Starting phenix.real_space_refine on Sat Feb 24 03:13:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emy_31198/02_2024/7emy_31198_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emy_31198/02_2024/7emy_31198.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emy_31198/02_2024/7emy_31198_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emy_31198/02_2024/7emy_31198_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emy_31198/02_2024/7emy_31198_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emy_31198/02_2024/7emy_31198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emy_31198/02_2024/7emy_31198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emy_31198/02_2024/7emy_31198_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7emy_31198/02_2024/7emy_31198_neut_trim_updated.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 70 5.16 5 C 12924 2.51 5 N 3778 2.21 5 O 3740 1.98 5 H 20502 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 831": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41020 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 20444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 20444 Classifications: {'peptide': 1334} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 1248} Chain: "B" Number of atoms: 20444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 20444 Classifications: {'peptide': 1334} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 1248} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' MG': 1, 'PNS': 1, 'SAL': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'NH1NOTPRO': 1, 'rna2p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Planarities with less than four sites: {'SAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' MG': 1, 'PNS': 1, 'SAL': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'NH1NOTPRO': 1, 'rna2p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Planarities with less than four sites: {'SAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N PHE B 741 " occ=0.50 ... (18 atoms not shown) pdb=" HZ PHE B 741 " occ=0.50 residue: pdb=" C1 SAL A1502 " occ=0.00 ... (7 atoms not shown) pdb=" O2 SAL A1502 " occ=0.00 residue: pdb=" C1 SAL B1502 " occ=0.00 ... (7 atoms not shown) pdb=" O2 SAL B1502 " occ=0.00 Time building chain proxies: 18.19, per 1000 atoms: 0.44 Number of scatterers: 41020 At special positions: 0 Unit cell: (160, 129, 139, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 70 16.00 P 4 15.00 Mg 2 11.99 O 3740 8.00 N 3778 7.00 C 12924 6.00 H 20502 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.88 Conformation dependent library (CDL) restraints added in 4.5 seconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 30 sheets defined 41.2% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.95 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 87 removed outlier: 4.194A pdb=" N ARG A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.654A pdb=" N ARG A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 241 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 269 through 297 removed outlier: 5.240A pdb=" N GLU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 404 through 423 removed outlier: 4.029A pdb=" N ASP A 420 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.865A pdb=" N ALA A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 522 Processing helix chain 'A' and resid 535 through 545 Processing helix chain 'A' and resid 558 through 566 Processing helix chain 'A' and resid 582 through 598 Processing helix chain 'A' and resid 615 through 626 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 711 through 725 removed outlier: 3.869A pdb=" N LEU A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 removed outlier: 3.587A pdb=" N LEU A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 749 " --> pdb=" O PHE A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 769 through 779 Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 956 through 964 Processing helix chain 'A' and resid 1009 through 1032 removed outlier: 4.155A pdb=" N ALA A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'A' and resid 1035 through 1047 removed outlier: 4.008A pdb=" N ALA A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1067 