Starting phenix.real_space_refine on Tue Jul 7 00:46:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7en1_31199/07_2026/7en1_31199_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7en1_31199/07_2026/7en1_31199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7en1_31199/07_2026/7en1_31199_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7en1_31199/07_2026/7en1_31199_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7en1_31199/07_2026/7en1_31199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7en1_31199/07_2026/7en1_31199.map" } resolution = 3.47 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 69 5.16 5 C 12880 2.51 5 N 3772 2.21 5 O 3716 1.98 5 H 20419 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 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: 40862 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 20280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 20280 Classifications: {'peptide': 1320} Link IDs: {'PCIS': 1, 'PTRANS': 83, 'TRANS': 1235} Chain breaks: 1 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 71 Unusual residues: {' MG': 1, 'AMP%rna2p': 1, 'J9F': 1, 'PNS': 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 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'J9F:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {' MG': 1, 'AMP%rna2p': 1, 'PNS': 1, 'SAL': 1} Classifications: {'RNA_mixed': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, '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: 2 residue: pdb=" C28 PNS A1501 " occ=0.00 ... (19 atoms not shown) pdb=" S44 PNS A1501 " occ=0.00 residue: pdb=" C1 SAL B1502 " occ=0.00 ... (7 atoms not shown) pdb=" O2 SAL B1502 " occ=0.00 Time building chain proxies: 5.95, per 1000 atoms: 0.15 Number of scatterers: 40862 At special positions: 0 Unit cell: (133, 148, 137, 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 69 16.00 P 4 15.00 Mg 2 11.99 O 3716 8.00 N 3772 7.00 C 12880 6.00 H 20419 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4906 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 24 sheets defined 47.6% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 108 through 118 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 206 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 240 through 257 removed outlier: 4.135A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 268 through 280 removed outlier: 3.948A pdb=" N ALA A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 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 removed outlier: 3.802A pdb=" N ILE A 313 " --> pdb=" O PRO A 310 " (cutoff:3.500A) 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 383 Processing helix chain 'A' and resid 403 through 422 removed outlier: 4.016A pdb=" N ASP A 420 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 3.876A 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: 3.723A pdb=" N ALA A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 522 Processing helix chain 'A' and resid 534 through 546 removed outlier: 3.590A pdb=" N GLN A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) 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 650 Processing helix chain 'A' and resid 670 through 676 Processing helix chain 'A' and resid 711 through 726 removed outlier: 4.319A pdb=" N LEU A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.774A pdb=" N PHE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 755 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: 3.551A pdb=" N LEU A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 removed outlier: 4.658A pdb=" N GLY A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 906 through 913 Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 1008 through 1027 removed outlier: 3.771A pdb=" N ALA A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 6.706A pdb=" N LEU A1031 " --> pdb=" O GLU A1028 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1033 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1048 removed outlier: 4.367A pdb=" N ALA A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1064 removed outlier: 3.910A 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 1089 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 1145 removed outlier: 3.522A pdb=" N GLY A1144 " --> pdb=" O TRP A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1148 No H-bonds generated for 'chain 'A' and resid 1146 through 1148' Processing helix chain 'A' and resid 1161 through 1172 removed outlier: 4.126A pdb=" N LEU A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1167 " --> pdb=" O VAL A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 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 1202 through 1206 Processing helix chain 'A' and resid 1208 through 1219 Processing helix chain 'A' and resid 1235 through 1246 Processing helix chain 'A' and resid 1248 through 1252 removed outlier: 3.640A pdb=" N ARG A1251 " --> pdb=" O ARG A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1265 Processing helix chain 'A' and resid 1291 through 1303 Processing helix chain 'A' and resid 1304 through 1308 Processing helix chain 'A' and resid 1327 through 1339 Processing helix chain 'A' and resid 1353 through 1368 Processing helix chain 'A' and resid 1377 through 1382 Processing helix chain 'A' and resid 1384 through 1399 removed outlier: 