Starting phenix.real_space_refine on Fri May 17 22:30:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si2_40496/05_2024/8si2_40496_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si2_40496/05_2024/8si2_40496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si2_40496/05_2024/8si2_40496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si2_40496/05_2024/8si2_40496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si2_40496/05_2024/8si2_40496_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si2_40496/05_2024/8si2_40496_neut.pdb" } resolution = 2.19 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= 0.010 sd= 0.078 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: 6 Type Number sf(0) Gaussians P 56 5.49 5 S 240 5.16 5 Na 2 4.78 5 C 25768 2.51 5 N 6012 2.21 5 O 6944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 942": "NH1" <-> "NH2" Residue "A TYR 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1018": "NH1" <-> "NH2" Residue "A ARG 1198": "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 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 942": "NH1" <-> "NH2" Residue "B TYR 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 962": "NH1" <-> "NH2" Residue "B ARG 975": "NH1" <-> "NH2" Residue "B PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1018": "NH1" <-> "NH2" Residue "B ARG 1198": "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 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 942": "NH1" <-> "NH2" Residue "C TYR 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 962": "NH1" <-> "NH2" Residue "C ARG 975": "NH1" <-> "NH2" Residue "C PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1018": "NH1" <-> "NH2" Residue "C ARG 1198": "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 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 942": "NH1" <-> "NH2" Residue "D TYR 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 962": "NH1" <-> "NH2" Residue "D ARG 975": "NH1" <-> "NH2" Residue "D PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1018": "NH1" <-> "NH2" Residue "D ARG 1198": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 39022 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8928 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "B" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8928 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "C" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8928 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "D" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8928 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "A" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 787 Unusual residues: {' NA': 2, 'CLR': 1, 'DU0': 1, 'POV': 16} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 785 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 785 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 785 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Time building chain proxies: 19.78, per 1000 atoms: 0.51 Number of scatterers: 39022 At special positions: 0 Unit cell: (180.11, 180.11, 156.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 240 16.00 P 56 15.00 Na 2 11.00 O 6944 8.00 N 6012 7.00 C 25768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.06 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.01 Simple disulfide: pdb=" SG CYS A1056 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 44 " distance=2.06 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 44 " distance=2.02 Simple disulfide: pdb=" SG CYS B1056 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 44 " distance=2.06 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 44 " distance=2.02 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 44 " distance=2.06 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 44 " distance=2.02 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: 15.69 Conformation dependent library (CDL) restraints added in 6.5 seconds 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8368 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 12 sheets defined 64.8% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.587A pdb=" N GLN A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.550A pdb=" N ALA A 52 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 removed outlier: 3.898A pdb=" N TYR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.596A pdb=" N GLU A 76 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 removed outlier: 4.055A pdb=" N ILE A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 removed outlier: 3.841A pdb=" N GLN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.540A pdb=" N HIS A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.504A pdb=" N LEU A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 259 through 270 removed outlier: 3.568A pdb=" N ARG A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.508A pdb=" N LEU A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.549A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.857A pdb=" N LEU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.785A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 418 removed outlier: 3.657A pdb=" N THR A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.816A pdb=" N ALA A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 449 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 470 through 480 removed outlier: 3.603A pdb=" N TYR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 498 removed outlier: 4.057A pdb=" N HIS A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN A 498 " --> pdb=" O ARG A 494 " (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 removed outlier: 3.565A pdb=" N ASN A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.806A pdb=" N GLU A 624 " --> pdb=" O TYR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 647 through 667 Processing helix chain 'A' and resid 675 through 701 removed outlier: 3.603A pdb=" N LEU A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 709 removed outlier: 3.621A pdb=" N LEU A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 730 through 735 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: 3.766A pdb=" N LEU A 774 " --> pdb=" O ILE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 794 removed outlier: 3.779A pdb=" N MET A 794 " --> pdb=" O ASP A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 850 removed outlier: 3.600A pdb=" N PHE A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 876 removed outlier: 3.642A 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 945 Processing helix chain 'A' and resid 955 through 975 removed outlier: 4.601A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 981 Processing helix chain 'A' and resid 985 through 1000 removed outlier: 3.970A pdb=" N TYR A 989 " --> pdb=" O GLN A 985 " (cutoff:3.500A) removed outlier: 3.753A 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 Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.850A pdb=" N ILE A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 removed outlier: 3.722A pdb=" N ILE A1053 " --> pdb=" O ALA A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1066 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 1086 Processing helix chain 'A' and resid 1087 through 1125 removed outlier: 5.101A pdb=" N LEU A1101 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLN A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A1122 " --> pdb=" O PHE A1118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A1124 " --> pdb=" O MET A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 removed outlier: 4.289A pdb=" N SER A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1190 Processing helix chain 'A' and resid 1192 through 1229 removed outlier: 3.582A pdb=" N ILE A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A1212 " --> pdb=" O SER A1208 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A1223 " --> pdb=" O ASN A1219 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.587A pdb=" N GLN B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.550A pdb=" N ALA B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 63 removed outlier: 3.898A pdb=" N TYR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.594A pdb=" N GLU B 76 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 126 removed outlier: 4.055A pdb=" N ILE