through 1082 Processing helix chain 'A' and resid 1088 through 1092 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1108 through 1116 Processing helix chain 'A' and resid 1121 through 1124 No H-bonds generated for 'chain 'A' and resid 1121 through 1124' Processing helix chain 'A' and resid 1139 through 1148 removed outlier: 5.704A pdb=" N ALA A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER A1147 " --> pdb=" O GLN A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1171 Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1188 through 1190 No H-bonds generated for 'chain 'A' and resid 1188 through 1190' Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1236 through 1245 removed outlier: 3.559A pdb=" N LEU A1240 " --> pdb=" O PRO A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1251 No H-bonds generated for 'chain 'A' and resid 1249 through 1251' Processing helix chain 'A' and resid 1255 through 1264 Processing helix chain 'A' and resid 1292 through 1302 Processing helix chain 'A' and resid 1328 through 1338 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 46 through 59 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 74 through 87 removed outlier: 4.194A pdb=" N ARG B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.687A pdb=" N ARG B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 155 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 241 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 269 through 297 removed outlier: 5.240A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 327 through 339 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 404 through 423 removed outlier: 4.041A pdb=" N ASP B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 458 through 463 removed outlier: 3.866A pdb=" N ALA B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 522 Processing helix chain 'B' and resid 535 through 545 Processing helix chain 'B' and resid 558 through 566 Processing helix chain 'B' and resid 582 through 598 Processing helix chain 'B' and resid 615 through 626 Processing helix chain 'B' and resid 640 through 650 Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 711 through 725 removed outlier: 3.862A pdb=" N LEU B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 753 removed outlier: 3.723A pdb=" N LEU B 748 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE B 749 " --> pdb=" O PHE B 746 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY B 750 " --> pdb=" O ASP B 747 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 751 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 752 " --> pdb=" O PHE B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 769 through 779 Processing helix chain 'B' and resid 788 through 795 Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 907 through 913 Processing helix chain 'B' and resid 956 through 964 Processing helix chain 'B' and resid 1009 through 1032 removed outlier: 4.155A pdb=" N ALA B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Proline residue: B1030 - end of helix Processing helix chain 'B' and resid 1035 through 1047 removed outlier: 4.008A pdb=" N ALA B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1063 Processing helix chain 'B' and resid 1067 through 1082 Processing helix chain 'B' and resid 1088 through 1092 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1108 through 1116 Processing helix chain 'B' and resid 1121 through 1124 No H-bonds generated for 'chain 'B' and resid 1121 through 1124' Processing helix chain 'B' and resid 1139 through 1148 removed outlier: 5.704A pdb=" N ALA B1146 " --> pdb=" O ASP B1142 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER B1147 " --> pdb=" O GLN B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1171 Processing helix chain 'B' and resid 1182 through 1184 No H-bonds generated for 'chain 'B' and resid 1182 through 1184' Processing helix chain 'B' and resid 1188 through 1190 No H-bonds generated for 'chain 'B' and resid 1188 through 1190' Processing helix chain 'B' and resid 1203 through 1205 No H-bonds generated for 'chain 'B' and resid 1203 through 1205' Processing helix chain 'B' and resid 1209 through 1219 Processing helix chain 'B' and