3.589A pdb=" N ARG A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1411 Processing helix chain 'A' and resid 1413 through 1423 removed outlier: 4.667A pdb=" N HIS A1420 " --> pdb=" O GLY A1416 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A1421 " --> pdb=" O LEU A1417 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 45 through 59 Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.692A pdb=" N CYS B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.779A pdb=" N GLY B 119 " --> pdb=" O TRP B 115 " (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 206 removed outlier: 3.525A pdb=" N HIS B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) 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: 4.781A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.450A 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 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: 4.381A pdb=" N ASP B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) removed outlier: 4.531A 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 462 Processing helix chain 'B' and resid 504 through 523 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 removed outlier: 3.731A pdb=" N GLY B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 711 through 726 removed outlier: 3.898A pdb=" N LEU B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.754A 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 797 removed outlier: 3.589A pdb=" N LEU B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 797 " --> pdb=" O MET B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 826 Processing helix chain 'B' and resid 841 through 845 removed outlier: 3.620A pdb=" N GLY B 845 " --> pdb=" O THR B 842 " (cutoff:3.500A) 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 1027 removed outlier: 4.156A pdb=" N ALA B1012 " --> pdb=" O PHE B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1033 removed outlier: 6.474A pdb=" N LEU B1031 " --> pdb=" O GLU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1048 removed outlier: 3.589A pdb=" N ASP B1043 " --> pdb=" O ARG B1039 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1064 removed outlier: 3.876A 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 removed outlier: 4.261A pdb=" N ASP B1093 " --> pdb=" O LEU B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1103 Processing helix chain 'B' and resid 1107 through 1116 removed outlier: 3.897A pdb=" N ARG B1114 " --> pdb=" O GLU B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1125 Processing helix chain 'B' and resid 1140 through 1143 Processing helix chain 'B' and resid 1144 through 1149 Processing helix chain 'B' and resid 1161 through 1170 removed outlier: 4.094A 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 1202 through 1206 Processing helix chain 'B' and resid 1208 through 1219 removed outlier: 3.722A pdb=" N GLY B1212 " --> pdb=" O ALA B1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 1235 through 1246 Processing helix 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: 3.724A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 325 removed outlier: 3.943A pdb=" N ARG A 485 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 372 Processing sheet with id=AA5, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.734A pdb=" N ALA A 572 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A 733 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN A 785 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TRP A 784 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N SER A 813 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER A 786 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 810 " --> pdb=" O HIS A 836 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU A 838 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 812 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 835 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 849 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.862A 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: 6.309A pdb=" N VAL A 607 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.006A 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: 6.255A pdb=" N GLU A 608 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 655 " --> pdb=" O LEU A 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.742A pdb=" N VAL A 709 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 694 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL A 707 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 3.651A 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: 4.790A pdb=" N ASP A 927 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE A 894 " --> pdb=" O THR A 925 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 925 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N GLY A 896 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N TYR A 923 " --> pdb=" O GLY A 896 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 872 through 877 removed outlier: 4.790A pdb=" N ASP A 927 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE A 894 " --> pdb=" O THR A 925 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 925 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N GLY A 896 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N TYR A 923 " --> pdb=" O GLY