27 outliers final: 12 residues processed: 115 average time/residue: 0.9353 time to fit residues: 129.8466 Evaluate side-chains 105 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 205 HIS 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 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 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: 1.9990 chunk 255 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** 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 = 0.3920 r_free = 0.3920 target = 0.106238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.070216 restraints weight = 138135.153| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.81 r_work: 0.3080 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3383 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= 0.185 Angle : 0.599 7.900 28538 Z= 0.295 Chirality : 0.038 0.195 3202 Planarity : 0.005 0.055 3796 Dihedral : 6.112 67.188 3008 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.03 % Allowed : 11.57 % Favored : 87.40 % 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: 1.49 (0.16), residues: 1098 sheet: -2.11 (0.22), residues: 510 loop : -0.15 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 31 TYR 0.015 0.002 TYR B 696 PHE 0.014 0.002 PHE B 372 TRP 0.026 0.001 TRP B1140 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (20942) covalent geometry : angle 0.59903 / 0.30 (28538) hydrogen bonds : bond 0.03920 / 2.62 ( 1004) hydrogen bonds : angle 5.35343 / 3.88 ( 2820) Misc. bond : bond 0.00114 / 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 114 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.933 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: 0.8826 (OUTLIER) cc_final: 0.8615 (tm) REVERT: A 64 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8355 (t0) REVERT: A 392 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8921 (tp) REVERT: A 854 ASP cc_start: 0.8595 (p0) cc_final: 0.8150 (p0) REVERT: A 1185 LEU cc_start: 0.8132 (tp) cc_final: 0.7875 (mm) REVERT: A 1237 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8256 (mt) REVERT: A 1335 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.7663 (mtp) REVERT: B 368 ASN cc_start: 0.8591 (m-40) cc_final: 0.8265 (m110) REVERT: B 503 GLU cc_start: 0.7839 (tp30) cc_final: 0.7401 (tp30) REVERT: B 715 ILE cc_start: 0.9091 (tp) cc_final: 0.8798 (tp) REVERT: B 747 ASP cc_start: 0.8878 (m-30) cc_final: 0.8552 (m-30) REVERT: B 1109 ARG cc_start: 0.7842 (tpt170) cc_final: 0.7589 (tpm170) REVERT: B 1307 MET cc_start: 0.9144 (ptp) cc_final: 0.8785 (ptm) REVERT: B 1335 MET cc_start: 0.8905 (mtt) cc_final: 0.8646 (mpt) outliers start: 21 outliers final: 10 residues processed: 107 average time/residue: 0.8682 time to fit residues: 113.6565 Evaluate side-chains 103 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 205 HIS 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 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 954 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 200 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 99 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** 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 = 0.3929 r_free = 0.3929 target = 0.106720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070941 restraints weight = 138861.253| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.82 r_work: 0.3096 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20948 Z= 0.159 Angle : 0.589 7.975 28538 Z= 0.288 Chirality : 0.038 0.254 3202 Planarity : 0.005 0.070 3796 Dihedral : 6.024 67.485 3008 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.93 % Allowed : 11.62 % Favored : 87.45 % 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: 1.47 (0.16), residues: 1118 sheet: -2.13 (0.22), residues: 496 loop : -0.06 (0.21), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 31 TYR 0.014 0.002 TYR B 696 PHE 0.013 0.001 PHE B 560 TRP 0.050 0.001 TRP B1140 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (20942) covalent geometry : angle 0.58901 / 0.29 (28538) hydrogen bonds : bond 0.03790 / 2.54 ( 1004) hydrogen bonds : angle 5.30135 / 3.84 ( 2820) Misc. bond : bond 0.00095 / 0.05 ( 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 114 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.008 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: A 27 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8633 (tm) REVERT: A 392 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8893 (tp) REVERT: A 854 ASP cc_start: 0.8550 (p0) cc_final: 0.8106 (p0) REVERT: A 1185 LEU cc_start: 0.8143 (tp) cc_final: 0.7895 (mm) REVERT: A 1237 