resid 1236 through 1245 removed outlier: 3.558A pdb=" N LEU B1240 " --> pdb=" O PRO B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1249 through 1251 No H-bonds generated for 'chain 'B' and resid 1249 through 1251' Processing helix chain 'B' and resid 1255 through 1264 Processing helix chain 'B' and resid 1292 through 1302 Processing helix chain 'B' and resid 1328 through 1338 Processing sheet with id= A, first strand: chain 'A' and resid 469 through 472 removed outlier: 3.551A pdb=" N GLU A 227 " --> pdb=" O MET A 223 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 221 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 161 through 164 Processing sheet with id= C, first strand: chain 'A' and resid 318 through 325 Processing sheet with id= D, first strand: chain 'A' and resid 364 through 372 removed outlier: 3.562A pdb=" N LEU A 394 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 630 through 633 removed outlier: 6.470A pdb=" N LEU A 654 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N SER A 610 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 656 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR A 657 " --> pdb=" O PRO A 667 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU A 669 " --> pdb=" O THR A 657 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.547A pdb=" N SER A 757 " --> pdb=" O LEU A 733 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 783 through 786 removed outlier: 6.870A pdb=" N ALA A 809 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N SER A 786 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 811 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN A 849 " --> pdb=" O GLY A 839 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 872 through 877 Processing sheet with id= I, first strand: chain 'A' and resid 915 through 917 Processing sheet with id= J, first strand: chain 'A' and resid 929 through 931 Processing sheet with id= K, first strand: chain 'A' and resid 946 through 949 Processing sheet with id= L, first strand: chain 'A' and resid 1153 through 1157 removed outlier: 6.301A pdb=" N LEU A1128 " --> pdb=" O GLU A1154 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR A1156 " --> pdb=" O LEU A1128 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A1130 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG A1196 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG A1225 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N SER A1199 " --> pdb=" O ARG A1225 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A1227 " --> pdb=" O SER A1199 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.556A pdb=" N VAL A 580 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 691 through 697 removed outlier: 6.734A pdb=" N VAL A 709 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 694 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL A 707 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR A 696 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LYS A 705 " --> pdb=" O TYR A 696 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 969 through 976 removed outlier: 6.679A pdb=" N VAL A 989 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 972 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 987 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA A 974 " --> pdb=" O GLY A 985 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY A 985 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 469 through 472 removed outlier: 3.551A pdb=" N GLU B 227 " --> pdb=" O MET B 223 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 221 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= R, first strand: chain 'B' and resid 318 through 325 Processing sheet with id= S, first strand: chain 'B' and resid 364 through 372 removed outlier: 3.562A pdb=" N LEU B 394 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.429A pdb=" N LEU B 654 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 657 " --> pdb=" O PRO B 667 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU B 669 " --> pdb=" O THR B 657 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 732 through 734 removed outlier: 6.465A pdb=" N SER B 757 " --> pdb=" O LEU B 733 