A 896 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 941 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 930 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE A 939 " --> pdb=" O ARG A 930 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 946 through 949 removed outlier: 3.631A pdb=" N VAL A 947 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 969 through 976 removed outlier: 3.635A pdb=" N SER A 971 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 984 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TRP A1313 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 6.578A 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 1180 removed outlier: 8.238A pdb=" N VAL A1177 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A1155 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLN A1179 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU A1157 " --> pdb=" O GLN A1179 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG A1129 " --> pdb=" O ARG A1196 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE A1198 " --> pdb=" O ARG A1129 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA A1131 " --> pdb=" O ILE A1198 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N PHE A1200 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP A1195 " --> pdb=" O GLN A1223 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A1280 " --> pdb=" O LEU A1272 " (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 Processing sheet with id=AB6, first strand: chain 'B' and resid 318 through 325 removed outlier: 6.319A pdb=" N VAL B 445 " --> pdb=" O HIS B 481 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU B 483 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 447 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ARG B 485 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ASN B 449 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 364 through 372 Processing sheet with id=AB8, first strand: chain 'B' and resid 578 through 581 removed outlier: 6.775A pdb=" N ALA B 572 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU B 733 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG B 732 " --> pdb=" O LEU B 783 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASN B 785 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 734 " --> pdb=" O ASN B 785 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP B 784 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N SER B 813 " --> pdb=" O TRP B 784 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER B 786 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL B 810 " --> pdb=" O HIS B 836 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B 838 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 812 " --> pdb=" O LEU B 838 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 849 " --> pdb=" O GLY B 839 " (cutoff:3.500A) removed outlier: 3.832A 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: 6.461A pdb=" N VAL B 607 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 654 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 655 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 691 through 697 removed outlier: 3.785A 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: 5.040A pdb=" N ASP B 927 " --> pdb=" O LEU B 892 " (cutoff:3.500A) removed outlier: 5.334A 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: 6.648A pdb=" N LEU B 984 " --> pdb=" O ARG B1311 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N TRP B1313 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA B 986 " --> pdb=" O TRP B1313 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1177 through 1178 removed outlier: 6.643A pdb=" N ARG B1129 " --> pdb=" O ARG B1196 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILE B1198 " --> pdb=" O ARG B1129 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA B1131 " --> pdb=" O ILE B1198 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE B1200 " --> pdb=" O ALA B1131 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR B1194 " --> pdb=" O ARG B1221 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLN B1223 " --> pdb=" O TYR B1194 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG B1196 " --> pdb=" O GLN B1223 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG B1225 " --> pdb=" O ARG B1196 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE B1198 " --> pdb=" O ARG B1225 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B1227 " --> pdb=" O ILE B1198 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHE B1200 " --> pdb=" O LEU B1227 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B1229 " --> pdb=" O PHE B1200 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B1230 " --> pdb=" O ALA B1279 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B1279 " --> pdb=" O ASP B1230 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B1280 " --> pdb=" O LEU B1272 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2796 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: 11.69 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.08: 7353 1.08 - 1.28: 16500 1.28 - 1.47: 7948 1.47 - 1.66: 9393 1.66 - 1.86: 94 Bond restraints: 41288 Sorted by residual: bond pdb=" N CYS A1505 " pdb=" H CYS A1505 " ideal model delta sigma weight residual 0.860 1.018 -0.158 2.00e-02 2.50e+03 6.24e+01 