B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 removed outlier: 3.840A pdb=" N GLN B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 removed outlier: 3.541A pdb=" N HIS B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.503A pdb=" N LEU B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 217' Processing helix chain 'B' and resid 259 through 270 removed outlier: 3.568A pdb=" N ARG B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 removed outlier: 3.508A pdb=" N LEU B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.549A pdb=" N THR B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 372 removed outlier: 3.856A pdb=" N LEU B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 391 through 399 removed outlier: 3.786A pdb=" N LEU B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 418 removed outlier: 3.656A pdb=" N THR B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.815A pdb=" N ALA B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 449 Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 470 through 480 removed outlier: 3.603A pdb=" N TYR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 498 removed outlier: 4.057A pdb=" N HIS B 491 " --> pdb=" O PRO B 487 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN B 498 " --> pdb=" O ARG B 494 " (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 removed outlier: 3.565A pdb=" N ASN B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 632 removed outlier: 3.806A pdb=" N GLU B 624 " --> pdb=" O TYR B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 647 through 667 Processing helix chain 'B' and resid 675 through 701 removed outlier: 3.602A pdb=" N LEU B 679 " --> pdb=" O THR B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 709 removed outlier: 3.621A pdb=" N LEU B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 730 through 735 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: 3.767A pdb=" N LEU B 774 " --> pdb=" O ILE B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 794 removed outlier: 3.779A pdb=" N MET B 794 " --> pdb=" O ASP B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 850 removed outlier: 3.600A pdb=" N PHE B 845 " --> pdb=" O ILE B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 876 removed outlier: 3.643A 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 945 Processing helix chain 'B' and resid 955 through 975 removed outlier: 4.602A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 981 Processing helix chain 'B' and resid 985 through 1000 removed outlier: 3.970A pdb=" N TYR B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) removed outlier: 3.752A 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 Processing helix chain 'B' and resid 1037 through 1044 removed outlier: 3.850A pdb=" N ILE B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1053 removed outlier: 3.723A pdb=" N ILE B1053 " --> pdb=" O ALA B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1062 through 1066 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 1086 Processing helix chain 'B' and resid 1087 through 1125 removed outlier: 5.101A pdb=" N LEU B1101 " --> pdb=" O ASN B1097 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN B1102 " --> pdb=" O ASN B1098 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B1122 " --> pdb=" O PHE B1118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS B1123 " --> pdb=" O ILE B1119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B1124 " --> pdb=" O MET B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1146 removed outlier: 4.288A pdb=" N SER B1136 " --> pdb=" O LEU B1132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1190 Processing helix chain 'B' and resid 1192 through 1229 removed outlier: 3.582A pdb=" N ILE B1209 " --> pdb=" O GLU B1205 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B1212 " --> pdb=" O SER B1208 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B1223 " --> pdb=" O ASN B1219 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B1224 " --> pdb=" O TYR B1220 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.587A pdb=" N GLN C 37 " --> pdb=" O CYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.549A pdb=" N ALA C 52 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.898A pdb=" N TYR C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.594A pdb=" N GLU C 76 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 126 removed outlier: 4.055A pdb=" N ILE C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 166 removed outlier: 3.841A pdb=" N GLN C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 157 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.541A pdb=" N HIS C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.503A pdb=" N LEU C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 259 through 270 removed outlier: 3.568A pdb=" N ARG C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.509A pdb=" N LEU C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.548A pdb=" N THR C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 372 removed outlier: 3.857A pdb=" N LEU C 364 " --> pdb=" O GLU C 360 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.785A pdb=" N LEU C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 3.656A pdb=" N THR C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 427 removed outlier: 3.815A pdb=" N ALA C 423 " --> pdb=" O ARG C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 449 Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 464 through 469 Processing helix chain 'C' and resid 470 through 480 removed outlier: 3.603A pdb=" N TYR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 498 removed outlier: 4.056A pdb=" N HIS C 491 " --> pdb=" O PRO C 487 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN C 498 " --> pdb=" O ARG C 494 " (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 removed outlier: 3.565A pdb=" N ASN C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.806A pdb=" N GLU C 624 " --> pdb=" O TYR C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'C' and resid 647 through 667 Processing helix chain 'C' and resid 675 through 701 removed outlier: 3.603A pdb=" N LEU C 679 " --> pdb=" O THR C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 709 removed outlier: 3.620A pdb=" N LEU C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 Processing helix chain 'C' and resid 730 through 735 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: 3.768A pdb=" N LEU C 774 " --> pdb=" O ILE C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 794 removed outlier: 3.779A pdb=" N MET C 794 " --> pdb=" O ASP C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 850 removed outlier: 3.600A pdb=" N PHE C 845 " --> pdb=" O ILE C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 876 removed outlier: 3.643A 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 945 Processing helix chain 'C' and resid 955 through 975 removed outlier: 4.602A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 981 Processing helix chain 'C' and resid 985 through 1000 removed outlier: 3.971A pdb=" N TYR C 989 " --> pdb=" O GLN C 985 " (cutoff:3.500A) removed outlier: 3.752A 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 Processing helix chain 'C' and resid 1037 through 1044 removed outlier: 3.850A pdb=" N ILE C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1053 removed outlier: 3.722A pdb=" N ILE C1053 " --> pdb=" O ALA C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1062 through 1066 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 1086 Processing helix chain 'C' and resid 1087 through 1125 removed outlier: 5.102A pdb=" N LEU C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN C1102 " --> pdb=" O ASN C1098 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C1122 " --> pdb=" O PHE C1118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS C1123 " --> pdb=" O ILE C1119 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C1124 " --> pdb=" O MET C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1146 removed outlier: 4.289A pdb=" N SER C1136 " --> pdb=" O LEU C1132 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1190 Processing helix chain 'C' and resid 1192 through 1229 removed outlier: 3.583A pdb=" N ILE C1209 " --> pdb=" O GLU C1205 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C1212 " --> pdb=" O SER C1208 