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'B' and resid 783 through 786 removed outlier: 6.911A pdb=" N ALA B 809 " --> pdb=" O TRP B 784 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N SER B 786 " --> pdb=" O ALA B 809 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 811 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 849 " --> pdb=" O GLY B 839 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 872 through 877 Processing sheet with id= X, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= Y, first strand: chain 'B' and resid 929 through 931 Processing sheet with id= Z, first strand: chain 'B' and resid 946 through 949 Processing sheet with id= AA, first strand: chain 'B' and resid 1153 through 1157 removed outlier: 6.300A pdb=" N LEU B1128 " --> pdb=" O GLU B1154 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR B1156 " --> pdb=" O LEU B1128 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL B1130 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG B1196 " --> pdb=" O ALA B1131 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG B1225 " --> pdb=" O VAL B1197 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N SER B1199 " --> pdb=" O ARG B1225 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU B1227 " --> pdb=" O SER B1199 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 571 through 574 removed outlier: 6.488A pdb=" N VAL B 580 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 691 through 697 removed outlier: 6.750A pdb=" N VAL B 709 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 694 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL B 707 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR B 696 " --> pdb=" O LYS B 705 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS B 705 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 969 through 976 removed outlier: 6.677A pdb=" N VAL B 989 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA B 972 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 987 " --> pdb=" O ALA B 972 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA B 974 " --> pdb=" O GLY B 985 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY B 985 " --> pdb=" O ALA B 974 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2301 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: 18.00 Time building geometry restraints manager: 36.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10405 1.04 - 1.24: 13106 1.24 - 1.44: 8149 1.44 - 1.64: 9690 1.64 - 1.84: 94 Bond restraints: 41444 Sorted by residual: bond pdb=" CA ALA B 442 " pdb=" CB ALA B 442 " ideal model delta sigma weight residual 1.529 1.422 0.108 1.13e-02 7.83e+03 9.07e+01 bond pdb=" CA ALA A 442 " pdb=" CB ALA A 442 " ideal model delta sigma weight residual 1.529 1.422 0.107 1.13e-02 7.83e+03 8.95e+01 bond pdb=" ND1 HIS B 481 " pdb=" CE1 HIS B 481 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.92e+01 bond pdb=" ND1 HIS B 156 " pdb=" CE1 HIS B 156 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.92e+01 bond pdb=" ND1 HIS B 880 " pdb=" CE1 HIS B 880 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.91e+01 ... (remaining 41439 not shown) Histogram of bond angle deviations from ideal: 78.55 - 90.19: 12 90.19 - 101.83: 103 101.83 - 113.46: 46622 113.46 - 125.10: 26156 125.10 - 136.73: 2107 Bond angle restraints: 75000 Sorted by residual: angle pdb="HG11 VAL A1229 " pdb=" CG1 VAL A1229 " pdb="HG12 VAL A1229 " ideal model delta sigma weight residual 110.00 78.55 31.45 3.00e+00 1.11e-01 1.10e+02 angle pdb=" CA ALA A 996 " pdb=" CB ALA A 996 " pdb=" HB3 ALA A 996 " ideal model delta sigma weight residual 109.00 78.87 30.13 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CA ALA A1123 " pdb=" CB ALA A1123 " pdb=" HB3 ALA A1123 " ideal model delta sigma weight residual 109.00 79.08 29.92 3.00e+00 1.11e-01 9.94e+01 angle pdb=" CA ALA A 996 " pdb=" CB ALA A 996 " pdb=" HB1 ALA A 996 " ideal model delta sigma weight residual 109.00 79.