bond pdb=" N CYS B1505 " pdb=" H CYS B1505 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C4 AMP A1504 " pdb=" C5 AMP A1504 " ideal model delta sigma weight residual 1.490 1.338 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N ALA A 794 " pdb=" H ALA A 794 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N TYR B 804 " pdb=" H TYR B 804 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 41283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.54: 74385 7.54 - 15.07: 307 15.07 - 22.61: 6 22.61 - 30.15: 0 30.15 - 37.68: 3 Bond angle restraints: 74701 Sorted by residual: angle pdb=" N GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 110.00 72.32 37.68 3.00e+00 1.11e-01 1.58e+02 angle pdb=" C GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 109.00 77.63 31.37 3.00e+00 1.11e-01 1.09e+02 angle pdb=" CB GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 109.00 78.51 30.49 3.00e+00 1.11e-01 1.03e+02 angle pdb=" CA PHE A 741 " pdb=" CB PHE A 741 " pdb=" CG PHE A 741 " ideal model delta sigma weight residual 113.80 122.27 -8.47 1.00e+00 1.00e+00 7.17e+01 angle pdb=" N PRO B 174 " pdb=" CA PRO B 174 " pdb=" CB PRO B 174 " ideal model delta sigma weight residual 103.22 107.09 -3.87 5.20e-01 3.70e+00 5.53e+01 ... (remaining 74696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 17522 21.16 - 42.33: 1081 42.33 - 63.49: 547 63.49 - 84.65: 120 84.65 - 105.82: 7 Dihedral angle restraints: 19277 sinusoidal: 10717 harmonic: 8560 Sorted by residual: dihedral pdb=" CA VAL A 486 " pdb=" C VAL A 486 " pdb=" N GLY A 487 " pdb=" CA GLY A 487 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA VAL B 486 " pdb=" C VAL B 486 " pdb=" N GLY B 487 " pdb=" CA GLY B 487 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER B 813 " pdb=" C SER B 813 " pdb=" N GLY B 814 " pdb=" CA GLY B 814 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 19274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2115 0.094 - 0.189: 886 0.189 - 0.283: 144 0.283 - 0.377: 29 0.377 - 0.472: 5 Chirality restraints: 3179 Sorted by residual: chirality pdb=" CA GLN B 689 " pdb=" N GLN B 689 " pdb=" C GLN B 689 " pdb=" CB GLN B 689 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA ASP B 742 " pdb=" N ASP B 742 " pdb=" C ASP B 742 " pdb=" CB ASP B 742 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASP A1246 " pdb=" N ASP A1246 " pdb=" C ASP A1246 " pdb=" CB ASP A1246 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3176 not shown) Planarity restraints: 6264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 953 " 0.572 9.50e-02 1.11e+02 2.83e-01 1.02e+03 pdb=" NE ARG B 953 " 0.142 2.00e-02 2.50e+03 pdb=" CZ ARG B 953 " 0.126 2.00e-02 2.50e+03 pdb=" NH1 ARG B 953 " 0.176 2.00e-02 2.50e+03 pdb=" NH2 ARG B 953 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG B 953 " -0.486 2.00e-02 2.50e+03 pdb="HH12 ARG B 953 " 0.247 2.00e-02 2.50e+03 pdb="HH21 ARG B 953 " -0.156 2.00e-02 2.50e+03 pdb="HH22 ARG B 953 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.356 2.00e-02 2.50e+03 1.27e-01 6.43e+02 pdb=" CG TRP A 816 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.128 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.042 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " 0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " 0.057 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP A 816 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 816 " 0.116 2.00e-02 2.50e+03 pdb=" HE3 TRP A 816 " 0.141 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 816 " -0.138 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 816 " 0.059 2.00e-02 2.50e+03 pdb=" HH2 TRP A 816 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 602 " -0.285 9.50e-02 1.11e+02 1.79e-01 5.24e+02 pdb=" NE ARG A 602 " -0.117 2.00e-02 2.50e+03 pdb=" CZ ARG A 602 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 602 " 0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG A 602 " 0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 602 " 0.261 2.00e-02 2.50e+03 pdb="HH12 ARG A 602 " -0.316 2.00e-02 2.50e+03 pdb="HH21 ARG A 602 " 0.013 2.00e-02 2.50e+03 pdb="HH22 ARG A 602 " 0.149 2.00e-02 2.50e+03 ... (remaining 6261 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 3002 2.16 - 2.77: 75789 2.77 - 3.38: 130085 3.38 - 3.99: 173450 3.99 - 4.60: 254695 Nonbonded interactions: 637021 Sorted by model distance: nonbonded pdb=" OE2 GLU A 608 " pdb=" HG SER A 610 " model vdw 1.552 2.450 nonbonded pdb=" HG1 THR B 343 " pdb=" O26 PNS B1501 " model vdw 1.572 2.450 nonbonded pdb=" OE1 GLU B1015 " pdb=" HG SER B1235 " model vdw 1.580 2.450 nonbonded pdb=" HG SER A 472 " pdb=" OD2 ASP A 480 " model vdw 1.586 2.450 nonbonded pdb=" OD2 ASP B1134 " pdb=" HG SER B1199 " model vdw 1.593 2.450 ... (remaining 637016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 99 through 1340 or resid 1501 or resid 1503 through 1505)) \ selection = (chain 'B' and (resid 99 through 1501 or resid 1503 through 1504 or (resid 1505 \ and (name N or name CA or name C or name O or name CB or name SG or name H or na \ me H2 or name HA or name HB2 or name HB3 or name HG )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.290 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 37.020 Find NCS groups from input model: 0.600 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 : 