Starting phenix.real_space_refine on Fri May 17 04:31:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2l_43751/05_2024/8w2l_43751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2l_43751/05_2024/8w2l_43751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2l_43751/05_2024/8w2l_43751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2l_43751/05_2024/8w2l_43751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2l_43751/05_2024/8w2l_43751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w2l_43751/05_2024/8w2l_43751.pdb" } resolution = 2.45 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= 0.104 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 Ca 1 9.91 5 P 48 5.49 5 S 196 5.16 5 Cl 4 4.86 5 C 23688 2.51 5 N 5508 2.21 5 O 6352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 530": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 750": "NH1" <-> "NH2" Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 902": "NH1" <-> "NH2" Residue "A ARG 942": "NH1" <-> "NH2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 1018": "NH1" <-> "NH2" Residue "A ARG 1198": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B ARG 525": "NH1" <-> "NH2" Residue "B ARG 530": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 639": "NH1" <-> "NH2" Residue "B ARG 699": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 750": "NH1" <-> "NH2" Residue "B TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 902": "NH1" <-> "NH2" Residue "B ARG 942": "NH1" <-> "NH2" Residue "B ARG 962": "NH1" <-> "NH2" Residue "B ARG 975": "NH1" <-> "NH2" Residue "B ARG 1018": "NH1" <-> "NH2" Residue "B ARG 1198": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 530": "NH1" <-> "NH2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C ARG 639": "NH1" <-> "NH2" Residue "C ARG 699": "NH1" <-> "NH2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "C PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 750": "NH1" <-> "NH2" Residue "C TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 902": "NH1" <-> "NH2" Residue "C ARG 942": "NH1" <-> "NH2" Residue "C ARG 962": "NH1" <-> "NH2" Residue "C ARG 975": "NH1" <-> "NH2" Residue "C ARG 1018": "NH1" <-> "NH2" Residue "C ARG 1198": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 419": "NH1" <-> "NH2" Residue "D ARG 525": "NH1" <-> "NH2" Residue "D ARG 530": "NH1" <-> "NH2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D ARG 639": "NH1" <-> "NH2" Residue "D ARG 699": "NH1" <-> "NH2" Residue "D ARG 729": "NH1" <-> "NH2" Residue "D PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 750": "NH1" <-> "NH2" Residue "D TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 902": "NH1" <-> "NH2" Residue "D ARG 942": "NH1" <-> "NH2" Residue "D ARG 962": "NH1" <-> "NH2" Residue "D ARG 975": "NH1" <-> "NH2" Residue "D ARG 1018": "NH1" <-> "NH2" Residue "D ARG 1198": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 35797 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8199 Classifications: {'peptide': 1014} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 972} Chain breaks: 3 Chain: "B" Number of atoms: 8199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8199 Classifications: {'peptide': 1014} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 972} Chain breaks: 3 Chain: "C" Number of atoms: 8199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8199 Classifications: {'peptide': 1014} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 972} Chain breaks: 3 Chain: "D" Number of atoms: 8199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8199 Classifications: {'peptide': 1014} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 972} Chain breaks: 3 Chain: "A" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 710 Unusual residues: {' CA': 1, 'CLR': 1, 'DU0': 1, 'M05': 1, 'POV': 13} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 709 Unusual residues: {'CLR': 1, 'DU0': 1, 'M05': 1, 'POV': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 709 Unusual residues: {'CLR': 1, 'DU0': 1, 'M05': 1, 'POV': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 709 Unusual residues: {'CLR': 1, 'DU0': 1, 'M05': 1, 'POV': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Time building chain proxies: 19.09, per 1000 atoms: 0.53 Number of scatterers: 35797 At special positions: 0 Unit cell: (145, 145, 156, 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) Ca 1 19.99 Cl 4 17.00 S 196 16.00 P 48 15.00 O 6352 8.00 N 5508 7.00 C 23688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1056 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B1056 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS D1056 " - pdb=" SG CYS D1066 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 13.98 Conformation dependent library (CDL) restraints added in 6.7 seconds 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7664 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 8 sheets defined 68.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 149 through 166 removed outlier: 3.636A pdb=" N GLN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.597A pdb=" N ARG A 197 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.645A pdb=" N ASP A 215 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 216 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 217 " --> pdb=" O ASN A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.571A pdb=" N ARG A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.666A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.619A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.634A pdb=" N PHE A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 372 Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.513A pdb=" N LEU A 377 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.862A pdb=" N ALA A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.555A pdb=" N ALA A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 449 removed outlier: 3.531A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.644A pdb=" N TYR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 498 removed outlier: 4.256A pdb=" N HIS A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 495 " --> pdb=" O HIS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 526 through 529 Processing helix chain 'A' and resid 530 through 540 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.734A pdb=" N GLU A 624 " --> pdb=" O TYR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.677A pdb=" N HIS A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 668 Processing helix chain 'A' and resid 675 through 701 Processing helix chain 'A' and resid 701 through 709 Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 730 through 735 removed outlier: 3.575A pdb=" N VAL A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 749 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 768 through 774 removed outlier: 3.503A pdb=" N MET A 773 " --> pdb=" O ALA A 770 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 774 " --> pdb=" O ILE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 removed outlier: 3.681A pdb=" N SER A 783 " --> pdb=" O ALA A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 840 through 850 removed outlier: 3.741A pdb=" N PHE A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 876 removed outlier: 3.855A pdb=" N ALA A 862 " --> pdb=" O PHE A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 905 Processing helix chain 'A' and resid 911 through 920 Processing helix chain 'A' and resid 922 through 944 Processing helix chain 'A' and resid 955 through 975 removed outlier: 4.757A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 981 removed outlier: 3.594A pdb=" N PHE A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1000 removed outlier: 4.118A pdb=" N TYR A 989 " --> pdb=" O GLN A 985 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1023 Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1030 through 1036 removed outlier: 3.661A pdb=" N LYS A1034 " --> pdb=" O TRP A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.878A pdb=" N ILE A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 3.543A pdb=" N CYS A1066 " --> pdb=" O PRO A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1071 No H-bonds generated for 'chain 'A' and resid 1069 through 1071' Processing helix chain 'A' and resid 1072 through 1087 Processing helix chain 'A' and resid 1087 through 1125 removed outlier: 5.465A pdb=" N LEU A1101 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A1122 " --> pdb=" O PHE A1118 