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" CA ALA A1123 " pdb=" CB ALA A1123 " pdb=" HB2 ALA A1123 " ideal model delta sigma weight residual 109.00 79.52 29.48 3.00e+00 1.11e-01 9.66e+01 ... (remaining 74995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.85: 18141 22.85 - 45.69: 776 45.69 - 68.54: 381 68.54 - 91.38: 44 91.38 - 114.23: 2 Dihedral angle restraints: 19344 sinusoidal: 10754 harmonic: 8590 Sorted by residual: dihedral pdb=" C1' AMP A1504 " pdb=" C4' AMP A1504 " pdb=" O4' AMP A1504 " pdb=" C5' AMP A1504 " ideal model delta sinusoidal sigma weight residual -123.00 -79.69 -43.31 1 8.00e+00 1.56e-02 4.09e+01 dihedral pdb=" C1' AMP B1504 " pdb=" C4' AMP B1504 " pdb=" O4' AMP B1504 " pdb=" C5' AMP B1504 " ideal model delta sinusoidal sigma weight residual -123.00 -79.97 -43.03 1 8.00e+00 1.56e-02 4.04e+01 dihedral pdb=" CA SER A 786 " pdb=" C SER A 786 " pdb=" N ALA A 787 " pdb=" CA ALA A 787 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 19341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1810 0.152 - 0.305: 81 0.305 - 0.457: 166 0.457 - 0.609: 886 0.609 - 0.761: 259 Chirality restraints: 3202 Sorted by residual: chirality pdb=" CG LEU B 483 " pdb=" CB LEU B 483 " pdb=" CD1 LEU B 483 " pdb=" CD2 LEU B 483 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" CG LEU A 483 " pdb=" CB LEU A 483 " pdb=" CD1 LEU A 483 " pdb=" CD2 LEU A 483 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CG LEU A 574 " pdb=" CB LEU A 574 " pdb=" CD1 LEU A 574 " pdb=" CD2 LEU A 574 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.40e+01 ... (remaining 3199 not shown) Planarity restraints: 6292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AMP A1504 " -0.348 2.00e-02 2.50e+03 1.48e-01 6.06e+02 pdb=" C2 AMP A1504 " 0.053 2.00e-02 2.50e+03 pdb=" C4 AMP A1504 " 0.110 2.00e-02 2.50e+03 pdb=" C5 AMP A1504 " 0.082 2.00e-02 2.50e+03 pdb=" C6 AMP A1504 " -0.034 2.00e-02 2.50e+03 pdb=" C8 AMP A1504 " 0.104 2.00e-02 2.50e+03 pdb=" N1 AMP A1504 " -0.102 2.00e-02 2.50e+03 pdb=" N3 AMP A1504 " 0.174 2.00e-02 2.50e+03 pdb=" N6 AMP A1504 " -0.188 2.00e-02 2.50e+03 pdb=" N7 AMP A1504 " 0.095 2.00e-02 2.50e+03 pdb=" N9 AMP A1504 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AMP B1504 " 0.324 2.00e-02 2.50e+03 1.39e-01 5.31e+02 pdb=" C2 AMP B1504 " -0.054 2.00e-02 2.50e+03 pdb=" C4 AMP B1504 " -0.102 2.00e-02 2.50e+03 pdb=" C5 AMP B1504 " -0.074 2.00e-02 2.50e+03 pdb=" C6 AMP B1504 " 0.032 2.00e-02 2.50e+03 pdb=" C8 AMP B1504 " -0.100 2.00e-02 2.50e+03 pdb=" N1 AMP B1504 " 0.095 2.00e-02 2.50e+03 pdb=" N3 AMP B1504 " -0.162 2.00e-02 2.50e+03 pdb=" N6 AMP B1504 " 0.178 2.00e-02 2.50e+03 pdb=" N7 AMP B1504 " -0.091 2.00e-02 2.50e+03 pdb=" N9 AMP B1504 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 953 " -0.172 9.50e-02 1.11e+02 1.58e-01 4.89e+02 pdb=" NE ARG B 953 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 953 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG B 953 " 0.152 2.00e-02 2.50e+03 pdb=" NH2 ARG B 953 " 0.023 2.00e-02 2.50e+03 pdb="HH11 ARG B 953 " -0.309 2.00e-02 2.50e+03 pdb="HH12 ARG B 953 " 0.203 2.00e-02 2.50e+03 pdb="HH21 ARG B 953 " -0.054 2.00e-02 2.50e+03 pdb="HH22 ARG B 953 " -0.147 2.00e-02 2.50e+03 ... (remaining 6289 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 1764 2.10 - 2.73: 73899 2.73 - 3.35: 132411 3.35 - 3.98: 173398 3.98 - 4.60: 265483 Nonbonded interactions: 646955 Sorted by model distance: nonbonded pdb="HE22 GLN A 538 " pdb=" O GLN B 919 " model vdw 1.477 1.850 nonbonded pdb=" H LEU A 887 " pdb=" O TYR A 931 " model vdw 1.496 1.850 nonbonded pdb=" O ALA B 649 " pdb="HD21 ASN B 905 " model vdw 1.513 1.850 nonbonded pdb=" O ALA A 649 " pdb="HD21 ASN A 905 " model vdw 1.513 1.850 nonbonded pdb=" H ALA A 66 " pdb=" OD2 ASP A 420 " model vdw 1.514 1.850 ... (remaining 646950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.690 Extract box with map and model: 5.530 Check model and map are aligned: 0.560 Set scattering table: 0.360 Process input model: 136.350 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.150 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.037 0.150 20942 Z= 2.501 Angle : 2.792 17.993 28538 Z= 1.814 Chirality : 0.360 0.761 3202 Planarity : 0.012 0.148 3796 Dihedral : 12.070 114.229 7726 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.46 % Rotamer: Outliers : 0.88 % Allowed : 3.53 % Favored : 95.59 % Cbeta Deviations : 19.21 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.16), residues: 