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C1223 " --> pdb=" O ASN C1219 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C1224 " --> pdb=" O TYR C1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 11 Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.587A pdb=" N GLN D 37 " --> pdb=" O CYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.550A pdb=" N ALA D 52 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.898A pdb=" N TYR D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 removed outlier: 3.595A pdb=" N GLU D 76 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 126 removed outlier: 4.055A pdb=" N ILE D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 121 " --> pdb=" O PRO D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 166 removed outlier: 3.841A pdb=" N GLN D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 190 removed outlier: 3.541A pdb=" N HIS D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 3.503A pdb=" N LEU D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 217' Processing helix chain 'D' and resid 259 through 270 removed outlier: 3.568A pdb=" N ARG D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 removed outlier: 3.509A pdb=" N LEU D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 329 Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.548A pdb=" N THR D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 removed outlier: 3.856A pdb=" N LEU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 370 " --> pdb=" O GLN D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.785A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 418 removed outlier: 3.657A pdb=" N THR D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 427 removed outlier: 3.815A pdb=" N ALA D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 449 Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 470 through 480 removed outlier: 3.603A pdb=" N TYR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 498 removed outlier: 4.056A pdb=" N HIS D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN D 498 " --> pdb=" O ARG D 494 " (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 removed outlier: 3.565A pdb=" N ASN D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 632 removed outlier: 3.806A pdb=" N GLU D 624 " --> pdb=" O TYR D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 647 through 667 Processing helix chain 'D' and resid 675 through 701 removed outlier: 3.603A pdb=" N LEU D 679 " --> pdb=" O THR D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 709 removed outlier: 3.621A pdb=" N LEU D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 730 through 735 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: 3.767A pdb=" N LEU D 774 " --> pdb=" O ILE D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 794 removed outlier: 3.780A pdb=" N MET D 794 " --> pdb=" O ASP D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 850 removed outlier: 3.600A pdb=" N PHE D 845 " --> pdb=" O ILE D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 876 removed outlier: 3.642A 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 945 Processing helix chain 'D' and resid 955 through 975 removed outlier: 4.602A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 981 Processing helix chain 'D' and resid 985 through 1000 removed outlier: 3.970A pdb=" N TYR D 989 " --> pdb=" O GLN D 985 " (cutoff:3.500A) removed outlier: 3.753A 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 Processing helix chain 'D' and resid 1037 through 1044 removed outlier: 3.849A pdb=" N ILE D1044 " --> pdb=" O PRO D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1053 removed outlier: 3.722A pdb=" N ILE D1053 " --> pdb=" O ALA D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1062 through 1066 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 1086 Processing helix chain 'D' and resid 1087 through 1125 removed outlier: 5.102A pdb=" N LEU D1101 " --> pdb=" O ASN D1097 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLN D1102 " --> pdb=" O ASN D1098 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D1122 " --> pdb=" O PHE D1118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS D1123 " --> pdb=" O ILE D1119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D1124 " --> pdb=" O MET D1120 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1146 removed outlier: 4.289A pdb=" N SER D1136 " --> pdb=" O LEU D1132 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1190 Processing helix chain 'D' and resid 1192 through 1229 removed outlier: 3.581A pdb=" N ILE D1209 " --> pdb=" O GLU D1205 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D1212 " --> pdb=" O SER D1208 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG D1223 " --> pdb=" O ASN D1219 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D1224 " --> pdb=" O TYR D1220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.538A pdb=" N SER A 87 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 15 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 85 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.860A pdb=" N TYR A 92 " --> pdb=" O GLY A 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 245 removed outlier: 6.199A pdb=" N VAL A 136 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 288 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 138 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N VAL A 313 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 287 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N CYS A 315 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE A 289 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A 312 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE A 381 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 314 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 16 removed outlier: 3.538A pdb=" N SER B 87 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 15 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 85 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.860A pdb=" N TYR B 92 " --> pdb=" O GLY B 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 244 through 245 removed outlier: 6.199A pdb=" N VAL B 136 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 288 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER B 138 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N VAL B 313 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 287 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N CYS B 315 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE B 289 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL B 312 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 381 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 314 " --> pdb=" O PHE B 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 16 removed outlier: 3.537A pdb=" N SER C 87 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU C 15 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 85 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.860A pdb=" N TYR C 92 " --> pdb=" O GLY C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 244 through 245 removed outlier: 6.199A pdb=" N VAL C 136 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU C 288 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER C 138 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N VAL C 313 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 287 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N CYS C 315 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE C 289 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL C 312 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE C 381 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL C 314 " --> pdb=" O PHE C 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 13 through 16 removed outlier: 3.537A pdb=" N SER D 87 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU D 15 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 85 " --> pdb=" O GLU D 15 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.860A pdb=" N TYR D 92 " --> pdb=" O GLY D 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 244 through 245 removed outlier: 6.198A pdb=" N VAL D 136 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU D 288 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER D 138 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N VAL D 313 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA D 287 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N CYS D 315 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE D 289 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL D 312 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE D 381 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL D 314 " --> pdb=" O PHE D 381 " (cutoff:3.500A) 1796 hydrogen bonds defined for protein. 