0.013 0.155 20874 Z= 0.862 Angle : 1.977 21.372 28429 Z= 1.290 Chirality : 0.101 0.472 3179 Planarity : 0.022 0.206 3782 Dihedral : 15.111 105.818 7712 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.17 % Favored : 94.56 % Rotamer: Outliers : 1.72 % Allowed : 5.72 % Favored : 92.56 % Cbeta Deviations : 0.29 % 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: -2.33 (0.15), residues: 2648 helix: -1.68 (0.13), residues: 1092 sheet: -1.98 (0.24), residues: 422 loop : -0.97 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG B 953 TYR 0.205 0.034 TYR B 923 PHE 0.132 0.024 PHE B 372 TRP 0.229 0.035 TRP A 816 HIS 0.028 0.006 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.01285 / 0.84 (20869) covalent geometry : angle 1.97743 / 1.29 (28429) hydrogen bonds : bond 0.14432 / 9.57 ( 995) hydrogen bonds : angle 8.30724 / 5.96 ( 2796) Misc. bond : bond 0.12772 / 6.72 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.668 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1055 SER cc_start: 0.1741 (OUTLIER) cc_final: 0.1355 (t) REVERT: A 1073 MET cc_start: 0.5360 (mtp) cc_final: 0.4996 (mtm) REVERT: A 1207 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: B 715 ILE cc_start: 0.9224 (tp) cc_final: 0.8909 (tp) REVERT: B 1000 MET cc_start: 0.5895 (tmm) cc_final: 0.5600 (tmm) REVERT: B 1505 CYS cc_start: 0.5004 (m) cc_final: 0.4773 (m) outliers start: 35 outliers final: 10 residues processed: 266 average time/residue: 0.4774 time to fit residues: 175.0742 Evaluate side-chains 150 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1109 ARG Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN B 449 ASN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.087762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.063206 restraints weight = 188663.990| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.20 r_work: 0.3114 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20874 Z= 0.289 Angle : 0.822 9.264 28429 Z= 0.424 Chirality : 0.043 0.432 3179 Planarity : 0.007 0.056 3782 Dihedral : 9.333 93.520 3039 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.63 % Allowed : 7.93 % Favored : 90.44 % 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: -1.65 (0.16), residues: 2648 helix: -0.58 (0.14), residues: 1113 sheet: -2.00 (0.24), residues: 426 loop : -1.05 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1210 TYR 0.016 0.002 TYR A1194 PHE 0.021 0.002 PHE B 560 TRP 0.022 0.002 TRP B 535 HIS 0.008 0.002 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.29 (20869) covalent geometry : angle 0.82231 / 0.42 (28429) hydrogen bonds : bond 0.05793 / 3.84 ( 995) hydrogen bonds : angle 6.51552 / 4.72 ( 2796) Misc. bond : bond 0.00180 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.964 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: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.9090 (ttp) cc_final: 0.8875 (ttm) REVERT: A 1055 SER cc_start: 0.1657 (OUTLIER) cc_final: 0.1367 (t) REVERT: A 1073 MET cc_start: 0.4821 (mtp) cc_final: 0.4579 (mtm) REVERT: A 1219 LEU cc_start: 0.9093 (tp) cc_final: 0.8846 (tp) REVERT: B 346 SER cc_start: 0.8666 (m) cc_final: 0.8243 (p) REVERT: B 428 GLU cc_start: 0.8668 (tp30) cc_final: 0.8463 (mm-30) REVERT: B 924 ARG cc_start: 0.8614 (ttt-90) cc_final: 0.8269 (ttp80) REVERT: B 1000 MET cc_start: 0.6098 (tmm) cc_final: 0.5824 (tmm) REVERT: B 1335 MET cc_start: 0.8865 (mtm) cc_final: 0.8641 (mtm) outliers start: 33 outliers final: 21 residues processed: 177 average time/residue: 0.4233 time to fit residues: 106.1914 Evaluate side-chains 140 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 0.0030 chunk 103 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 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 = 0.3868 r_free = 0.3868 target = 0.088526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064060 restraints weight = 186962.771| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.20 r_work: 0.3136 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20874 Z= 0.180 Angle : 0.680 7.481 28429 Z= 0.348 Chirality : 0.040 0.398 3179 Planarity : 0.006 0.114 3782 Dihedral : 7.884 74.855 3025 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.38 % Allowed : 8.97 % Favored : 89.65 % 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: -1.15 (0.16), residues: 2648 helix: 0.07 (0.15), residues: 1110 sheet: -2.16 (0.22), residues: 453 loop : -0.82 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1308 TYR 0.015 0.002 TYR B 290 PHE 0.021 0.002 PHE B1200 TRP 0.019 0.001 TRP B 535 HIS 0.006 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (20869) covalent geometry : angle 0.67990 / 0.35 (28429) hydrogen bonds : bond 0.04505 / 3.01 ( 995) hydrogen bonds : angle 5.96947 / 4.34 ( 2796) Misc. bond : bond 0.00107 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.017 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: symmetry clash revert: 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 394 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8850 (tt) REVERT: A 1055 SER cc_start: 0.1573 (OUTLIER) cc_final: 0.1272 (t) REVERT: A 1073 MET cc_start: 0.4968 (mtp) cc_final: 0.4737 (mtm) REVERT: A 1145 MET cc_start: 0.6567 (ttt) cc_final: 0.5376 (ppp) REVERT: A 1219 LEU cc_start: 0.9032 (tp) cc_final: 0.8825 (tp) REVERT: B 346 SER cc_start: 0.8456 (m) cc_final: 0.8084 (p) REVERT: B 428 GLU cc_start: 0.8679 (tp30) cc_final: 0.8455 (mm-30) REVERT: B 924 ARG cc_start: 0.8613 (ttt-90) cc_final: 0.8272 (ttp80) REVERT: B 1073 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7407 (mtp) REVERT: B 1329 ARG cc_start: 0.8502 (ttp80) cc_final: 0.8288 (tmm-80) outliers start: 28 outliers final: 16 residues processed: 157 average time/residue: 0.4406 time to fit residues: 98.6155 Evaluate side-chains 146 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 229 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1355 HIS ** B 716 ASN ** 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 = 0.3806 r_free = 0.3806 target = 0.085527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060074 restraints weight = 188618.147| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.03 r_work: 0.3059 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 20874 Z= 0.363 Angle : 0.734 8.439 28429 Z= 0.376 Chirality : 0.042 0.411 3179 Planarity : 0.006 0.075 3782 Dihedral : 7.636 85.435 3020 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.77 % Allowed : 9.76 % Favored : 88.47 % 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: -1.18 (0.16), residues: 2648 helix: 0.19 (0.15), residues: 1109 sheet: -2.40 (0.21), residues: 470 loop : -0.86 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 320 TYR 0.016 0.002 TYR A1194 PHE 0.018 0.002 PHE A1200 TRP 0.017 0.002 TRP A 922 HIS 0.008 0.002 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.36 (20869) covalent geometry : angle 0.73372 / 0.38 (28429) hydrogen bonds : bond 0.04739 / 3.14 ( 995) hydrogen bonds : angle 5.99508 / 4.34 ( 2796) Misc. bond : bond 0.00201 / 0.10 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.014 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: symmetry clash REVERT: A 394 LEU cc_start: 0.9195 (tp) cc_final: 0.8982 (tt) REVERT: A 757 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 849 ASN cc_start: 0.8269 (m110) cc_final: 0.7657 (m110) REVERT: A 865 TYR cc_start: 0.8783 (m-10) cc_final: 0.8171 (m-10) REVERT: A 1055 SER cc_start: 0.1676 (OUTLIER) cc_final: 0.1407 (t) REVERT: A 1073 MET cc_start: 0.4818 (mtp) cc_final: 0.4572 (mtm) REVERT: A 1300 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7948 (tm-30) REVERT: B 216 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.9073 (p90) REVERT: B 346 SER cc_start: 0.8866 (m) cc_final: 0.8411 (p) REVERT: B 428 GLU cc_start: 0.8884 (tp30) cc_final: 0.8581 (mm-30) REVERT: B 1505 CYS cc_start: 0.5543 (m) cc_final: 0.5139 (m) outliers start: 36 outliers final: 26 residues processed: 148 average time/residue: 0.4370 time to fit residues: 92.3537 Evaluate side-chains 136 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1230 ASP Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 250 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 161 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 239 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 HIS B 716 ASN B1223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.088267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.065876 restraints weight = 186548.671| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.83 r_work: 0.3162 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20874 Z= 0.137 Angle : 0.626 6.962 28429 Z= 0.313 Chirality : 0.039 0.383 3179 Planarity : 0.005 0.058 3782 Dihedral : 7.207 79.540 3020 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.28 % Allowed : 9.91 % Favored : 88.81 % 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: -0.77 (0.16), residues: 2648 helix: 0.55 (0.16), residues: 1117 sheet: -2.24 (0.22), residues: 457 loop : -0.68 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 320 TYR 0.023 0.002 TYR A1194 PHE 0.016 0.002 PHE B 372 TRP 0.018 0.001 TRP B 535 HIS 0.006 0.001 HIS B 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (20869) covalent geometry : angle 0.62644 / 0.31 (28429) hydrogen bonds : bond 0.03901 / 2.62 ( 995) hydrogen bonds : angle 5.64374 / 4.08 ( 2796) Misc. bond : bond 0.00041 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.879 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8493 (pt0) REVERT: A 849 ASN cc_start: 0.7923 (m110) cc_final: 0.7508 (m110) REVERT: A 865 TYR cc_start: 0.8619 (m-10) cc_final: 0.8129 (m-10) REVERT: A 1055 SER cc_start: 0.1850 (OUTLIER) cc_final: 0.1571 (t) REVERT: A 1073 MET cc_start: 0.5023 (mtp) cc_final: 0.4771 (mtm) REVERT: A 1145 MET cc_start: 0.6616 (ttt) cc_final: 0.5570 (ppp) REVERT: B 346 SER cc_start: 0.8626 (m) cc_final: 0.8352 (p) REVERT: B 480 ASP cc_start: 0.8210 (t0) cc_final: 0.7993 (t0) outliers start: 26 outliers final: 20 residues processed: 143 average time/residue: 0.3972 time to fit residues: 82.0663 Evaluate side-chains 136 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 161 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 211 optimal weight: 0.0870 chunk 51 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.087665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.065502 restraints weight = 187660.092| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.93 r_work: 0.3134 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20874 Z= 0.127 Angle : 0.597 6.744 28429 Z= 0.296 Chirality : 0.038 0.382 3179 Planarity : 0.005 0.053 3782 Dihedral : 6.874 83.646 3020 