2664 helix: -0.18 (0.14), residues: 1088 sheet: -1.40 (0.23), residues: 478 loop : -0.15 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.176 0.013 TRP A 816 HIS 0.026 0.003 HIS A 130 PHE 0.074 0.013 PHE B 372 TYR 0.194 0.025 TYR A 923 ARG 0.013 0.001 ARG B 953 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 244 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8936 (tpt) cc_final: 0.8726 (tpt) REVERT: A 1157 LEU cc_start: 0.9108 (mt) cc_final: 0.8874 (mt) REVERT: A 1185 LEU cc_start: 0.8147 (tp) cc_final: 0.7913 (mt) REVERT: B 346 SER cc_start: 0.8810 (m) cc_final: 0.8392 (p) REVERT: B 368 ASN cc_start: 0.7693 (m-40) cc_final: 0.7445 (m110) REVERT: B 1307 MET cc_start: 0.8504 (ptp) cc_final: 0.8276 (ptm) outliers start: 18 outliers final: 5 residues processed: 259 average time/residue: 3.5568 time to fit residues: 1030.7119 Evaluate side-chains 126 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20942 Z= 0.233 Angle : 0.625 9.120 28538 Z= 0.311 Chirality : 0.038 0.154 3202 Planarity : 0.005 0.057 3796 Dihedral : 7.251 101.614 3019 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.13 % Allowed : 8.14 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2664 helix: 1.20 (0.15), residues: 1096 sheet: -1.02 (0.25), residues: 440 loop : -0.05 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 535 HIS 0.009 0.001 HIS A 130 PHE 0.013 0.001 PHE A 560 TYR 0.018 0.002 TYR A 51 ARG 0.009 0.000 ARG B 726 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 3.102 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: A 368 ASN cc_start: 0.8100 (m-40) cc_final: 0.7884 (m-40) REVERT: B 368 ASN cc_start: 0.7819 (m-40) cc_final: 0.7524 (m110) REVERT: B 1307 MET cc_start: 0.8601 (ptp) cc_final: 0.8395 (ptm) outliers start: 23 outliers final: 7 residues processed: 149 average time/residue: 2.6916 time to fit residues: 464.6834 Evaluate side-chains 115 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 241 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 239 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20942 Z= 0.341 Angle : 0.611 8.673 28538 Z= 0.303 Chirality : 0.038 0.137 3202 Planarity : 0.005 0.052 3796 Dihedral : 6.874 98.825 3016 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.98 % Allowed : 9.46 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2664 helix: 1.46 (0.16), residues: 1102 sheet: -1.39 (0.23), residues: 494 loop : 0.05 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1140 HIS 0.006 0.001 HIS B 375 PHE 0.018 0.002 PHE B 372 TYR 0.018 0.002 TYR B 696 ARG 0.014 0.001 ARG B 826 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.7998 (m-40) cc_final: 0.7762 (m-40) REVERT: A 989 VAL cc_start: 0.8586 (t) cc_final: 0.7864 (t) REVERT: A 1237 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 1335 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8124 (mtp) REVERT: B 223 MET cc_start: 0.8457 (mmm) cc_final: 0.8248 (mmm) REVERT: B 503 GLU cc_start: 0.6587 (tp30) cc_final: 0.6363 (tp30) REVERT: B 1307 MET cc_start: 0.8629 (ptp) cc_final: 0.8380 (ptm) outliers start: 20 outliers final: 8 residues processed: 118 average time/residue: 2.5817 time to fit residues: 357.5029 Evaluate side-chains 103 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 20.0000 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 242 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20942 Z= 0.295 Angle : 0.582 7.735 28538 Z= 0.287 Chirality : 0.037 0.143 3202 Planarity : 0.004 0.058 3796 Dihedral : 6.618 102.948 3014 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.03 % Allowed : 9.95 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.17), residues: 2664 helix: 1.56 (0.16), residues: 1102 sheet: -1.37 (0.23), residues: 494 loop : 0.11 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1140 HIS 0.005 0.001 HIS A 375 PHE 0.014 0.001 PHE B 372 TYR 0.014 0.002 TYR A 290 ARG 0.010 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1237 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8182 (mt) REVERT: A 1335 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8196 (mtp) REVERT: B 223 MET cc_start: 0.8470 (mmm) cc_final: 0.8252 (mmm) REVERT: B 1307 MET cc_start: 0.8623 (ptp) cc_final: 0.8361 (ptm) outliers start: 21 outliers final: 15 residues processed: 118 average time/residue: 2.4310 time to fit residues: 337.7844 Evaluate side-chains 111 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.4980 chunk 145 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20942 Z= 0.293 Angle : 0.575 6.772 28538 Z= 0.283 Chirality : 0.037 0.147 3202 Planarity : 0.004 0.042 3796 Dihedral : 6.474 103.021 3014 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.98 % Allowed : 10.00 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2664 helix: 1.61 (0.16), residues: 1104 sheet: -1.41 (0.23), residues: 494 loop : 0.12 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1140 HIS 0.006 0.001 HIS A 375 PHE 0.013 0.001 PHE B 372 TYR 0.014 0.002 TYR A 290 ARG 0.010 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1237 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8212 (mt) REVERT: A 1335 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8247 (mtp) REVERT: B 223 MET cc_start: 0.8431 (mmm) cc_final: 0.8201 (mmm) REVERT: B 503 GLU cc_start: 0.7055 (tp30) cc_final: 0.6821 (tp30) REVERT: B 1307 MET cc_start: 0.8624 (ptp) cc_final: 0.8362 (ptm) outliers start: 20 outliers final: 9 residues processed: 116 average time/residue: 2.6301 time to fit residues: 356.9959 Evaluate side-chains 102 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 257 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 85 optimal weight: 0.0170 chunk 135 optimal weight: 9.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20942 Z= 0.207 Angle : 0.553 6.698 28538 Z= 0.269 Chirality : 0.037 0.157 3202 Planarity : 0.004 0.065 3796 Dihedral : 6.268 103.266 3012 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.98 % Allowed : 10.44 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2664 helix: 1.70 (0.16), residues: 1104 sheet: -1.28 (0.24), residues: 474 loop : 0.15 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1140 HIS 0.005 0.001 HIS A 375 PHE 0.012 0.001 PHE B 560 TYR 0.013 0.002 TYR A 290 ARG 0.010 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8656 (tp) REVERT: A 1237 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8206 (mt) REVERT: A 1335 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8196 (mtp) REVERT: B 223 MET cc_start: 0.8390 (mmm) cc_final: 0.8154 (mmm) REVERT: B 1307 MET cc_start: 0.8595 (ptp) cc_final: 0.8321 (ptm) outliers start: 20 outliers final: 10 residues processed: 109 average time/residue: 2.3861 time to fit residues: 309.7176 Evaluate side-chains 105 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20942 Z= 0.370 Angle : 0.593 6.688 28538 Z= 0.291 Chirality : 0.037 0.153 3202 Planarity : 0.004 0.053 3796 Dihedral : 6.315 99.414 3012 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.88 % Allowed : 10.93 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2664 helix: 1.64 (0.16), residues: 1104 sheet: -1.49 (0.23), residues: 500 loop : 0.13 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1140 HIS 0.005 0.001 HIS A 375 PHE 0.015 0.002 PHE B 372 TYR 0.015 0.002 TYR B 696 ARG 0.009 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 3.133 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: A 392 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8748 (tp) REVERT: A 1237 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8245 (mt) REVERT: A 1335 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: B 223 MET cc_start: 0.8443 (mmm) cc_final: 0.8167 (mmm) REVERT: B 1109 ARG cc_start: 0.7803 (tpt170) cc_final: 0.7576 (tpm170) REVERT: B 1307 MET cc_start: 0.8601 (ptp) cc_final: 0.8329 (ptm) outliers start: 18 outliers final: 9 residues processed: 107 average time/residue: 2.1824 time to fit residues: 281.5556 Evaluate side-chains 100 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 162 optimal weight: 0.0670 chunk 174 optimal weight: 3.9990 chunk 126 optimal weight: 30.0000 chunk 23 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20942 Z= 0.176 Angle : 0.548 6.507 28538 Z= 0.266 Chirality : 0.037 0.164 3202 Planarity : 0.004 0.049 3796 Dihedral : 6.164 100.685 3012 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.78 % Allowed : 10.88 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2664 