5232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.73 Time building geometry restraints manager: 17.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6397 1.32 - 1.45: 10316 1.45 - 1.58: 22467 1.58 - 1.71: 112 1.71 - 1.84: 392 Bond restraints: 39684 Sorted by residual: bond pdb=" C29 POV C1308 " pdb="C210 POV C1308 " ideal model delta sigma weight residual 1.333 1.508 -0.175 2.00e-02 2.50e+03 7.63e+01 bond pdb=" C29 POV A1305 " pdb="C210 POV A1305 " ideal model delta sigma weight residual 1.333 1.507 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C29 POV D1309 " pdb="C210 POV D1309 " ideal model delta sigma weight residual 1.333 1.507 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" C29 POV B1308 " pdb="C210 POV B1308 " ideal model delta sigma weight residual 1.333 1.507 -0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" CG LEU A 722 " pdb=" CD2 LEU A 722 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.24e+01 ... (remaining 39679 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.18: 610 104.18 - 111.69: 16722 111.69 - 119.20: 16275 119.20 - 126.72: 18963 126.72 - 134.23: 682 Bond angle restraints: 53252 Sorted by residual: angle pdb=" N PRO C1130 " pdb=" CA PRO C1130 " pdb=" C PRO C1130 " ideal model delta sigma weight residual 110.70 116.77 -6.07 1.22e+00 6.72e-01 2.48e+01 angle pdb=" N PRO A1130 " pdb=" CA PRO A1130 " pdb=" C PRO A1130 " ideal model delta sigma weight residual 110.70 116.76 -6.06 1.22e+00 6.72e-01 2.47e+01 angle pdb=" N PRO D1130 " pdb=" CA PRO D1130 " pdb=" C PRO D1130 " ideal model delta sigma weight residual 110.70 116.74 -6.04 1.22e+00 6.72e-01 2.45e+01 angle pdb=" N PRO B1130 " pdb=" CA PRO B1130 " pdb=" C PRO B1130 " ideal model delta sigma weight residual 110.70 116.72 -6.02 1.22e+00 6.72e-01 2.43e+01 angle pdb=" C28 POV A1305 " pdb=" C29 POV A1305 " pdb="C210 POV A1305 " ideal model delta sigma weight residual 127.79 113.01 14.78 3.00e+00 1.11e-01 2.43e+01 ... (remaining 53247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 23804 35.81 - 71.62: 791 71.62 - 107.43: 161 107.43 - 143.24: 43 143.24 - 179.05: 45 Dihedral angle restraints: 24844 sinusoidal: 11876 harmonic: 12968 Sorted by residual: dihedral pdb=" CA SER C 22 " pdb=" C SER C 22 " pdb=" N SER C 23 " pdb=" CA SER C 23 " ideal model delta harmonic sigma weight residual -180.00 -145.38 -34.62 0 5.00e+00 4.00e-02 4.79e+01 dihedral pdb=" CA SER B 22 " pdb=" C SER B 22 " pdb=" N SER B 23 " pdb=" CA SER B 23 " ideal model delta harmonic sigma weight residual -180.00 -145.41 -34.59 0 5.00e+00 4.00e-02 4.79e+01 dihedral pdb=" CA SER D 22 " pdb=" C SER D 22 " pdb=" N SER D 23 " pdb=" CA SER D 23 " ideal model delta harmonic sigma weight residual -180.00 -145.42 -34.58 0 5.00e+00 4.00e-02 4.78e+01 ... (remaining 24841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3822 0.055 - 0.110: 1507 0.110 - 0.164: 275 0.164 - 0.219: 48 0.219 - 0.274: 24 Chirality restraints: 5676 Sorted by residual: chirality pdb=" CB VAL C1037 " pdb=" CA VAL C1037 " pdb=" CG1 VAL C1037 " pdb=" CG2 VAL C1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL B1037 " pdb=" CA VAL B1037 " pdb=" CG1 VAL B1037 " pdb=" CG2 VAL B1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL A1037 " pdb=" CA VAL A1037 " pdb=" CG1 VAL A1037 " pdb=" CG2 VAL A1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5673 not shown) Planarity restraints: 6364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D1310 " -0.069 2.00e-02 2.50e+03 1.48e-01 2.19e+02 pdb=" C29 POV D1310 " 0.196 2.00e-02 2.50e+03 pdb="C210 POV D1310 " -0.198 2.00e-02 2.50e+03 pdb="C211 POV D1310 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1309 " 0.069 2.00e-02 2.50e+03 1.47e-01 2.16e+02 pdb=" C29 POV B1309 " -0.195 2.00e-02 2.50e+03 pdb="C210 POV B1309 " 0.197 2.00e-02 2.50e+03 pdb="C211 POV B1309 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C1309 " 0.064 2.00e-02 2.50e+03 1.32e-01 1.74e+02 pdb=" C29 POV C1309 " -0.175 2.00e-02 2.50e+03 pdb="C210 POV C1309 " 0.175 2.00e-02 2.50e+03 pdb="C211 POV C1309 " -0.064 2.00e-02 2.50e+03 ... (remaining 6361 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 435 2.60 - 3.18: 34098 3.18 - 3.75: 58957 3.75 - 4.33: 88226 4.33 - 4.90: 140809 Nonbonded interactions: 322525 Sorted by model distance: nonbonded pdb=" OE1 GLU B 692 " pdb=" OH TYR B1181 " model vdw 2.026 2.440 nonbonded pdb=" OE1 GLU C 692 " pdb=" OH TYR C1181 " model vdw 2.026 2.440 nonbonded pdb=" OE1 GLU D 692 " pdb=" OH TYR D1181 " model vdw 2.026 2.440 nonbonded pdb=" OE1 GLU A 692 " pdb=" OH TYR A1181 " model vdw 2.027 2.440 nonbonded pdb=" O ILE A1221 " pdb=" OG SER A1224 " model vdw 2.033 2.440 ... (remaining 322520 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 3 through 1230 or resid 1301 or (resid 1303 and (name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C310 or name C311 or name C312 or name C313)) or (resid \ 1305 and (name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29)) or (resid 1306 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or \ name O32 or name P or name C210 or name C211 or name C212)) or (resid 1309 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 or name C213 or name C214 or \ name C215 or name C216)) or resid 1310 through 1313 or (resid 1315 and (name N \ or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C \ 2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or nam \ e C27 or name C28 or name C29 or name O11 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 C \ 213 or name C214 or name C215 or name C216 or name C217 or name C218)) or resid \ 1316)) selection = (chain 'B' and (resid 3 through 1230 or resid 1301 or (resid 1303 and (name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C310 or name C311 or name C312 or name C313)) or (resid \ 1305 and (name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29)) or (resid 1306 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or \ name O32 or name P or name C210 or name C211 or name C212)) or (resid 1309 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 or name C213 or name C214 or \ name C215 or name C216)) or resid 1310 or (resid 1311 and (name N or name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 \ or 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 O11 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 C \ 214 or name C215 or name C216 or name C217 or name C218)) or resid 1312 through \ 1313 or (resid 1315 and (name N or name C1 or name C11 or name C12 or name C13 o \ r name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C29 or name O11 or nam \ e 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 C216 or na \ me C217 or name C218)) or resid 1316)) selection = (chain 'C' and (resid 3 through 1230 or resid 1301 or (resid 1303 and (name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C310 or name C311 or name C312 or name C313)) or (resid \ 1305 and (name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29)) or (resid 1306 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or \ name O32 or name P or name C210 or name C211 or name C212)) or (resid 1309 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 or name C213 or name C214 or \ name C215 or name C216)) or resid 1310 or (resid 1311 and (name N or name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 \ or 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 O11 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 C \ 214 or name C215 or name C216 or name C217 or name C218)) or resid 1312 through \ 1313 or (resid 1315 and (name N or name C1 or name C11 or name C12 or name C13 o \ r name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C29 or name O11 or nam \ e 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 C216 or na \ me C217 or name C218)) or resid 1316)) selection = (chain 'D' and (resid 3 through 1230 or resid 1301 