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.33 % Allowed : 10.25 % Favored : 88.42 % 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: -0.44 (0.17), residues: 2648 helix: 0.86 (0.16), residues: 1119 sheet: -2.15 (0.22), residues: 461 loop : -0.50 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.015 0.002 TYR B 865 PHE 0.014 0.002 PHE A1200 TRP 0.018 0.001 TRP B 535 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (20869) covalent geometry : angle 0.59675 / 0.30 (28429) hydrogen bonds : bond 0.03629 / 2.43 ( 995) hydrogen bonds : angle 5.44877 / 3.94 ( 2796) Misc. bond : bond 0.00066 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.065 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 849 ASN cc_start: 0.7935 (m110) cc_final: 0.7593 (m110) REVERT: A 865 TYR cc_start: 0.8530 (m-10) cc_final: 0.7972 (m-10) REVERT: A 1027 LEU cc_start: 0.2959 (OUTLIER) cc_final: 0.2526 (tp) REVERT: A 1055 SER cc_start: 0.1783 (OUTLIER) cc_final: 0.1519 (t) REVERT: A 1073 MET cc_start: 0.4964 (mtp) cc_final: 0.4700 (mtm) REVERT: A 1145 MET cc_start: 0.6533 (ttt) cc_final: 0.5410 (ppp) REVERT: B 346 SER cc_start: 0.8560 (m) cc_final: 0.8291 (p) REVERT: B 511 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8478 (mt-10) REVERT: B 736 VAL cc_start: 0.9605 (m) cc_final: 0.9329 (p) REVERT: B 924 ARG cc_start: 0.8732 (ttt-90) cc_final: 0.8347 (ttp80) outliers start: 27 outliers final: 19 residues processed: 153 average time/residue: 0.4262 time to fit residues: 94.1512 Evaluate side-chains 137 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1505 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 228 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.086932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.061677 restraints weight = 188295.627| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.13 r_work: 0.3096 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20874 Z= 0.168 Angle : 0.598 6.814 28429 Z= 0.296 Chirality : 0.038 0.387 3179 Planarity : 0.005 0.051 3782 Dihedral : 6.725 82.787 3016 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.43 % Allowed : 10.55 % Favored : 88.02 % 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: -0.39 (0.17), residues: 2648 helix: 0.96 (0.16), residues: 1120 sheet: -2.25 (0.21), residues: 478 loop : -0.42 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.014 0.002 TYR B 272 PHE 0.015 0.002 PHE B 372 TRP 0.015 0.001 TRP B 535 HIS 0.005 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (20869) covalent geometry : angle 0.59754 / 0.30 (28429) hydrogen bonds : bond 0.03627 / 2.43 ( 995) hydrogen bonds : angle 5.38998 / 3.88 ( 2796) Misc. bond : bond 0.00096 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.001 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 849 ASN cc_start: 0.7717 (m110) cc_final: 0.7349 (m110) REVERT: A 865 TYR cc_start: 0.8345 (m-10) cc_final: 0.7772 (m-10) REVERT: A 1027 LEU cc_start: 0.3147 (OUTLIER) cc_final: 0.2719 (tp) REVERT: A 1055 SER cc_start: 0.1731 (OUTLIER) cc_final: 0.1471 (t) REVERT: A 1073 MET cc_start: 0.4947 (mtp) cc_final: 0.4686 (mtm) REVERT: A 1145 MET cc_start: 0.6585 (ttt) cc_final: 0.5525 (ppp) REVERT: B 346 SER cc_start: 0.8488 (m) cc_final: 0.8191 (p) REVERT: B 924 ARG cc_start: 0.8628 (ttt-90) cc_final: 0.8209 (ttp80) outliers start: 29 outliers final: 24 residues processed: 144 average time/residue: 0.4244 time to fit residues: 87.1138 Evaluate side-chains 140 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 240 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 193 optimal weight: 3.9990 chunk 257 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1179 GLN B1223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.085431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.061364 restraints weight = 189259.487| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.19 r_work: 0.3036 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20874 Z= 0.264 Angle : 0.638 7.211 28429 Z= 0.320 Chirality : 0.039 0.394 3179 Planarity : 0.005 0.051 3782 Dihedral : 6.795 85.034 3016 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.53 % Allowed : 10.79 % Favored : 87.68 % 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: -0.49 (0.17), residues: 2648 helix: 0.92 (0.16), residues: 1118 sheet: -2.37 (0.21), residues: 482 loop : -0.50 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.013 0.002 TYR B 272 PHE 0.015 0.002 PHE B 560 TRP 0.013 0.001 TRP B 535 HIS 0.004 0.001 HIS B 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.26 (20869) covalent geometry : angle 0.63810 / 0.32 (28429) hydrogen bonds : bond 0.03887 / 2.59 ( 995) hydrogen bonds : angle 5.49705 / 3.95 ( 2796) Misc. bond : bond 0.00148 / 0.07 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.923 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 946 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8516 (pt0) REVERT: A 1027 LEU cc_start: 0.3182 (OUTLIER) cc_final: 0.2771 (tp) REVERT: A 1055 SER cc_start: 0.1433 (OUTLIER) cc_final: 0.1209 (t) REVERT: A 1073 MET cc_start: 0.4953 (mtp) cc_final: 0.4707 (mtm) REVERT: A 1145 MET cc_start: 0.6668 (ttt) cc_final: 0.5531 (ppp) REVERT: A 1300 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7882 (tm-30) REVERT: B 346 SER cc_start: 0.8683 (m) cc_final: 0.8340 (p) outliers start: 31 outliers