helix: 1.74 (0.16), residues: 1102 sheet: -1.34 (0.24), residues: 482 loop : 0.23 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1140 HIS 0.004 0.001 HIS A 375 PHE 0.013 0.001 PHE B 560 TYR 0.013 0.002 TYR A 290 ARG 0.007 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1237 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8239 (mt) REVERT: A 1335 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8165 (mtp) REVERT: B 223 MET cc_start: 0.8363 (mmm) cc_final: 0.8105 (mmm) REVERT: B 1109 ARG cc_start: 0.7781 (tpt170) cc_final: 0.7573 (tpm170) REVERT: B 1307 MET cc_start: 0.8578 (ptp) cc_final: 0.8288 (ptm) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 2.2473 time to fit residues: 290.8678 Evaluate side-chains 103 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 224 optimal weight: 0.5980 chunk 238 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 104 optimal weight: 0.2980 chunk 187 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20942 Z= 0.230 Angle : 0.550 6.862 28538 Z= 0.267 Chirality : 0.037 0.164 3202 Planarity : 0.004 0.046 3796 Dihedral : 6.119 99.585 3012 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.74 % Allowed : 11.08 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2664 helix: 1.87 (0.16), residues: 1090 sheet: -1.36 (0.24), residues: 482 loop : 0.24 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B1140 HIS 0.004 0.001 HIS A 375 PHE 0.012 0.001 PHE B 560 TYR 0.012 0.002 TYR B 290 ARG 0.006 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1237 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8200 (mt) REVERT: A 1335 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8178 (mtp) REVERT: B 223 MET cc_start: 0.8380 (mmm) cc_final: 0.8118 (mmm) REVERT: B 1307 MET cc_start: 0.8585 (ptp) cc_final: 0.8295 (ptm) outliers start: 15 outliers final: 9 residues processed: 104 average time/residue: 2.1029 time to fit residues: 266.4664 Evaluate side-chains 101 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 265 optimal weight: 0.0470 chunk 243 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 163 optimal weight: 0.0000 chunk 129 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20942 Z= 0.231 Angle : 0.552 6.356 28538 Z= 0.267 Chirality : 0.037 0.140 3202 Planarity : 0.004 0.046 3796 Dihedral : 6.084 99.402 3012 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.69 % Allowed : 11.18 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2664 helix: 1.89 (0.16), residues: 1090 sheet: -1.35 (0.24), residues: 482 loop : 0.26 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B1140 HIS 0.004 0.001 HIS A 375 PHE 0.012 0.001 PHE B 560 TYR 0.013 0.002 TYR A 290 ARG 0.006 0.000 ARG B 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1237 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8197 (mt) REVERT: A 1335 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8175 (mtp) REVERT: B 223 MET cc_start: 0.8387 (mmm) cc_final: 0.8122 (mmm) REVERT: B 1109 ARG cc_start: 0.7821 (tpt170) cc_final: 0.7572 (tpm170) REVERT: B 1307 MET cc_start: 0.8577 (ptp) cc_final: 0.8282 (ptm) outliers start: 14 outliers final: 11 residues processed: 106 average time/residue: 2.1337 time to fit residues: 274.4155 Evaluate side-chains 101 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 954 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.107720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072117 restraints weight = 138524.942| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.81 r_work: 0.3122 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20942 Z= 0.235 Angle : 0.554 6.956 28538 Z= 0.268 Chirality : 0.037 0.138 3202 Planarity : 0.004 0.045 3796 Dihedral : 6.051 99.134 3012 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.78 % Allowed : 11.13 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2664 helix: 1.90 (0.16), residues: 1088 sheet: -1.35 (0.24), residues: 482 loop : 0.24 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B1140 HIS 0.003 0.001 HIS A 130 PHE 0.012 0.001 PHE B 560 TYR 0.012 0.002 TYR A 290 ARG 0.006 0.000 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10510.65 seconds wall clock time: 186 minutes 37.76 seconds (11197.76 seconds total)