or resid 1303 or (resid 1305 \ and (name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C29)) or resid 1306 or resid 1309 through 1310 or (resid 1311 and \ (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name O11 or name O12 or name O13 or nam \ e O14 or name O21 or name O22 or name P or name C210 or name C211 or name C212 o \ r name C213 or name C214 or name C215 or name C216 or name C217 or name C218)) o \ r resid 1312 through 1313 or resid 1315 through 1316)) } 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: 1.620 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: 8.180 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 100.230 Find NCS groups from input model: 3.300 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 : 0.012 0.175 39684 Z= 0.757 Angle : 1.127 14.784 53252 Z= 0.576 Chirality : 0.059 0.274 5676 Planarity : 0.007 0.148 6364 Dihedral : 20.098 179.053 16440 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.75 % Favored : 90.98 % Rotamer: Outliers : 0.20 % Allowed : 3.58 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.93 (0.10), residues: 4388 helix: -2.11 (0.08), residues: 2492 sheet: -3.83 (0.25), residues: 172 loop : -3.10 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP C1042 HIS 0.011 0.003 HIS D 850 PHE 0.082 0.004 PHE B 858 TYR 0.071 0.004 TYR C 870 ARG 0.017 0.002 ARG B1115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 629 time to evaluate : 4.330 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 60 MET cc_start: -0.0322 (mpp) cc_final: -0.0673 (ppp) REVERT: A 906 MET cc_start: 0.6556 (mtt) cc_final: 0.6289 (mtp) REVERT: A 1161 PHE cc_start: 0.7621 (t80) cc_final: 0.7167 (m-80) REVERT: B 60 MET cc_start: -0.0410 (mpp) cc_final: -0.0732 (ppp) REVERT: B 906 MET cc_start: 0.6576 (mtt) cc_final: 0.6320 (mtp) REVERT: B 1161 PHE cc_start: 0.7597 (t80) cc_final: 0.7188 (m-80) REVERT: C 60 MET cc_start: -0.0628 (mpp) cc_final: -0.1092 (ppp) REVERT: C 906 MET cc_start: 0.6676 (mtt) cc_final: 0.6346 (mtp) REVERT: C 1161 PHE cc_start: 0.7631 (t80) cc_final: 0.7081 (m-80) REVERT: D 60 MET cc_start: -0.0355 (mpp) cc_final: -0.0679 (ppp) REVERT: D 422 ILE cc_start: 0.8177 (mm) cc_final: 0.7972 (mm) REVERT: D 906 MET cc_start: 0.6581 (mtt) cc_final: 0.6316 (mtp) REVERT: D 1161 PHE cc_start: 0.7615 (t80) cc_final: 0.7178 (m-80) outliers start: 8 outliers final: 5 residues processed: 633 average time/residue: 1.8424 time to fit residues: 1375.2613 Evaluate side-chains 365 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 360 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain C residue 951 ASN Chi-restraints excluded: chain D residue 951 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 2.9990 chunk 333 optimal weight: 0.0070 chunk 185 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 224 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 209 optimal weight: 0.9980 chunk 256 optimal weight: 20.0000 chunk 399 optimal weight: 4.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 177 ASN A 239 ASN A 242 HIS A 276 HIS ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS A 668 GLN A 948 ASN A 951 ASN A 968 ASN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN A1137 HIS A1210 GLN B 149 HIS B 177 ASN B 239 ASN B 242 HIS B 276 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS B 538 ASN B 668 GLN B 948 ASN B 951 ASN B 968 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN B1137 HIS B1210 GLN C 149 HIS C 177 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS C 276 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 HIS C 538 ASN C 668 GLN C 948 ASN C 951 ASN C 968 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1025 HIS C1098 ASN C1137 HIS C1210 GLN D 149 HIS D 177 ASN D 239 ASN D 242 HIS D 276 HIS ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS D 668 GLN D 948 ASN D 951 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1025 HIS D1098 ASN D1137 HIS D1210 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39684 Z= 0.209 Angle : 0.697 9.896 53252 Z= 0.349 Chirality : 0.043 0.184 5676 Planarity : 0.005 0.043 6364 Dihedral : 24.738 179.729 7774 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.63 % Favored : 93.09 % Rotamer: Outliers : 1.10 % Allowed : 9.17 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.79 (0.12), residues: 4388 helix: -0.11 (0.09), residues: 2628 sheet: -3.55 (0.28), residues: 180 loop : -2.72 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C1111 HIS 0.006 0.001 HIS C 329 PHE 0.028 0.002 PHE B 858 TYR 0.024 0.002 TYR B 18 ARG 0.009 0.001 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 409 time to evaluate : 4.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.0292 (mpp) cc_final: -0.0679 (ppp) REVERT: A 906 MET cc_start: 0.6563 (mtt) cc_final: 0.6359 (mtp) REVERT: A 1161 PHE cc_start: 0.7615 (t80) cc_final: 0.7186 (m-80) REVERT: B 60 MET cc_start: -0.0344 (mpp) cc_final: -0.0744 (ppp) REVERT: B 1161 PHE cc_start: 0.7580 (t80) cc_final: 0.7233 (m-80) REVERT: C 60 MET cc_start: -0.0569 (mpp) cc_final: -0.1105 (ppp) REVERT: C 906 MET cc_start: 0.6686 (mtt) cc_final: 0.6439 (mtp) REVERT: C 1161 PHE cc_start: 0.7642 (t80) cc_final: 0.7131 (m-80) REVERT: D 60 MET cc_start: -0.0184 (mpp) cc_final: -0.0594 (ppp) REVERT: D 906 MET cc_start: 0.6569 (mtt) cc_final: 0.6351 (mtp) REVERT: D 1161 PHE cc_start: 0.7602 (t80) cc_final: 0.7195 (m-80) outliers start: 43 outliers final: 11 residues processed: 443 average time/residue: 1.7537 time to fit residues: 926.6864 Evaluate side-chains 350 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 339 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 951 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 951 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 0.0570 chunk 124 optimal weight: 5.9990 chunk 332 optimal weight: 0.0980 chunk 272 optimal weight: 9.9990 chunk 110 optimal weight: 30.0000 chunk 400 optimal weight: 9.9990 chunk 432 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 396 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 overall best weight: 2.6304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN A 461 ASN A 538 ASN A 635 GLN A 718 ASN A 951 ASN A 955 ASN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN B 635 GLN B 718 ASN B 951 ASN B 955 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 635 GLN C 718 ASN C 951 ASN C 955 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN D 538 ASN D 635 GLN D 718 ASN D 951 ASN D 955 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 39684 Z= 0.249 Angle : 0.677 8.990 53252 Z= 0.341 Chirality : 0.044 0.192 5676 Planarity : 0.005 0.047 6364 Dihedral : 23.555 178.290 7774 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.95 % Favored : 92.78 % Rotamer: Outliers : 1.33 % Allowed : 10.09 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.91 (0.12), residues: 4388 helix: 0.63 (0.10), residues: 2624 sheet: -2.85 (0.32), residues: 188 loop : -2.47 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 78 HIS 0.007 0.001 HIS D 276 PHE 0.031 0.002 PHE C 858 TYR 0.021 0.002 TYR B 870 ARG 0.016 0.001 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 364 time to evaluate : 4.107 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 60 MET cc_start: -0.0284 (mpp) cc_final: -0.0722 (ppp) REVERT: A 289 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.6876 (mp) REVERT: A 473 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7128 (mtt-85) REVERT: A 481 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6757 (mptt) REVERT: A 843 ARG cc_start: 0.6615 (mtt-85) cc_final: 0.6398 (mtt180) REVERT: A 906 MET cc_start: 0.6646 (mtt) cc_final: 0.6421 (mtp) REVERT: A 1161 PHE cc_start: 0.7671 (t80) cc_final: 0.7177 (m-80) REVERT: B 60 MET cc_start: -0.0273 (mpp) cc_final: -0.0744 (ppp) REVERT: B 289 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6842 (mp) REVERT: B 473 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7111 (mtt-85) REVERT: B 481 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6807 (mptt) REVERT: B 637 MET cc_start: 0.8338 (tpp) cc_final: 0.8122 (tpp) REVERT: B 906 MET cc_start: 0.6927 (mtp) cc_final: 0.6633 (mtp) REVERT: B 1161 PHE cc_start: 0.7646 (t80) cc_final: 0.7227 (m-80) REVERT: C 60 MET cc_start: -0.0663 (mpp) cc_final: -0.1222 (ppp) REVERT: C 473 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7132 (mtt-85) REVERT: C 