final: 26 residues processed: 138 average time/residue: 0.4349 time to fit residues: 85.3011 Evaluate side-chains 131 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 946 GLN Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 239 optimal weight: 30.0000 chunk 163 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.086231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.060788 restraints weight = 189667.997| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.14 r_work: 0.3070 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20874 Z= 0.198 Angle : 0.608 7.140 28429 Z= 0.302 Chirality : 0.038 0.389 3179 Planarity : 0.005 0.050 3782 Dihedral : 6.664 81.265 3016 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.23 % Allowed : 11.58 % Favored : 87.19 % 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: -0.44 (0.17), residues: 2648 helix: 0.97 (0.16), residues: 1120 sheet: -2.43 (0.21), residues: 479 loop : -0.45 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.021 0.002 TYR B 865 PHE 0.015 0.002 PHE B 372 TRP 0.015 0.001 TRP B 535 HIS 0.005 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (20869) covalent geometry : angle 0.60815 / 0.30 (28429) hydrogen bonds : bond 0.03685 / 2.47 ( 995) hydrogen bonds : angle 5.42273 / 3.90 ( 2796) Misc. bond : bond 0.00105 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.858 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 1027 LEU cc_start: 0.3052 (OUTLIER) cc_final: 0.2634 (tp) REVERT: A 1055 SER cc_start: 0.1573 (OUTLIER) cc_final: 0.1347 (t) REVERT: A 1073 MET cc_start: 0.4915 (mtp) cc_final: 0.4661 (mtm) REVERT: A 1145 MET cc_start: 0.6620 (ttt) cc_final: 0.5464 (ppp) REVERT: A 1300 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7870 (tm-30) REVERT: B 50 MET cc_start: 0.8678 (mtp) cc_final: 0.8447 (mtp) REVERT: B 346 SER cc_start: 0.8643 (m) cc_final: 0.8281 (p) outliers start: 25 outliers final: 23 residues processed: 132 average time/residue: 0.4348 time to fit residues: 82.4943 Evaluate side-chains 127 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 147 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 237 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.086012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.060585 restraints weight = 188634.948| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.12 r_work: 0.3064 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20874 Z= 0.212 Angle : 0.612 7.143 28429 Z= 0.305 Chirality : 0.039 0.389 3179 Planarity : 0.005 0.050 3782 Dihedral : 6.644 83.563 3016 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.23 % Allowed : 11.83 % Favored : 86.94 % 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: -0.45 (0.17), residues: 2648 helix: 1.01 (0.16), residues: 1114 sheet: -2.46 (0.21), residues: 474 loop : -0.49 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.017 0.002 TYR B 865 PHE 0.014 0.002 PHE B 560 TRP 0.019 0.001 TRP B1041 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 (20869) covalent geometry : angle 0.61234 / 0.31 (28429) hydrogen bonds : bond 0.03685 / 2.46 ( 995) hydrogen bonds : angle 5.41999 / 3.89 ( 2796) Misc. bond : bond 0.00111 / 0.05 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.070 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: A 1027 LEU cc_start: 0.2986 (OUTLIER) cc_final: 0.2577 (tp) REVERT: A 1055 SER cc_start: 0.1601 (OUTLIER) cc_final: 0.1379 (t) REVERT: A 1073 MET cc_start: 0.4913 (mtp) cc_final: 0.4660 (mtm) REVERT: A 1145 MET cc_start: 0.6616 (ttt) cc_final: 0.5462 (ppp) REVERT: A 1300 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7868 (tm-30) REVERT: B 346 SER cc_start: 0.8689 (m) cc_final: 0.8319 (p) outliers start: 25 outliers final: 23 residues processed: 127 average time/residue: 0.4994 time to fit residues: 90.2438 Evaluate side-chains 128 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 153 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 217 optimal weight: 0.2980 chunk 111 optimal weight: 9.9990 chunk 219 optimal weight: 0.0870 chunk 173 optimal weight: 5.9990 overall best weight: 2.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 GLN B1223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.086437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.060926 restraints weight = 189779.058| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.27 r_work: 0.3070 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20874 Z= 0.174 Angle : 0.598 7.043 28429 Z= 0.296 Chirality : 0.039 0.383 3179 Planarity : 0.005 0.050 3782 Dihedral : 6.606 82.751 3016 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.28 % Allowed : 11.83 % Favored : 86.89 % 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: -0.37 (0.17), residues: 2648 helix: 1.09 (0.16), residues: 1113 sheet: -2.44 (0.21), residues: 472 loop : -0.47 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.015 0.002 TYR B 865 PHE 0.014 0.002 PHE B 560 TRP 0.030 0.001 TRP B1041 HIS 0.004 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (20869) covalent geometry : angle 0.59849 / 0.30 (28429) hydrogen bonds : bond 0.03556 / 2.39 ( 995) hydrogen bonds : angle 5.36376 / 3.85 ( 2796) Misc. bond : bond 0.00084 / 0.04 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8864.07 seconds wall clock time: 150 minutes 50.17 seconds (9050.17 seconds total)