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A1124 " --> pdb=" O MET A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1141 removed outlier: 4.076A pdb=" N SER A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1190 Processing helix chain 'A' and resid 1192 through 1228 removed outlier: 3.842A pdb=" N ARG A1198 " --> pdb=" O GLU A1194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG A1217 " --> pdb=" O GLU A1213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A1222 " --> pdb=" O VAL A1218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A1223 " --> pdb=" O ASN A1219 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A1225 " --> pdb=" O ILE A1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 149 through 166 removed outlier: 3.636A pdb=" N GLN B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.597A pdb=" N ARG B 197 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.644A pdb=" N ASP B 215 " --> pdb=" O ASN B 212 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 216 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 217 " --> pdb=" O ASN B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 217' Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.572A pdb=" N ARG B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.668A pdb=" N LEU B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 removed outlier: 3.619A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.634A pdb=" N PHE B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 372 Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.512A pdb=" N LEU B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 378' Processing helix chain 'B' and resid 390 through 398 removed outlier: 3.862A pdb=" N ALA B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.554A pdb=" N ALA B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 449 removed outlier: 3.530A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 470 through 479 removed outlier: 3.644A pdb=" N TYR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 498 removed outlier: 4.255A pdb=" N HIS B 491 " --> pdb=" O PRO B 487 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP B 495 " --> pdb=" O HIS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 530 through 540 Processing helix chain 'B' and resid 620 through 632 removed outlier: 3.733A pdb=" N GLU B 624 " --> pdb=" O TYR B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 644 removed outlier: 3.677A pdb=" N HIS B 644 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 668 Processing helix chain 'B' and resid 675 through 701 Processing helix chain 'B' and resid 701 through 709 Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 730 through 735 removed outlier: 3.575A pdb=" N VAL B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 749 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 768 through 774 removed outlier: 3.503A pdb=" N MET B 773 " --> pdb=" O ALA B 770 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 774 " --> pdb=" O ILE B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 783 removed outlier: 3.682A pdb=" N SER B 783 " --> pdb=" O ALA B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 797 Processing helix chain 'B' and resid 840 through 850 removed outlier: 3.741A pdb=" N PHE B 848 " --> pdb=" O LYS B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 876 removed outlier: 3.856A pdb=" N ALA B 862 " --> pdb=" O PHE B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 905 Processing helix chain 'B' and resid 911 through 920 Processing helix chain 'B' and resid 922 through 944 Processing helix chain 'B' and resid 955 through 975 removed outlier: 4.756A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 981 removed outlier: 3.594A pdb=" N PHE B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1000 removed outlier: 4.119A pdb=" N TYR B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 994 " --> pdb=" O VAL B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1023 Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1030 through 1036 removed outlier: 3.661A pdb=" N LYS B1034 " --> pdb=" O TRP B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1044 removed outlier: 3.878A pdb=" N ILE B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1053 Processing helix chain 'B' and resid 1062 through 1066 removed outlier: 3.544A pdb=" N CYS B1066 " --> pdb=" O PRO B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1071 No H-bonds generated for 'chain 'B' and resid 1069 through 1071' Processing helix chain 'B' and resid 1072 through 1087 Processing helix chain 'B' and resid 1087 through 1125 removed outlier: 5.465A pdb=" N LEU B1101 " --> pdb=" O ASN B1097 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLN B1102 " --> pdb=" O ASN B1098 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B1122 " --> pdb=" O PHE B1118 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS B1123 " --> pdb=" O ILE B1119 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU B1124 " --> pdb=" O MET B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1141 removed outlier: 4.076A pdb=" N SER B1136 " --> pdb=" O LEU B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1190 Processing helix chain 'B' and resid 1192 through 1228 removed outlier: 3.842A pdb=" N ARG B1198 " --> pdb=" O GLU B1194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B1209 " --> pdb=" O GLU B1205 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG B1217 " --> pdb=" O GLU B1213 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B1219 " --> pdb=" O GLY B1215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B1222 " --> pdb=" O VAL B1218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B1223 " --> pdb=" O ASN B1219 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER B1224 " --> pdb=" O TYR B1220 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B1225 " --> pdb=" O ILE B1221 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 Processing helix chain 'C' and resid 149 through 166 removed outlier: 3.636A pdb=" N GLN C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 191 Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.597A pdb=" N ARG C 197 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.645A pdb=" N ASP C 215 " --> pdb=" O ASN C 212 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 216 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 217 " --> pdb=" O ASN C 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 259 through 271 removed outlier: 3.571A pdb=" N ARG C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 305 removed outlier: 3.667A pdb=" N LEU C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 removed outlier: 3.619A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.634A pdb=" N PHE C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 372 Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.512A pdb=" N LEU C 377 " --> pdb=" O LYS C 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 374 through 378' Processing helix chain 'C' and resid 390 through 398 removed outlier: 3.862A pdb=" N ALA C 394 " --> pdb=" O ASP C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 418 Processing helix chain 'C' and resid 419 through 427 removed outlier: 3.555A pdb=" N ALA C 423 " --> pdb=" O ARG C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 449 removed outlier: 3.531A pdb=" N VAL C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 461 Processing helix chain 'C' and resid 464 through 469 Processing helix chain 'C' and resid 470 through 479 removed outlier: 3.644A pdb=" N TYR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 498 removed outlier: 4.255A pdb=" N HIS C 491 " --> pdb=" O PRO C 487 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP C 495 " --> pdb=" O HIS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 526 through 529 Processing helix chain 'C' and resid 530 through 540 Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.733A pdb=" N GLU C 624 " --> pdb=" O TYR C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 644 removed outlier: 3.676A pdb=" N HIS C 644 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 668 Processing helix chain 'C' and resid 675 through 701 Processing helix chain 'C' and resid 701 through 709 Processing helix chain 'C' and resid 720 through 728 Processing helix chain 'C' and resid 730 through 735 removed outlier: 3.575A pdb=" N VAL C 734 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 749 Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 768 through 774 removed outlier: 3.503A pdb=" N MET C 773 " --> pdb=" O ALA C 770 