481 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6881 (mptt) REVERT: C 637 MET cc_start: 0.8390 (tpp) cc_final: 0.8161 (tpp) REVERT: C 906 MET cc_start: 0.6762 (mtt) cc_final: 0.6482 (mtp) REVERT: C 1161 PHE cc_start: 0.7685 (t80) cc_final: 0.7135 (m-80) REVERT: D 60 MET cc_start: -0.0284 (mpp) cc_final: -0.0745 (ppp) REVERT: D 107 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7166 (ttpt) REVERT: D 473 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7117 (mtt-85) REVERT: D 481 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6799 (mptt) REVERT: D 637 MET cc_start: 0.8380 (tpp) cc_final: 0.8160 (tpp) REVERT: D 906 MET cc_start: 0.6660 (mtt) cc_final: 0.6428 (mtp) REVERT: D 1161 PHE cc_start: 0.7665 (t80) cc_final: 0.7199 (m-80) outliers start: 52 outliers final: 11 residues processed: 405 average time/residue: 1.8105 time to fit residues: 873.1540 Evaluate side-chains 354 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 332 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 951 ASN Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 951 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 0.9990 chunk 300 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 401 optimal weight: 6.9990 chunk 425 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 380 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 272 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 668 GLN A 787 GLN A 951 ASN A 955 ASN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 GLN B 50 GLN B 272 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 668 GLN B 787 GLN B 951 ASN B 955 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN C 272 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 668 GLN C 787 GLN C 951 ASN C 955 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN D 272 GLN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN D 668 GLN D 787 GLN D 951 ASN D 955 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 39684 Z= 0.382 Angle : 0.759 9.009 53252 Z= 0.379 Chirality : 0.049 0.239 5676 Planarity : 0.006 0.066 6364 Dihedral : 23.620 177.873 7772 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.25 % Favored : 92.48 % Rotamer: Outliers : 2.30 % Allowed : 10.37 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.97 (0.12), residues: 4388 helix: 0.53 (0.10), residues: 2648 sheet: -2.49 (0.35), residues: 188 loop : -2.49 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 78 HIS 0.009 0.002 HIS D 276 PHE 0.024 0.003 PHE C 858 TYR 0.026 0.003 TYR D1122 ARG 0.009 0.001 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 347 time to evaluate : 4.332 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 60 MET cc_start: -0.0293 (mpp) cc_final: -0.0703 (ppp) REVERT: A 265 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6151 (tp30) REVERT: A 289 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.6897 (mp) REVERT: A 473 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7721 (mtt-85) REVERT: A 481 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6775 (mptt) REVERT: A 746 MET cc_start: 0.8511 (mtp) cc_final: 0.8310 (mtp) REVERT: A 843 ARG cc_start: 0.6596 (mtt-85) cc_final: 0.6386 (mpp80) REVERT: A 906 MET cc_start: 0.6812 (mtt) cc_final: 0.6550 (mtp) REVERT: A 1161 PHE cc_start: 0.7788 (t80) cc_final: 0.7159 (m-80) REVERT: A 1188 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7639 (tmmm) REVERT: B 60 MET cc_start: -0.0179 (mpp) cc_final: -0.0651 (ppp) REVERT: B 265 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6159 (tp30) REVERT: B 289 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.6876 (mp) REVERT: B 473 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7718 (mtt-85) REVERT: B 481 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6781 (mptt) REVERT: B 1027 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: B 1161 PHE cc_start: 0.7761 (t80) cc_final: 0.7194 (m-80) REVERT: B 1188 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7620 (tmmm) REVERT: C 60 MET cc_start: -0.0494 (mpp) cc_final: -0.1039 (ppp) REVERT: C 183 HIS cc_start: 0.5924 (m-70) cc_final: 0.5643 (m-70) REVERT: C 473 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7734 (mtt-85) REVERT: C 481 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6875 (mptt) REVERT: C 746 MET cc_start: 0.8545 (mtp) cc_final: 0.8343 (mtp) REVERT: C 773 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6341 (mmm) REVERT: C 906 MET cc_start: 0.6884 (mtt) cc_final: 0.6575 (mtp) REVERT: C 1027 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: C 1161 PHE cc_start: 0.7800 (t80) cc_final: 0.7112 (m-80) REVERT: C 1188 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7658 (tmmm) REVERT: D 60 MET cc_start: -0.0184 (mpp) cc_final: -0.0669 (ppp) REVERT: D 473 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7738 (mtt-85) REVERT: D 481 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6785 (mptt) REVERT: D 906 MET cc_start: 0.6800 (mtt) cc_final: 0.6541 (mtp) REVERT: D 1027 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: D 1161 PHE cc_start: 0.7782 (t80) cc_final: 0.7182 (m-80) REVERT: D 1188 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7636 (tmmm) outliers start: 90 outliers final: 18 residues processed: 411 average time/residue: 1.7400 time to fit residues: 855.3143 Evaluate side-chains 358 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 320 time to evaluate : 4.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 773 MET Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 1027 GLU Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 6 optimal weight: 0.1980 chunk 316 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 362 optimal weight: 8.9990 chunk 293 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 217 optimal weight: 9.9990 chunk 381 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 955 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39684 Z= 0.212 Angle : 0.624 8.643 53252 Z= 0.313 Chirality : 0.042 0.221 5676 Planarity : 0.004 0.052 6364 Dihedral : 22.885 174.278 7764 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.59 % Favored : 93.14 % Rotamer: Outliers : 1.28 % Allowed : 12.28 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4388 helix: 0.97 (0.10), residues: 2624 sheet: -2.33 (0.37), residues: 188 loop : -2.46 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 78 HIS 0.005 0.001 HIS D 329 PHE 0.016 0.002 PHE C 936 TYR 0.016 0.002 TYR D1122 ARG 0.009 0.001 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 349 time to evaluate : 3.957 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: A 39 LEU cc_start: 0.1143 (OUTLIER) cc_final: 0.0711 (tt) REVERT: A 60 MET cc_start: -0.0160 (mpp) cc_final: -0.0644 (ppp) REVERT: A 289 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6856 (mp) REVERT: A 473 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7715 (mtt-85) REVERT: A 481 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6714 (mptt) REVERT: A 906 MET cc_start: 0.6710 (mtt) cc_final: 0.6494 (mtp) REVERT: A 1161 PHE cc_start: 0.7792 (t80) cc_final: 0.7188 (m-80) REVERT: A 1188 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7659 (tmmm) REVERT: B 39 LEU cc_start: 0.1149 (OUTLIER) cc_final: 0.0713 (tt) REVERT: B 60 MET cc_start: -0.0187 (mpp) cc_final: -0.0722 (ppp) REVERT: B 289 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6817 (mp) REVERT: B 473 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7690 (mtt-85) REVERT: B 481 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6690 (mptt) REVERT: B 906 MET cc_start: 0.6922 (mtp) cc_final: 0.6602 (mtp) REVERT: B 1161 PHE cc_start: 0.7750 (t80) cc_final: 0.7206 (m-80) REVERT: B 1188 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7628 (tmmm) REVERT: C 39 LEU cc_start: 0.0856 (OUTLIER) cc_final: 0.0485 (tt) REVERT: C 60 MET cc_start: -0.0615 (mpp) cc_final: -0.1148 (ppp) REVERT: C 473 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7735 (mtt-85) REVERT: C 481 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6817 (mptt) REVERT: C 906 MET cc_start: 0.6796 (mtt) cc_final: 0.6529 (mtp) REVERT: C 1161 PHE cc_start: 0.7809 (t80) cc_final: 0.7139 (m-80) REVERT: C 1188 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7672 (tmmm) REVERT: D 39 LEU cc_start: 0.1121 (OUTLIER) cc_final: 0.0677 (tt) REVERT: D 60 MET cc_start: -0.0118 (mpp) cc_final: -0.0650 (ppp) REVERT: D 473 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7710 (mtt-85) REVERT: D 481 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6733 (mptt) REVERT: D 906 MET cc_start: 0.6697 (mtt) cc_final: 0.6481 (mtp) REVERT: D 1161 PHE cc_start: 0.7790 (t80) cc_final: 0.7200 (m-80) REVERT: D 1188 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7658 (tmmm) outliers start: 50 outliers final: 17 residues processed: 390 average time/residue: 1.7673 time to fit residues: 823.7319 Evaluate side-chains 363 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 328 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 0.0060 chunk 383 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 249 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 425 optimal weight: 0.2980 chunk 353 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 35 optimal weight: 40.0000 chunk 140 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 overall best weight: 3.