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8236 (mt) REVERT: A 1335 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.7647 (mtp) REVERT: B 503 GLU cc_start: 0.7680 (tp30) cc_final: 0.7288 (tp30) REVERT: B 715 ILE cc_start: 0.9067 (tp) cc_final: 0.8774 (tp) REVERT: B 747 ASP cc_start: 0.8862 (m-30) cc_final: 0.8539 (m-30) REVERT: B 1307 MET cc_start: 0.9178 (ptp) cc_final: 0.8781 (ptm) REVERT: B 1335 MET cc_start: 0.8878 (mtt) cc_final: 0.8532 (mpt) outliers start: 19 outliers final: 10 residues processed: 109 average time/residue: 0.7720 time to fit residues: 103.8782 Evaluate side-chains 99 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 205 HIS 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 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: 10.0000 chunk 144 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 66 optimal weight: 0.0470 chunk 108 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** 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 = 0.3894 r_free = 0.3894 target = 0.104730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.068405 restraints weight = 137960.959| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.79 r_work: 0.3042 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20948 Z= 0.297 Angle : 0.647 8.102 28538 Z= 0.319 Chirality : 0.039 0.187 3202 Planarity : 0.005 0.071 3796 Dihedral : 6.063 65.414 3008 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.93 % Allowed : 11.67 % Favored : 87.40 % 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: 1.45 (0.16), residues: 1118 sheet: -2.17 (0.22), residues: 506 loop : -0.10 (0.21), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 31 TYR 0.020 0.002 TYR B 696 PHE 0.013 0.002 PHE B 749 TRP 0.048 0.002 TRP B1140 HIS 0.007 0.002 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.30 (20942) covalent geometry : angle 0.64737 / 0.32 (28538) hydrogen bonds : bond 0.04138 / 2.78 ( 1004) hydrogen bonds : angle 5.37071 / 3.89 ( 2820) Misc. bond : bond 0.00161 / 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 111 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.022 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 64 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8404 (t0) REVERT: A 205 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8700 (m90) REVERT: A 392 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8935 (tp) REVERT: A 1185 LEU cc_start: 0.8170 (tp) cc_final: 0.7940 (mm) REVERT: A 1237 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8311 (mt) REVERT: A 1335 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.7708 (mtp) REVERT: B 503 GLU cc_start: 0.7970 (tp30) cc_final: 0.7524 (tp30) REVERT: B 715 ILE cc_start: 0.9097 (tp) cc_final: 0.8792 (tp) REVERT: B 747 ASP cc_start: 0.8898 (m-30) cc_final: 0.8561 (m-30) REVERT: B 1109 ARG cc_start: 0.7790 (tpt170) cc_final: 0.7563 (tpm170) REVERT: B 1307 MET cc_start: 0.9151 (ptp) cc_final: 0.8799 (ptm) outliers start: 19 outliers final: 10 residues processed: 108 average time/residue: 0.9494 time to fit residues: 123.9520 Evaluate side-chains 98 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 205 HIS 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 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: 9.9990 chunk 205 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 261 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 219 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** 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 = 0.3935 r_free = 0.3935 target = 0.107074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.071593 restraints weight = 138430.077| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.81 r_work: 0.3113 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20948 Z= 0.129 Angle : 0.588 7.620 28538 Z= 0.287 Chirality : 0.038 0.218 3202 Planarity : 0.005 0.083 3796 Dihedral : 5.962 67.407 3008 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.83 % Allowed : 12.06 % Favored : 87.11 % 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: 0.19 (0.17), residues: 2664 helix: 1.48 (0.16), residues: 1118 sheet: -2.18 (0.22), residues: 490 loop : -0.01 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 991 TYR 0.012 0.002 TYR B 696 PHE 0.015 0.002 PHE B 560 TRP 0.048 0.001 TRP B1140 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (20942) covalent geometry : angle 0.58820 / 0.29 (28538) hydrogen bonds : bond 0.03670 / 2.45 ( 1004) hydrogen bonds : angle 5.26068 / 3.82 ( 2820) Misc. bond : bond 0.00073 / 0.04 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12757.86 seconds wall clock time: 216 minutes 12.37 seconds (12972.37 seconds total)