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 774 " --> pdb=" O ILE C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 783 removed outlier: 3.681A pdb=" N SER C 783 " --> pdb=" O ALA C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 797 Processing helix chain 'C' and resid 840 through 850 removed outlier: 3.741A pdb=" N PHE C 848 " --> pdb=" O LYS C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 876 removed outlier: 3.856A pdb=" N ALA C 862 " --> pdb=" O PHE C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 905 Processing helix chain 'C' and resid 911 through 920 Processing helix chain 'C' and resid 922 through 944 Processing helix chain 'C' and resid 955 through 975 removed outlier: 4.756A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 981 removed outlier: 3.593A pdb=" N PHE C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1000 removed outlier: 4.118A pdb=" N TYR C 989 " --> pdb=" O GLN C 985 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY C 994 " --> pdb=" O VAL C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1023 Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1030 through 1036 removed outlier: 3.661A pdb=" N LYS C1034 " --> pdb=" O TRP C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1044 removed outlier: 3.877A pdb=" N ILE C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1053 Processing helix chain 'C' and resid 1062 through 1066 removed outlier: 3.544A pdb=" N CYS C1066 " --> pdb=" O PRO C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1071 No H-bonds generated for 'chain 'C' and resid 1069 through 1071' Processing helix chain 'C' and resid 1072 through 1087 Processing helix chain 'C' and resid 1087 through 1125 removed outlier: 5.464A pdb=" N LEU C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN C1102 " --> pdb=" O ASN C1098 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR C1122 " --> pdb=" O PHE C1118 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS C1123 " --> pdb=" O ILE C1119 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU C1124 " --> pdb=" O MET C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1141 removed outlier: 4.076A pdb=" N SER C1136 " --> pdb=" O LEU C1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1190 Processing helix chain 'C' and resid 1192 through 1228 removed outlier: 3.842A pdb=" N ARG C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C1209 " --> pdb=" O GLU C1205 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG C1217 " --> pdb=" O GLU C1213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C1219 " --> pdb=" O GLY C1215 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C1222 " --> pdb=" O VAL C1218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C1223 " --> pdb=" O ASN C1219 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER C1224 " --> pdb=" O TYR C1220 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C1225 " --> pdb=" O ILE C1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 Processing helix chain 'D' and resid 149 through 166 removed outlier: 3.635A pdb=" N GLN D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.597A pdb=" N ARG D 197 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 3.645A pdb=" N ASP D 215 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 216 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 217 " --> pdb=" O ASN D 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 217' Processing helix chain 'D' and resid 259 through 271 removed outlier: 3.572A pdb=" N ARG D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 305 removed outlier: 3.667A pdb=" N LEU D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 331 removed outlier: 3.620A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN D 331 " --> pdb=" O TYR D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.634A pdb=" N PHE D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 Processing helix chain 'D' and resid 374 through 378 removed outlier: 3.512A pdb=" N LEU D 377 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 378 " --> pdb=" O LYS D 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 374 through 378' Processing helix chain 'D' and resid 390 through 398 removed outlier: 3.862A pdb=" N ALA D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 418 Processing helix chain 'D' and resid 419 through 427 removed outlier: 3.555A pdb=" N ALA D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 449 removed outlier: 3.530A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 461 Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 470 through 479 removed outlier: 3.644A pdb=" N TYR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 498 removed outlier: 4.255A pdb=" N HIS D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP D 495 " --> pdb=" O HIS D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 526 through 529 Processing helix chain 'D' and resid 530 through 540 Processing helix chain 'D' and resid 620 through 632 removed outlier: 3.733A pdb=" N GLU D 624 " --> pdb=" O TYR D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 644 removed outlier: 3.678A pdb=" N HIS D 644 " --> pdb=" O PHE D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 668 Processing helix chain 'D' and resid 675 through 701 Processing helix chain 'D' and resid 701 through 709 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 730 through 735 removed outlier: 3.575A pdb=" N VAL D 734 " --> pdb=" O LEU D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 749 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 768 through 774 removed outlier: 3.504A pdb=" N MET D 773 " --> pdb=" O ALA D 770 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 774 " --> pdb=" O ILE D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 783 removed outlier: 3.682A pdb=" N SER D 783 " --> pdb=" O ALA D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 797 Processing helix chain 'D' and resid 840 through 850 removed outlier: 3.741A pdb=" N PHE D 848 " --> pdb=" O LYS D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 876 removed outlier: 3.855A pdb=" N ALA D 862 " --> pdb=" O PHE D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 905 Processing helix chain 'D' and resid 911 through 920 Processing helix chain 'D' and resid 922 through 944 Processing helix chain 'D' and resid 955 through 975 removed outlier: 4.756A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 981 removed outlier: 3.594A pdb=" N PHE D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1000 removed outlier: 4.118A pdb=" N TYR D 989 " --> pdb=" O GLN D 985 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY D 994 " --> pdb=" O VAL D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1023 Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1030 through 1036 removed outlier: 3.662A pdb=" N LYS D1034 " --> pdb=" O TRP D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1044 removed outlier: 3.878A pdb=" N ILE D1044 " --> pdb=" O PRO D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1053 Processing helix chain 'D' and resid 1062 through 1066 removed outlier: 3.544A pdb=" N CYS D1066 " --> pdb=" O PRO D1063 " (cutoff:3.500A) Processing helix chain 'D' and resid 1069 through 1071 No H-bonds generated for 'chain 'D' and resid 1069 through 1071' Processing helix chain 'D' and resid 1072 through 1087 Processing helix chain 'D' and resid 1087 through 1125 removed outlier: 5.464A pdb=" N LEU D1101 " --> pdb=" O ASN D1097 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN D1102 " --> pdb=" O ASN D1098 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR D1122 " --> pdb=" O PHE D1118 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS D1123 " --> pdb=" O ILE D1119 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU D1124 " --> pdb=" O MET D1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1141 removed outlier: 4.076A pdb=" N SER D1136 " --> pdb=" O LEU D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1190 Processing helix chain 'D' and resid 1192 through 1228 removed outlier: 3.842A pdb=" N ARG D1198 " --> pdb=" O GLU D1194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D1209 " --> pdb=" O GLU D1205 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG D1217 " --> pdb=" O GLU D1213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN D1219 " --> pdb=" O GLY D1215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D1222 " --> pdb=" O VAL D1218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D1223 " --> pdb=" O ASN D1219 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER D1224 " --> pdb=" O TYR D1220 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D1225 " --> pdb=" O ILE D1221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 removed outlier: 7.521A pdb=" N TYR A 92 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 222 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 94 " --> pdb=" O VAL A 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 248 removed outlier: 6.084A pdb=" N GLY A 203 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 248 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA A 205 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A 202 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 171 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE A 204 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 173 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL A 136 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU A 288 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER A 138 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL A 313 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 287 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N CYS A 315 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A 289 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N PHE A 381 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 314 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 7.521A pdb=" N TYR B 92 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 222 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 94 " --> pdb=" O VAL B 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 244 through 248 removed outlier: 6.085A pdb=" N GLY B 203 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL B 248 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA B 205 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE B 202 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 171 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 204 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR B 173 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL B 136 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU B 288 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER B 138 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL B 313 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA B 287 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N CYS B 315 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE B 289 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N PHE B 381 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL B 314 " --> pdb=" O PHE B 381 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 7.519A pdb=" N TYR C 92 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 222 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 94 " --> pdb=" O VAL C 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 244 through 248 removed outlier: 6.084A pdb=" N GLY C 203 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL C 248 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA C 205 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE C 202 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 171 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE C 204 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR C 173 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL C 136 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU C 288 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER C 138 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL C 313 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 287 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N CYS C 315 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE C 289 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N PHE C 381 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL C 314 " --> pdb=" O PHE C 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 91 through 94 removed outlier: 7.520A pdb=" N TYR D 92 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 222 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL D 94 " --> pdb=" O VAL D 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 244 through 248 removed outlier: 6.084A pdb=" N GLY D 203 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL D 248 " --> pdb=" O GLY D 203 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA D 205 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE D 202 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE D 171 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE D 204 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR D 173 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL D 136 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU D 288 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER D 138 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL D 313 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA D 287 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N CYS D 315 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE D 289 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N PHE D 381 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL D 314 " --> pdb=" O PHE D 381 " (cutoff:3.500A) 1764 hydrogen bonds defined for protein. 5184 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: 13.90 Time building geometry restraints manager: 15.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5413 1.32 - 1.44: 9313 1.44 - 1.57: 21245 1.57 - 1.69: 101 1.69 - 1.81: 348 Bond restraints: 36420 Sorted by residual: bond pdb=" C29 POV C1313 " pdb="C210 POV C1313 " ideal model delta sigma weight residual 1.333 1.517 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C29 POV B1313 " pdb="C210 POV B1313 " ideal model delta sigma weight residual 1.333 1.516 -0.183 2.00e-02 2.50e+03 8.42e+01 bond pdb=" C29 POV A1311 " pdb="C210 POV A1311 " ideal model delta sigma weight residual 1.333 1.516 -0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C29 POV D1315 " pdb="C210 POV D1315 " ideal model delta sigma weight residual 1.333 1.516 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" O12 POV D1303 " pdb=" P POV D1303 " ideal model delta sigma weight residual 1.657 1.591 0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 36415 not shown) Histogram of bond angle deviations from ideal: 94.81 - 103.72: 571 103.72 - 112.63: 18433 112.63 - 121.54: 21670 121.54 - 130.45: 8043 130.45 - 139.35: 223 Bond angle restraints: 48940 Sorted by residual: angle pdb=" C29 POV D1315 " pdb="C210 POV D1315 " pdb="C211 POV D1315 " ideal model delta sigma weight residual 127.67 113.37 14.30 3.00e+00 1.11e-01 2.27e+01 angle pdb=" C29 POV B1313 " pdb="C210 POV B1313 " pdb="C211 POV B1313 " ideal model delta sigma weight residual 127.67 113.39 14.28 3.00e+00 1.11e-01 2.27e+01 angle pdb=" C29 POV C1313 " pdb="C210 POV C1313 " pdb="C211 POV C1313 " ideal model delta sigma weight residual 127.67 113.42 14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" C29 POV A1311 " pdb="C210 POV A1311 " pdb="C211 POV A1311 " ideal model delta sigma weight residual 127.67 113.53 14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C28 POV C1313 " pdb=" C29 POV C1313 " pdb="C210 POV C1313 " ideal model delta sigma weight residual 127.79 114.08 13.71 3.00e+00 1.11e-01 2.09e+01 ... (remaining 48935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 21782 35.79 - 71.58: 682 71.58 - 107.36: 186 107.36 - 143.15: 62 143.15 - 178.94: 32 Dihedral angle restraints: 22744 sinusoidal: 10852 harmonic: 11892 Sorted by residual: dihedral pdb=" CA TYR C 949 " pdb=" C TYR C 949 " pdb=" N ILE C 950 " pdb=" CA ILE C 950 " ideal model delta harmonic sigma weight residual -180.00 -131.84 -48.16 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA TYR B 949 " pdb=" C TYR B 949 " pdb=" N ILE B 950 " pdb=" CA ILE B 950 " ideal model delta harmonic sigma weight residual 180.00 -131.85 -48.15 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA TYR D 949 " pdb=" C TYR D 949 " pdb=" N ILE D 950 " pdb=" CA ILE D 950 " ideal model delta harmonic sigma weight residual -180.00 -131.86 -48.14 0 5.00e+00 4.00e-02 9.27e+01 ... (remaining 22741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3828 0.053 - 0.105: 1105 0.105 - 0.158: 248 0.158 - 0.211: 43 0.211 - 0.264: 12 Chirality restraints: 5236 Sorted by residual: chirality pdb=" CG LEU B1128 " pdb=" CB LEU B1128 " pdb=" CD1 LEU B1128 " pdb=" CD2 LEU B1128 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU C1128 " pdb=" CB LEU C1128 " pdb=" CD1 LEU C1128 " pdb=" CD2 LEU C1128 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CG LEU A1128 " pdb=" CB LEU A1128 " pdb=" CD1 LEU A1128 " pdb=" CD2 LEU A1128 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 5233 not shown) Planarity restraints: 5840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D1315 " 0.156 2.00e-02 2.50e+03 3.16e-01 9.99e+02 pdb=" C29 POV D1315 " -0.425 2.00e-02 2.50e+03 pdb="C210 POV D1315 " 0.416 2.00e-02 2.50e+03 pdb="C211 POV D1315 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C1313 " 0.155 2.00e-02 2.50e+03 3.14e-01 9.84e+02 pdb=" C29 POV C1313 " -0.420 2.00e-02 2.50e+03 pdb="C210 POV C1313 " 0.413 2.00e-02 2.50e+03 pdb="C211 POV C1313 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1313 " -0.156 2.00e-02 2.50e+03 3.13e-01 9.80e+02 pdb=" C29 POV B1313 " 0.420 2.00e-02 2.50e+03 pdb="C210 POV B1313 " -0.412 2.00e-02 2.50e+03 pdb="C211 POV B1313 " 0.148 2.00e-02 2.50e+03 ... (remaining 5837 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 325 2.56 - 3.14: 28164 3.14 - 3.73: 52619 3.73 - 4.31: 80482 4.31 - 4.90: 129027 Nonbonded interactions: 290617 Sorted by model distance: nonbonded pdb=" OG1 THR B 895 " pdb=" O PRO B1130 " model vdw 1.970 2.440 nonbonded pdb=" OG1 THR D 895 " pdb=" O PRO D1130 " model vdw 1.971 2.440 nonbonded pdb=" OG1 THR A 895 " pdb=" O PRO A1130 " model vdw 1.972 2.440 nonbonded pdb=" OG1 THR C 895 " pdb=" O PRO C1130 " model vdw 1.972 2.440 nonbonded pdb=" OH TYR D 505 " pdb=" OD2 ASP D 511 " model vdw 2.014 2.440 ... (remaining 290612 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' and (resid 87 through 1229 or resid 1301 or resid 1303 or resid 1305 \ or resid 1307 or resid 1309 through 1311 or (resid 1313 and (name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C210 or name C211 or name C212 or name C213 or name C214 or name C215 or name \ C216)) or (resid 1315 and (name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C210 or name C211 or name C212 o \ r name C213 or name C214 or name C215 or name C216)))) selection = (chain 'B' and (resid 87 through 1229 or resid 1301 or resid 1303 or resid 1305 \ or resid 1307 or (resid 1309 and (name N or name C1 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 o \ r name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name O \ 11 or name O12 or name O13 or name O14 or name O21 or name O22 or name P or name \ C210 or name C211 or name C212 or name C213 or name C214 or name C215 or name C \ 216 or name C217 or name C218)) or resid 1310 or (resid 1311 and (name C22 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C210 or name C211 or name C212 or name C213 or name C214 or name C215 or \ name C216)) or resid 1313 or (resid 1315 and (name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C210 or name \ C211 or name C212 or name C213 or name C214 or name C215 or name C216)))) selection = (chain 'C' and (resid 87 through 1229 or resid 1301 or resid 1303 or resid 1305 \ or resid 1307 or (resid 1309 and (name N or name C1 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 o \ r name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name O \ 11 or name O12 or name O13 or name O14 or name O21 or name O22 or name P or name \ C210 or name C211 or name C212 or name C213 or name C214 or name C215 or name C \ 216 or name C217 or name C218)) or resid 1310 or (resid 1311 and (name C22 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C210 or name C211 or name C212 or name C213 or name C214 or name C215 or \ name C216)) or resid 1313 or (resid 1315 and (name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C210 or name \ C211 or name C212 or name C213 or name C214 or name C215 or name C216)))) selection = (chain 'D' and (resid 87 through 1229 or resid 1301 or resid 1303 or resid 1305 \ or resid 1307 or (resid 1309 and (name N or name C1 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 o \ r name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name O \ 11 or name O12 or name O13 or name O14 or name O21 or name O22 or name P or name \ C210 or name C211 or name C212 or name C213 or name C214 or name C215 or name C \ 216 or name C217 or name C218)) or resid 1310 or (resid 1311 and (name C22 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C210 or name C211 or name C212 or name C213 or name C214 or name C215 or \ name C216)) or (resid 1313 and (name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C210 or name C211 or name C \ 212 or name C213 or name C214 or name C215 or name C216)) or resid 1315)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.030 Extract box with map and model: 9.190 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 93.360 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.220 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.009 0.184 36420 Z= 0.556 Angle : 1.185 14.303 48940 Z= 0.591 Chirality : 0.053 0.264 5236 Planarity : 0.011 0.316 5840 Dihedral : 20.381 178.938 15068 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.18 % Favored : 92.22 % Rotamer: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % 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: -4.03 (0.11), residues: 4024 helix: -2.48 (0.08), residues: 2492 sheet: -2.56 (0.31), residues: 204 loop : -2.71 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A1042 HIS 0.012 0.002 HIS A 329 PHE 0.063 0.003 PHE B 858 TYR 0.055 0.003 TYR C 870 ARG 0.013 0.002 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 777 time to evaluate : 4.035 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: A 616 LYS cc_start: 0.7479 (ptpp) cc_final: 0.7223 (ptpp) REVERT: A 1189 PHE cc_start: 0.8323 (t80) cc_final: 0.8114 (t80) REVERT: B 369 MET cc_start: 0.6968 (tmt) cc_final: 0.6464 (tpt) REVERT: B 465 MET cc_start: 0.8181 (mmt) cc_final: 0.7811 (mmt) REVERT: B 467 LYS cc_start: 0.8293 (mmmm) cc_final: 0.8053 (mmmt) REVERT: B 649 MET cc_start: 0.9020 (ttp) cc_final: 0.8761 (ttp) REVERT: B 1084 GLN cc_start: 0.8169 (mm110) cc_final: 0.7468 (mm-40) REVERT: B 1085 TYR cc_start: 0.7055 (m-10) cc_final: 0.6796 (m-10) REVERT: B 1120 MET cc_start: 0.8400 (mmm) cc_final: 0.8175 (mmp) REVERT: B 1128 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8571 (mt) REVERT: B 1175 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6812 (pt0) REVERT: B 1189 PHE cc_start: 0.8491 (t80) cc_final: 0.8171 (t80) REVERT: B 1207 MET cc_start: 0.8788 (mtp) cc_final: 0.8558 (mtp) REVERT: C 421 ASP cc_start: 0.7356 (p0) cc_final: 0.7147 (p0) REVERT: C 649 MET cc_start: 0.8976 (ttp) cc_final: 0.8630 (ttp) REVERT: C 1084 GLN cc_start: 0.8071 (mm110) cc_final: 0.7267 (mm-40) REVERT: C 1120 MET cc_start: 0.8395 (mmm) cc_final: 0.8182 (mmm) REVERT: C 1128 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8749 (mt) REVERT: D 421 ASP cc_start: 0.7398 (p0) cc_final: 0.7187 (p0) REVERT: D 465 MET cc_start: 0.8096 (mmt) cc_final: 0.7856 (mmt) REVERT: D 649 MET cc_start: 0.8968 (ttp) cc_final: 0.8638 (ttp) REVERT: D 1084 GLN cc_start: 0.8142 (mm110) cc_final: 0.7397 (mm-40) REVERT: D 1085 TYR cc_start: 0.7049 (m-10) cc_final: 0.6772 (m-10) REVERT: D 1128 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8699 (mt) REVERT: D 1189 PHE cc_start: 0.8633 (t80) cc_final: 0.8406 (t80) outliers start: 4 outliers final: 0 residues processed: 781 average time/residue: 1.6431 time to fit residues: 1519.5228 Evaluate side-chains 468 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 465 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 1128 LEU Chi-restraints excluded: chain D residue 1128 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 2.9990 chunk 306 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 163 optimal weight: 0.0370 chunk 316 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 192 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 366 optimal weight: 6.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 183 HIS A 242 HIS A 276 HIS A 281 GLN A 329 HIS A 668 GLN A 718 ASN A 787 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN A1097 ASN ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 177 ASN B 183 HIS B 242 HIS B 276 HIS B 329 HIS B 482 GLN B 498 GLN B 635 GLN B 681 GLN B 787 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 ASN C 129 GLN C 177 ASN C 183 HIS C 242 HIS C 276 HIS C 329 HIS C 635 GLN C 668 GLN C 681 GLN C 914 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 ASN D 177 ASN D 183 HIS D 242 HIS D 276 HIS D 329 HIS D 482 GLN D 681 GLN D 700 GLN D 914 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36420 Z= 0.301 Angle : 0.770 8.381 48940 Z= 0.388 Chirality : 0.048 0.207 5236 Planarity : 0.006 0.078 5840 Dihedral : 22.851 173.242 7126 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.01 % Favored : 93.51 % Rotamer: Outliers : 2.21 % Allowed : 10.00 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.12), residues: 4024 helix: -0.02 (0.09), residues: 2528 sheet: -1.70 (0.33), residues: 204 loop : -2.12 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 857 HIS 0.012 0.002 HIS C1137 PHE 0.027 0.003 PHE C 935 TYR 0.054 0.003 TYR C 953 ARG 0.006 0.001 ARG D1115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 534 time to evaluate : 3.077 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: A 906 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6959 (mtm) REVERT: A 1189 PHE cc_start: 0.8368 (t80) cc_final: 0.8137 (t80) REVERT: B 369 MET cc_start: 0.6983 (tmt) cc_final: 0.6589 (tpt) REVERT: B 418 ASP cc_start: 0.7881 (t0) cc_final: 0.7667 (t0) REVERT: B 467 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7903 (mmmt) REVERT: B 763 LEU cc_start: 0.8588 (tt) cc_final: 0.8344 (tm) REVERT: B 906 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6655 (mtm) REVERT: B 1043 MET cc_start: 0.9033 (mtt) cc_final: 0.8767 (mtt) REVERT: B 1175 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6819 (pt0) REVERT: B 1189 PHE cc_start: 0.8629 (t80) cc_final: 0.8327 (t80) REVERT: C 421 ASP cc_start: 0.7697 (p0) cc_final: 0.7450 (p0) REVERT: C 906 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6735 (mtm) REVERT: C 1185 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8344 (ttmm) REVERT: C 1189 PHE cc_start: 0.8701 (t80) cc_final: 0.8458 (t80) REVERT: D 418 ASP cc_start: 0.7952 (t0) cc_final: 0.7744 (t0) REVERT: D 421 ASP cc_start: 0.7732 (p0) cc_final: 0.7490 (p0) REVERT: D 906 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6722 (mtm) REVERT: D 1189 PHE cc_start: 0.8741 (t80) cc_final: 0.8509 (t80) outliers start: 79 outliers final: 20 residues processed: 585 average time/residue: 1.5889 time to fit residues: 1110.3160 Evaluate side-chains 480 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 455 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1185 LYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1099 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 305 optimal weight: 20.0000 chunk 249 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 367 optimal weight: 0.9990 chunk 397 optimal weight: 7.9990 chunk 327 optimal weight: 20.0000 chunk 364 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 183 HIS A 236 ASN A 281 GLN A 331 GLN A 914 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN B 102 HIS B 122 GLN B 183 HIS B 236 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 ASN B1098 ASN C 183 HIS C 787 GLN C 968 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN D 102 HIS D 183 HIS D 236 ASN D 668 GLN D 787 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 ASN ** D1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 36420 Z= 0.313 Angle : 0.706 8.032 48940 Z= 0.362 Chirality : 0.047 0.225 5236 Planarity : 0.006 0.089 5840 Dihedral : 22.063 159.816 7120 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.99 % Favored : 93.46 % Rotamer: Outliers : 3.30 % Allowed : 10.87 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.24 (0.13), residues: 4024 helix: 0.78 (0.10), residues: 2540 sheet: -1.03 (0.36), residues: 204 loop : -1.88 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 947 HIS 0.010 0.002 HIS B1137 PHE 0.026 0.003 PHE C 935 TYR 0.046 0.003 TYR C 953 ARG 0.007 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 488 time to evaluate : 3.837 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: A 320 ARG cc_start: 0.5553 (OUTLIER) cc_final: 0.5218 (mtt180) REVERT: A 488 MET cc_start: 0.7687 (ptm) cc_final: 0.7468 (ptm) REVERT: A 906 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6770 (mtm) REVERT: A 1189 PHE cc_start: 0.8554 (t80) cc_final: 0.8301 (t80) REVERT: B 320 ARG cc_start: 0.5060 (OUTLIER) cc_final: 0.4273 (mtt180) REVERT: B 369 MET cc_start: 0.6738 (tmt) cc_final: 0.6413 (tpt) REVERT: B 420 VAL cc_start: 0.8331 (t) cc_final: 0.8031 (p) REVERT: B 506 LYS cc_start: 0.8145 (mmpt) cc_final: 0.7838 (mmtt) REVERT: B 906 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6567 (mtm) REVERT: B 1175 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6973 (pt0) REVERT: B 1189 PHE cc_start: 0.8549 (t80) cc_final: 0.8223 (t80) REVERT: C 421 ASP cc_start: 0.7680 (p0) cc_final: 0.7473 (p0) REVERT: C 906 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6669 (mtm) REVERT: C 1189 PHE cc_start: 0.8704 (t80) cc_final: 0.8447 (t80) REVERT: D 906 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6662 (mtm) REVERT: D 1189 PHE cc_start: 0.8719 (t80) cc_final: 0.8478 (t80) outliers start: 118 outliers final: 50 residues processed: 574 average time/residue: 1.5333 time to fit residues: 1056.2465 Evaluate side-chains 507 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 451 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 796 MET Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 754 ARG Chi-restraints excluded: chain D residue 796 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1037 VAL Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 368 optimal weight: 0.9990 chunk 390 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 183 HIS C 331 GLN C 914 GLN ** C 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36420 Z= 0.191 Angle : 0.609 10.347 48940 Z= 0.310 Chirality : 0.042 0.174 5236 Planarity : 0.005 0.080 5840 Dihedral : 21.038 159.012 7120 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.04 % Favored : 93.71 % Rotamer: Outliers : 2.57 % Allowed : 12.85 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.40 (0.13), residues: 4024 helix: 1.32 (0.10), residues: 2556 sheet: -0.50 (0.38), residues: 200 loop : -1.82 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 747 HIS 0.006 0.001 HIS B1137 PHE 0.019 0.002 PHE D 935 TYR 0.028 0.002 TYR B1122 ARG 0.005 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 470 time to evaluate : 4.157 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: A 320 ARG cc_start: 0.5400 (OUTLIER) cc_final: 0.5023 (mtt180) REVERT: A 531 LYS cc_start: 0.7615 (mppt) cc_final: 0.7273 (mppt) REVERT: A 906 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6618 (mtm) REVERT: A 975 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7622 (ttt-90) REVERT: A 1189 PHE cc_start: 0.8409 (t80) cc_final: 0.8204 (t80) REVERT: B 320 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4289 (mtt180) REVERT: B 369 MET cc_start: 0.6682 (tmt) cc_final: 0.6375 (tpt) REVERT: B 420 VAL cc_start: 0.8358 (t) cc_final: 0.8068 (p) REVERT: B 506 LYS cc_start: 0.8067 (mmpt) cc_final: 0.7775 (mmmt) REVERT: B 763 LEU cc_start: 0.8454 (tt) cc_final: 0.8153 (tm) REVERT: B 906 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6402 (mtm) REVERT: B 1043 MET cc_start: 0.8931 (mtt) cc_final: 0.8610 (mtt) REVERT: B 1184 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: B 1189 PHE cc_start: 0.8458 (t80) cc_final: 0.8137 (t80) REVERT: B 1206 GLN cc_start: 0.7837 (mt0) cc_final: 0.7509 (mm110) REVERT: C 906 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6524 (mtm) REVERT: C 1184 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: C 1189 PHE cc_start: 0.8608 (t80) cc_final: 0.8358 (t80) REVERT: D 320 ARG cc_start: 0.5064 (OUTLIER) cc_final: 0.4812 (mtt180) REVERT: D 494 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7582 (mtp180) REVERT: D 906 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6482 (mtm) REVERT: D 1189 PHE cc_start: 0.8543 (t80) cc_final: 0.8330 (t80) outliers start: 92 outliers final: 35 residues processed: 533 average time/residue: 1.5799 time to fit residues: 1011.4302 Evaluate side-chains 491 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 445 time to evaluate : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 841 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 290 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 199 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 789 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 HIS B 461 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1137 HIS C 236 ASN C 461 ASN C 914 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 HIS C1210 GLN D 461 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1137 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36420 Z= 0.255 Angle : 0.656 11.235 48940 Z= 0.332 Chirality : 0.044 0.187 5236 Planarity : 0.006 0.090 5840 Dihedral : 21.024 156.377 7120 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.11 % Favored : 93.59 % Rotamer: Outliers : 2.99 % Allowed : 12.82 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.53 (0.13), residues: 4024 helix: 1.39 (0.10), residues: 2572 sheet: -0.49 (0.38), residues: 204 loop : -1.73 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 947 HIS 0.006 0.001 HIS D1137 PHE 0.024 0.002 PHE D 935 TYR 0.035 0.002 TYR B1122 ARG 0.006 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 464 time to evaluate : 3.668 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: A 320 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.5011 (mtt180) REVERT: A 906 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6741 (mtm) REVERT: A 975 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7682 (ttt-90) REVERT: A 1189 PHE cc_start: 0.8610 (t80) cc_final: 0.8359 (t80) REVERT: B 320 ARG cc_start: 0.5021 (OUTLIER) cc_final: 0.4373 (mtt180) REVERT: B 420 VAL cc_start: 0.8292 (t) cc_final: 0.8089 (p) REVERT: B 506 LYS cc_start: 0.8063 (mmpt) cc_final: 0.7842 (mmmt) REVERT: B 906 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6563 (mtm) REVERT: B 1175 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6979 (pt0) REVERT: B 1184 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: B 1189 PHE cc_start: 0.8517 (t80) cc_final: 0.8170 (t80) REVERT: B 1206 GLN cc_start: 0.7821 (mt0) cc_final: 0.7565 (mm110) REVERT: C 494 ARG cc_start: 0.7446 (mtp180) cc_final: 0.7243 (mtm180) REVERT: C 906 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6721 (mtm) REVERT: C 1184 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: C 1189 PHE cc_start: 0.8669 (t80) cc_final: 0.8395 (t80) REVERT: D 320 ARG cc_start: 0.5017 (OUTLIER) cc_final: 0.4815 (mtt180) REVERT: D 906 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6640 (mtm) REVERT: D 1189 PHE cc_start: 0.8664 (t80) cc_final: 0.8411 (t80) outliers start: 107 outliers final: 58 residues processed: 537 average time/residue: 1.4521 time to fit residues: 947.7410 Evaluate side-chains 513 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 445 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 643 GLN Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 841 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1037 VAL Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 0.6980 chunk 351 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 229 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 390 optimal weight: 3.9990 chunk 324 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36420 Z= 0.232 Angle : 0.635 10.698 48940 Z= 0.322 Chirality : 0.043 0.176 5236 Planarity : 0.005 0.082 5840 Dihedral : 20.712 156.185 7120 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 2.82 % Allowed : 13.60 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.72 (0.13), residues: 4024 helix: 1.54 (0.10), residues: 2576 sheet: -0.36 (0.38), residues: 204 loop : -1.68 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 947 HIS 0.005 0.001 HIS B 850 PHE 0.021 0.002 PHE C 935 TYR 0.026 0.002 TYR B1122 ARG 0.006 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 452 time to evaluate : 3.644 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: A 320 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.5100 (mtt180) REVERT: A 368 MET cc_start: 0.6174 (ttm) cc_final: 0.5912 (tmm) REVERT: A 906 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6729 (mtm) REVERT: A 975 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7648 (ttt-90) REVERT: A 1189 PHE cc_start: 0.8540 (t80) cc_final: 0.8271 (t80) REVERT: B 320 ARG cc_start: 0.4962 (OUTLIER) cc_final: 0.4348 (mtt180) REVERT: B 506 LYS cc_start: 0.8080 (mmpt) cc_final: 0.7849 (mmmt) REVERT: B 906 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6550 (mtm) REVERT: B 1175 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6973 (pt0) REVERT: B 1184 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: B 1189 PHE cc_start: 0.8485 (t80) cc_final: 0.8158 (t80) REVERT: B 1206 GLN cc_start: 0.7905 (mt0) cc_final: 0.7562 (mm110) REVERT: C 320 ARG cc_start: 0.5569 (OUTLIER) cc_final: 0.5116 (mtt180) REVERT: C 906 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6717 (mtm) REVERT: C 1184 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: C 1189 PHE cc_start: 0.8620 (t80) cc_final: 0.8364 (t80) REVERT: D 494 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7569 (mtm180) REVERT: D 906 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6625 (mtm) REVERT: D 1189 PHE cc_start: 0.8618 (t80) cc_final: 0.8376 (t80) outliers start: 101 outliers final: 55 residues processed: 519 average time/residue: 1.4837 time to fit residues: 937.2130 Evaluate side-chains 506 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 440 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 643 GLN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 841 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 754 ARG Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1037 VAL Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 222 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 329 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 389 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36420 Z= 0.284 Angle : 0.668 9.853 48940 Z= 0.338 Chirality : 0.045 0.199 5236 Planarity : 0.006 0.091 5840 Dihedral : 20.761 157.099 7120 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.46 % Favored : 93.36 % Rotamer: Outliers : 3.41 % Allowed : 13.46 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.68 (0.13), residues: 4024 helix: 1.47 (0.10), residues: 2576 sheet: -0.22 (0.38), residues: 204 loop : -1.64 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 947 HIS 0.006 0.001 HIS B 850 PHE 0.024 0.002 PHE C 935 TYR 0.026 0.002 TYR B1122 ARG 0.008 0.001 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 452 time to evaluate : 4.243 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: A 320 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.5107 (mtt180) REVERT: A 368 MET cc_start: 0.6217 (ttm) cc_final: 0.5916 (ttm) REVERT: A 906 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6767 (mtm) REVERT: A 975 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7717 (ttt-90) REVERT: A 1189 PHE cc_start: 0.8633 (t80) cc_final: 0.8351 (t80) REVERT: B 320 ARG cc_start: 0.5043 (OUTLIER) cc_final: 0.4410 (mtt180) REVERT: B 506 LYS cc_start: 0.8126 (mmpt) cc_final: 0.7881 (mmtt) REVERT: B 906 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6603 (mtm) REVERT: B 1184 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: B 1189 PHE cc_start: 0.8522 (t80) cc_final: 0.8162 (t80) REVERT: B 1206 GLN cc_start: 0.7775 (mt0) cc_final: 0.7516 (mm110) REVERT: C 320 ARG cc_start: 0.5564 (OUTLIER) cc_final: 0.5123 (mtt180) REVERT: C 906 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6765 (mtm) REVERT: C 1189 PHE cc_start: 0.8661 (t80) cc_final: 0.8375 (t80) REVERT: D 494 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7485 (mtm180) REVERT: D 906 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6680 (mtm) REVERT: D 1189 PHE cc_start: 0.8662 (t80) cc_final: 0.8394 (t80) outliers start: 122 outliers final: 70 residues processed: 536 average time/residue: 1.4821 time to fit residues: 964.2727 Evaluate side-chains 528 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 448 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 643 GLN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 841 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 754 ARG Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 796 MET Chi-restraints excluded: chain D residue 841 ILE Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1037 VAL Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 306 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36420 Z= 0.283 Angle : 0.667 9.866 48940 Z= 0.338 Chirality : 0.045 0.194 5236 Planarity : 0.006 0.084 5840 Dihedral : 20.548 157.932 7120 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 3.24 % Allowed : 14.08 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.13), residues: 4024 helix: 1.49 (0.10), residues: 2568 sheet: -0.21 (0.38), residues: 204 loop : -1.72 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 947 HIS 0.006 0.001 HIS C 850 PHE 0.023 0.002 PHE C 935 TYR 0.026 0.002 TYR C 953 ARG 0.009 0.001 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 451 time to evaluate : 3.930 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: A 320 ARG cc_start: 0.5441 (OUTLIER) cc_final: 0.5023 (mtt180) REVERT: A 368 MET cc_start: 0.6228 (ttm) cc_final: 0.5876 (tmm) REVERT: A 616 LYS cc_start: 0.7943 (mtmm) cc_final: 0.7498 (mttm) REVERT: A 906 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6789 (mtm) REVERT: A 975 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7709 (ttt-90) REVERT: A 1189 PHE cc_start: 0.8608 (t80) cc_final: 0.8334 (t80) REVERT: B 320 ARG cc_start: 0.5006 (OUTLIER) cc_final: 0.4407 (mtt180) REVERT: B 421 ASP cc_start: 0.8156 (p0) cc_final: 0.7741 (p0) REVERT: B 506 LYS cc_start: 0.8125 (mmpt) cc_final: 0.7853 (mmmt) REVERT: B 906 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6600 (mtm) REVERT: B 1184 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: B 1189 PHE cc_start: 0.8512 (t80) cc_final: 0.8161 (t80) REVERT: B 1213 GLU cc_start: 0.8094 (tp30) cc_final: 0.7826 (tm-30) REVERT: C 320 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.5146 (mtt180) REVERT: C 906 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6770 (mtm) REVERT: C 1189 PHE cc_start: 0.8665 (t80) cc_final: 0.8389 (t80) REVERT: D 906 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6680 (mtm) REVERT: D 1189 PHE cc_start: 0.8661 (t80) cc_final: 0.8408 (t80) REVERT: D 1213 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7056 (tm-30) outliers start: 116 outliers final: 74 residues processed: 528 average time/residue: 1.4743 time to fit residues: 947.7016 Evaluate side-chains 527 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 443 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 643 GLN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 796 MET Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 754 ARG Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 796 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1037 VAL Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1194 GLU Chi-restraints excluded: chain D residue 1213 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 9.9990 chunk 373 optimal weight: 0.7980 chunk 340 optimal weight: 6.9990 chunk 362 optimal weight: 5.9990 chunk 372 optimal weight: 0.6980 chunk 218 optimal weight: 0.3980 chunk 158 optimal weight: 2.9990 chunk 284 optimal weight: 0.4980 chunk 111 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 343 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1210 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 968 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1210 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36420 Z= 0.148 Angle : 0.570 10.660 48940 Z= 0.289 Chirality : 0.040 0.160 5236 Planarity : 0.005 0.082 5840 Dihedral : 19.305 156.971 7120 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.96 % Favored : 93.94 % Rotamer: Outliers : 2.09 % Allowed : 15.22 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 4024 helix: 1.84 (0.10), residues: 2580 sheet: 0.13 (0.40), residues: 192 loop : -1.61 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 947 HIS 0.004 0.001 HIS A 850 PHE 0.015 0.001 PHE C 935 TYR 0.018 0.001 TYR C 953 ARG 0.011 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 469 time to evaluate : 4.015 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: A 320 ARG cc_start: 0.5045 (OUTLIER) cc_final: 0.4747 (mtt180) REVERT: A 368 MET cc_start: 0.6182 (ttm) cc_final: 0.5929 (tmm) REVERT: A 616 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7422 (mttm) REVERT: A 906 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6580 (mtm) REVERT: A 975 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7536 (ttt-90) REVERT: B 320 ARG cc_start: 0.4810 (OUTLIER) cc_final: 0.4331 (mtt180) REVERT: B 421 ASP cc_start: 0.8205 (p0) cc_final: 0.7787 (p0) REVERT: B 506 LYS cc_start: 0.8050 (mmpt) cc_final: 0.7798 (mmmt) REVERT: B 906 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6363 (mtm) REVERT: B 1184 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: B 1189 PHE cc_start: 0.8307 (t80) cc_final: 0.8043 (t80) REVERT: C 320 ARG cc_start: 0.5150 (OUTLIER) cc_final: 0.4928 (mtt180) REVERT: C 906 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6604 (mtm) REVERT: C 1189 PHE cc_start: 0.8442 (t80) cc_final: 0.8240 (t80) REVERT: D 906 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6443 (mtm) outliers start: 75 outliers final: 34 residues processed: 518 average time/residue: 1.5310 time to fit residues: 955.4671 Evaluate side-chains 502 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 459 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 3.9990 chunk 238 optimal weight: 0.7980 chunk 383 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 402 optimal weight: 7.9990 chunk 370 optimal weight: 0.3980 chunk 320 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 305 GLN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN C 281 GLN C 968 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1210 GLN D 305 GLN ** D 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36420 Z= 0.245 Angle : 0.641 10.769 48940 Z= 0.325 Chirality : 0.044 0.183 5236 Planarity : 0.005 0.087 5840 Dihedral : 19.415 155.327 7120 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.24 % Favored : 93.66 % Rotamer: Outliers : 1.59 % Allowed : 16.12 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.96 (0.14), residues: 4024 helix: 1.72 (0.10), residues: 2568 sheet: -0.04 (0.39), residues: 204 loop : -1.60 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 947 HIS 0.005 0.001 HIS C 491 PHE 0.021 0.002 PHE C 935 TYR 0.022 0.002 TYR C 953 ARG 0.010 0.001 ARG C 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8048 Ramachandran restraints generated. 4024 Oldfield, 0 Emsley, 4024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 458 time to evaluate : 4.024 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: A 320 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.4984 (mtt180) REVERT: A 368 MET cc_start: 0.6178 (ttm) cc_final: 0.5886 (tmm) REVERT: A 496 VAL cc_start: 0.8248 (t) cc_final: 0.8021 (t) REVERT: A 616 LYS cc_start: 0.7837 (mtmm) cc_final: 0.7416 (mttm) REVERT: A 906 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6622 (mtm) REVERT: A 975 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7656 (ttt-90) REVERT: B 320 ARG cc_start: 0.4833 (OUTLIER) cc_final: 0.4310 (mtt180) REVERT: B 421 ASP cc_start: 0.8185 (p0) cc_final: 0.7769 (p0) REVERT: B 496 VAL cc_start: 0.8085 (t) cc_final: 0.7874 (t) REVERT: B 506 LYS cc_start: 0.8059 (mmpt) cc_final: 0.7831 (mmmt) REVERT: B 906 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6556 (mtm) REVERT: B 1184 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: B 1189 PHE cc_start: 0.8466 (t80) cc_final: 0.8130 (t80) REVERT: C 320 ARG cc_start: 0.5351 (OUTLIER) cc_final: 0.5070 (mtt180) REVERT: C 906 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6648 (mtm) REVERT: C 1189 PHE cc_start: 0.8596 (t80) cc_final: 0.8334 (t80) REVERT: D 496 VAL cc_start: 0.8120 (t) cc_final: 0.7889 (t) REVERT: D 906 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6629 (mtm) outliers start: 57 outliers final: 29 residues processed: 500 average time/residue: 1.4832 time to fit residues: 895.0379 Evaluate side-chains 491 residues out of total 3580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 453 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 0.4980 chunk 254 optimal weight: 7.9990 chunk 341 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 295 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 329 optimal weight: 30.0000 chunk 40 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1210 GLN ** D 983 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 = 0.4281 r_free = 0.4281 target = 0.201849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132086 restraints weight = 37006.625| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.96 r_work: 0.3224 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 36420 Z= 0.144 Angle : 0.566 10.596 48940 Z= 0.287 Chirality : 0.040 0.155 5236 Planarity : 0.005 0.079 5840 Dihedral : 18.438 151.570 7120 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.06 % Favored : 93.76 % Rotamer: Outliers : 1.28 % Allowed : 16.45 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.14), residues: 4024 helix: 1.93 (0.10), residues: 2588 sheet: 0.40 (0.41), residues: 188 loop : -1.54 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 417 HIS 0.003 0.000 HIS A 850 PHE 0.015 0.001 PHE C 935 TYR 0.018 0.001 TYR C 953 ARG 0.009 0.000 ARG B 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15417.01 seconds wall clock time: 275 minutes 45.14 seconds (16545.14 seconds total)