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN C 955 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN D 955 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39684 Z= 0.255 Angle : 0.646 8.435 53252 Z= 0.324 Chirality : 0.043 0.229 5676 Planarity : 0.005 0.054 6364 Dihedral : 22.560 172.153 7764 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.68 % Favored : 93.05 % Rotamer: Outliers : 1.71 % Allowed : 12.41 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.48 (0.13), residues: 4388 helix: 0.96 (0.10), residues: 2660 sheet: -2.65 (0.33), residues: 228 loop : -2.30 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 78 HIS 0.005 0.001 HIS A 329 PHE 0.017 0.002 PHE A 936 TYR 0.019 0.002 TYR C1122 ARG 0.008 0.001 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 339 time to evaluate : 4.309 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: A 39 LEU cc_start: 0.1145 (OUTLIER) cc_final: 0.0720 (tt) REVERT: A 60 MET cc_start: -0.0144 (mpp) cc_final: -0.0663 (ppp) REVERT: A 289 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6875 (mp) REVERT: A 473 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7730 (mtt-85) REVERT: A 481 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6658 (mptt) REVERT: A 906 MET cc_start: 0.6766 (mtt) cc_final: 0.6540 (mtp) REVERT: A 1027 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: A 1161 PHE cc_start: 0.7789 (t80) cc_final: 0.7181 (m-80) REVERT: A 1188 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7637 (tmmm) REVERT: B 39 LEU cc_start: 0.1150 (OUTLIER) cc_final: 0.0720 (tt) REVERT: B 60 MET cc_start: -0.0179 (mpp) cc_final: -0.0734 (ppp) REVERT: B 289 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.6824 (mp) REVERT: B 473 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7697 (mtt-85) REVERT: B 481 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6658 (mptt) REVERT: B 906 MET cc_start: 0.7006 (mtp) cc_final: 0.6667 (mtp) REVERT: B 1027 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: B 1161 PHE cc_start: 0.7769 (t80) cc_final: 0.7212 (m-80) REVERT: B 1188 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7605 (tmmm) REVERT: C 39 LEU cc_start: 0.0862 (OUTLIER) cc_final: 0.0511 (tt) REVERT: C 60 MET cc_start: -0.0552 (mpp) cc_final: -0.1119 (ppp) REVERT: C 473 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7753 (mtt-85) REVERT: C 481 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6738 (mptt) REVERT: C 906 MET cc_start: 0.6842 (mtt) cc_final: 0.6566 (mtp) REVERT: C 1027 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: C 1161 PHE cc_start: 0.7810 (t80) cc_final: 0.7127 (m-80) REVERT: C 1188 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7665 (tmmm) REVERT: D 39 LEU cc_start: 0.1164 (OUTLIER) cc_final: 0.0723 (tt) REVERT: D 60 MET cc_start: -0.0169 (mpp) cc_final: -0.0718 (ppp) REVERT: D 473 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7719 (mtt-85) REVERT: D 481 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6661 (mptt) REVERT: D 906 MET cc_start: 0.6754 (mtt) cc_final: 0.6548 (mtp) REVERT: D 1027 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: D 1161 PHE cc_start: 0.7793 (t80) cc_final: 0.7190 (m-80) REVERT: D 1188 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7624 (tmmm) outliers start: 67 outliers final: 16 residues processed: 398 average time/residue: 1.7316 time to fit residues: 825.5141 Evaluate side-chains 364 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 326 time to evaluate : 4.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 1027 GLU Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 1027 GLU Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 310 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 chunk 358 optimal weight: 6.9990 chunk 237 optimal weight: 0.0570 chunk 424 optimal weight: 4.9990 chunk 265 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39684 Z= 0.249 Angle : 0.644 9.871 53252 Z= 0.323 Chirality : 0.043 0.231 5676 Planarity : 0.005 0.054 6364 Dihedral : 22.367 172.330 7764 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.70 % Favored : 93.03 % Rotamer: Outliers : 1.71 % Allowed : 12.51 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.39 (0.13), residues: 4388 helix: 1.03 (0.10), residues: 2660 sheet: -2.57 (0.34), residues: 228 loop : -2.28 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 78 HIS 0.006 0.001 HIS A 329 PHE 0.034 0.002 PHE B 365 TYR 0.021 0.002 TYR C 776 ARG 0.008 0.001 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 336 time to evaluate : 4.134 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: A 39 LEU cc_start: 0.1155 (OUTLIER) cc_final: 0.0720 (tt) REVERT: A 60 MET cc_start: -0.0180 (mpp) cc_final: -0.0728 (ppp) REVERT: A 289 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6878 (mp) REVERT: A 401 LYS cc_start: 0.6552 (mmmm) cc_final: 0.6330 (mmmm) REVERT: A 473 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7739 (mtt-85) REVERT: A 481 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6649 (mptt) REVERT: A 906 MET cc_start: 0.6773 (mtt) cc_final: 0.6556 (mtp) REVERT: A 1027 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: A 1161 PHE cc_start: 0.7793 (t80) cc_final: 0.7179 (m-80) REVERT: A 1188 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7635 (tmmm) REVERT: B 39 LEU cc_start: 0.1158 (OUTLIER) cc_final: 0.0722 (tt) REVERT: B 60 MET cc_start: -0.0257 (mpp) cc_final: -0.0799 (ppp) REVERT: B 105 ARG cc_start: 0.6681 (mtm110) cc_final: 0.6376 (mtm-85) REVERT: B 289 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6813 (mp) REVERT: B 473 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7714 (mtt-85) REVERT: B 481 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6651 (mptt) REVERT: B 906 MET cc_start: 0.6985 (mtp) cc_final: 0.6678 (mtp) REVERT: B 1027 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: B 1161 PHE cc_start: 0.7766 (t80) cc_final: 0.7212 (m-80) REVERT: B 1188 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7619 (tmmm) REVERT: C 39 LEU cc_start: 0.0919 (OUTLIER) cc_final: 0.0576 (tt) REVERT: C 60 MET cc_start: -0.0650 (mpp) cc_final: -0.1225 (ppp) REVERT: C 401 LYS cc_start: 0.6724 (mmmm) cc_final: 0.6466 (mmmm) REVERT: C 473 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7763 (mtt-85) REVERT: C 481 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6730 (mptt) REVERT: C 906 MET cc_start: 0.6851 (mtt) cc_final: 0.6581 (mtp) REVERT: C 1027 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: C 1161 PHE cc_start: 0.7801 (t80) cc_final: 0.7115 (m-80) REVERT: C 1188 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7656 (tmmm) REVERT: D 39 LEU cc_start: 0.1212 (OUTLIER) cc_final: 0.0772 (tt) REVERT: D 60 MET cc_start: -0.0196 (mpp) cc_final: -0.0735 (ppp) REVERT: D 473 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7737 (mtt-85) REVERT: D 481 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6666 (mptt) REVERT: D 906 MET cc_start: 0.6760 (mtt) cc_final: 0.6546 (mtp) REVERT: D 1027 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: D 1161 PHE cc_start: 0.7789 (t80) cc_final: 0.7182 (m-80) REVERT: D 1188 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7630 (tmmm) outliers start: 67 outliers final: 20 residues processed: 394 average time/residue: 1.8459 time to fit residues: 866.7978 Evaluate side-chains 362 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 320 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 1027 GLU Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 1027 GLU Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 5.9990 chunk 169 optimal weight: 0.0000 chunk 253 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 269 optimal weight: 0.0980 chunk 288 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 333 optimal weight: 6.9990 overall best weight: 3.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** 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: 0.7280 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39684 Z= 0.261 Angle : 0.655 8.414 53252 Z= 0.326 Chirality : 0.044 0.255 5676 Planarity : 0.005 0.055 6364 Dihedral : 22.245 171.565 7764 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.16 % Favored : 92.57 % Rotamer: Outliers : 1.48 % Allowed : 13.05 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.34 (0.13), residues: 4388 helix: 1.06 (0.10), residues: 2660 sheet: -2.11 (0.39), residues: 188 loop : -2.34 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 747 HIS 0.006 0.001 HIS A 329 PHE 0.041 0.002 PHE C 365 TYR 0.023 0.002 TYR C 776 ARG 0.006 0.000 ARG A 843 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 338 time to evaluate : 4.366 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 39 LEU cc_start: 0.1134 (OUTLIER) cc_final: 0.0729 (tt) REVERT: A 60 MET cc_start: -0.0238 (mpp) cc_final: -0.0774 (ppp) REVERT: A 289 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.6864 (mp) REVERT: A 473 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7741 (mtt-85) REVERT: A 481 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6614 (mptt) REVERT: A 906 MET cc_start: 0.6777 (mtt) cc_final: 0.6547 (mtp) REVERT: A 1027 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: A 1161 PHE cc_start: 0.7784 (t80) cc_final: 0.7165 (m-80) REVERT: A 1188 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7647 (tmmm) REVERT: B 39 LEU cc_start: 0.1085 (OUTLIER) cc_final: 0.0661 (tt) REVERT: B 60 MET cc_start: -0.0303 (mpp) cc_final: -0.0850 (ppp) REVERT: B 105 ARG cc_start: 0.6690 (mtm110) cc_final: 0.6385 (mtm-85) REVERT: B 289 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.6823 (mp) REVERT: B 473 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7717 (mtt-85) REVERT: B 481 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6649 (mptt) REVERT: B 906 MET cc_start: 0.6994 (mtp) cc_final: 0.6683 (mtp) REVERT: B 1027 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: B 1161 PHE cc_start: 0.7773 (t80) cc_final: 0.7207 (m-80) REVERT: B 1188 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7623 (tmmm) REVERT: C 39 LEU cc_start: 0.0874 (OUTLIER) cc_final: 0.0533 (tt) REVERT: C 60 MET cc_start: -0.0700 (mpp) cc_final: -0.1249 (ppp) REVERT: C 110 ARG cc_start: 0.5771 (tpt-90) cc_final: 0.5499 (tpt-90) REVERT: C 401 LYS cc_start: 0.6690 (mmmm) cc_final: 0.6478 (mmmm) REVERT: C 473 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7764 (mtt-85) REVERT: C 481 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6730 (mptt) REVERT: C 906 MET cc_start: 0.6870 (mtt) cc_final: 0.6607 (mtp) REVERT: C 1027 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: C 1161 PHE cc_start: 0.7800 (t80) cc_final: 0.7103 (m-80) REVERT: C 1188 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7661 (tmmm) REVERT: D 39 LEU cc_start: 0.1106 (OUTLIER) cc_final: 0.0674 (tt) REVERT: D 60 MET cc_start: -0.0273 (mpp) cc_final: -0.0827 (ppp) REVERT: D 473 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7738 (mtt-85) REVERT: D 481 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6653 (mptt) REVERT: D 906 MET cc_start: 0.6773 (mtt) cc_final: 0.6552 (mtp) REVERT: D 1027 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: D 1161 PHE cc_start: 0.7804 (t80) cc_final: 0.7185 (m-80) REVERT: D 1188 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7622 (tmmm) outliers start: 58 outliers final: 24 residues processed: 386 average time/residue: 1.7538 time to fit residues: 808.6386 Evaluate side-chains 371 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 325 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 1027 GLU Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 844 LYS Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1102 GLN Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 1027 GLU Chi-restraints excluded: chain D residue 1102 GLN Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 2.9990 chunk 406 optimal weight: 6.9990 chunk 370 optimal weight: 7.9990 chunk 395 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 121 optimal weight: 0.1980 chunk 357 optimal weight: 0.0670 chunk 373 optimal weight: 2.9990 chunk 393 optimal weight: 0.9990 overall best weight: 0.8524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN ** 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: 0.7220 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 39684 Z= 0.153 Angle : 0.582 8.982 53252 Z= 0.290 Chirality : 0.040 0.226 5676 Planarity : 0.004 0.053 6364 Dihedral : 21.502 172.135 7764 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.77 % Favored : 92.96 % Rotamer: Outliers : 1.15 % Allowed : 13.82 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.02 (0.13), residues: 4388 helix: 1.37 (0.10), residues: 2652 sheet: -1.07 (0.43), residues: 156 loop : -2.34 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 747 HIS 0.005 0.001 HIS C 329 PHE 0.063 0.001 PHE C 365 TYR 0.015 0.001 TYR C 776 ARG 0.008 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 352 time to evaluate : 4.417 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 60 MET cc_start: -0.0372 (mpp) cc_final: -0.0921 (ppp) REVERT: A 289 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6875 (mp) REVERT: A 449 MET cc_start: 0.8438 (mtp) cc_final: 0.8189 (mtp) REVERT: A 473 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: A 1161 PHE cc_start: 0.7789 (t80) cc_final: 0.7183 (m-80) REVERT: A 1188 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7612 (tmmm) REVERT: B 60 MET cc_start: -0.0436 (mpp) cc_final: -0.0988 (ppp) REVERT: B 110 ARG cc_start: 0.4726 (tpt-90) cc_final: 0.4203 (mmm160) REVERT: B 289 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6854 (mp) REVERT: B 473 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7723 (mtt-85) REVERT: B 1161 PHE cc_start: 0.7773 (t80) cc_final: 0.7225 (m-80) REVERT: B 1188 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7584 (tmmm) REVERT: C 60 MET cc_start: -0.0850 (mpp) cc_final: -0.1387 (ppp) REVERT: C 110 ARG cc_start: 0.5761 (tpt-90) cc_final: 0.5431 (tpt-90) REVERT: C 473 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7775 (mtt-85) REVERT: C 906 MET cc_start: 0.6730 (mtt) cc_final: 0.6521 (mtp) REVERT: C 1161 PHE cc_start: 0.7785 (t80) cc_final: 0.7117 (m-80) REVERT: C 1188 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7629 (tmmm) REVERT: D 60 MET cc_start: -0.0391 (mpp) cc_final: -0.0957 (ppp) REVERT: D 105 ARG cc_start: 0.6682 (mtm110) cc_final: 0.6388 (mtm-85) REVERT: D 110 ARG cc_start: 0.4859 (tpt-90) cc_final: 0.4143 (mmm160) REVERT: D 368 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.5540 (mpp) REVERT: D 473 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7745 (mtt-85) REVERT: D 1161 PHE cc_start: 0.7795 (t80) cc_final: 0.7195 (m-80) REVERT: D 1188 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7613 (tmmm) outliers start: 45 outliers final: 21 residues processed: 387 average time/residue: 1.6321 time to fit residues: 763.5008 Evaluate side-chains 352 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 320 time to evaluate : 4.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 1188 LYS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 1188 LYS Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 737 THR Chi-restraints excluded: chain D residue 1188 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 9.9990 chunk 417 optimal weight: 3.9990 chunk 255 optimal weight: 0.5980 chunk 198 optimal weight: 7.9990 chunk 290 optimal weight: 0.6980 chunk 438 optimal weight: 0.9980 chunk 403 optimal weight: 3.9990 chunk 349 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 269 optimal weight: 8.9990 chunk 214 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3887 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: