Starting phenix.real_space_refine on Fri Feb 23 14:08:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtc_6772/02_2024/5xtc_6772_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtc_6772/02_2024/5xtc_6772.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtc_6772/02_2024/5xtc_6772_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtc_6772/02_2024/5xtc_6772_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtc_6772/02_2024/5xtc_6772_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtc_6772/02_2024/5xtc_6772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtc_6772/02_2024/5xtc_6772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtc_6772/02_2024/5xtc_6772_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtc_6772/02_2024/5xtc_6772_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 246 5.16 5 C 25473 2.51 5 N 6270 2.21 5 O 6822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S ARG 50": "NH1" <-> "NH2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 82": "NH1" <-> "NH2" Residue "W ARG 88": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 43": "NH1" <-> "NH2" Residue "Y ARG 72": "NH1" <-> "NH2" Residue "Y GLU 79": "OE1" <-> "OE2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Z ARG 42": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "b ARG 58": "NH1" <-> "NH2" Residue "b GLU 92": "OE1" <-> "OE2" Residue "b ARG 103": "NH1" <-> "NH2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "c ARG 58": "NH1" <-> "NH2" Residue "d ARG 103": "NH1" <-> "NH2" Residue "d ARG 147": "NH1" <-> "NH2" Residue "d ARG 161": "NH1" <-> "NH2" Residue "e ARG 113": "NH1" <-> "NH2" Residue "g ARG 5": "NH1" <-> "NH2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 77": "NH1" <-> "NH2" Residue "g ARG 85": "NH1" <-> "NH2" Residue "h ARG 32": "NH1" <-> "NH2" Residue "h ARG 74": "NH1" <-> "NH2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "i ARG 232": "NH1" <-> "NH2" Residue "k ARG 23": "NH1" <-> "NH2" Residue "l PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 357": "NH1" <-> "NH2" Residue "l ARG 425": "NH1" <-> "NH2" Residue "l ARG 456": "NH1" <-> "NH2" Residue "n ARG 29": "NH1" <-> "NH2" Residue "o ARG 72": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 45": "NH1" <-> "NH2" Residue "p ARG 173": "NH1" <-> "NH2" Residue "p ARG 175": "NH1" <-> "NH2" Residue "r ARG 82": "NH1" <-> "NH2" Residue "r ARG 135": "NH1" <-> "NH2" Residue "r ARG 432": "NH1" <-> "NH2" Residue "s ARG 34": "NH1" <-> "NH2" Residue "s PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 281": "NH1" <-> "NH2" Residue "u ARG 47": "NH1" <-> "NH2" Residue "u ARG 98": "NH1" <-> "NH2" Residue "u ARG 101": "NH1" <-> "NH2" Residue "u ARG 119": "NH1" <-> "NH2" Residue "u ARG 145": "NH1" <-> "NH2" Residue "u ARG 166": "NH1" <-> "NH2" Residue "v ARG 7": "NH1" <-> "NH2" Residue "v ARG 71": "NH1" <-> "NH2" Residue "v ARG 104": "NH1" <-> "NH2" Residue "w ARG 295": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38835 Number of models: 1 Model: "" Number of chains: 40 Chain: "Q" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 381 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 7, 'TRANS': 38} Chain: "S" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 568 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "U" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 647 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 70} Chain: "V" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1038 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 132} Chain: "W" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 956 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "X" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 686 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 533 Classifications: {'peptide': 59} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 53} Chain: "Z" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "a" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1174 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "b" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1059 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 13, 'TRANS': 110} Chain: "c" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1236 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 133} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "d" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1418 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 161} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "e" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 810 Classifications: {'peptide': 97} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 88} Chain: "f" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 405 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 3, 'TRANS': 43} Chain: "g" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1004 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 11, 'TRANS': 107} Chain: "h" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 863 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "i" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2735 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 323} Chain: "j" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 919 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 740 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "l" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4717 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 570} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1313 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain: "n" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 473 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1066 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1495 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 16, 'TRANS': 155} Chain: "r" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3629 Classifications: {'peptide': 459} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 436} Chain: "s" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "u" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1394 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 13, 'TRANS': 155} Chain: "v" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 921 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "w" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2474 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 15, 'TRANS': 304} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "U" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 166 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'CDL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'PLX': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "l" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 228 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 74 Chain: "n" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "p" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'PLX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "s" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.01, per 1000 atoms: 0.49 Number of scatterers: 38835 At special positions: 0 Unit cell: (179.778, 202.521, 141.873, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 246 16.00 P 24 15.00 O 6822 8.00 N 6270 7.00 C 25473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS l 279 " distance=2.05 Simple disulfide: pdb=" SG CYS d 149 " - pdb=" SG CYS e 141 " distance=2.04 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.02 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.02 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=1.94 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.80 Conformation dependent library (CDL) restraints added in 6.5 seconds 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 206 helices and 1 sheets defined 63.6% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.34 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 48 removed outlier: 4.212A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 78 removed outlier: 3.764A pdb=" N ILE Q 76 " --> pdb=" O PRO Q 72 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL Q 77 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS Q 78 " --> pdb=" O ASP Q 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 30 Proline residue: S 7 - end of helix removed outlier: 3.716A pdb=" N VAL S 14 " --> pdb=" O VAL S 11 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU S 16 " --> pdb=" O GLY S 13 " (cutoff:3.500A) Proline residue: S 19 - end of helix removed outlier: 4.059A pdb=" N ALA S 24 " --> pdb=" O LEU S 21 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS S 27 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG S 28 " --> pdb=" O TYR S 25 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 55 removed outlier: 3.649A pdb=" N ILE S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 69 Processing helix chain 'U' and resid 3 through 14 removed outlier: 3.917A pdb=" N PHE U 8 " --> pdb=" O ARG U 4 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP U 14 " --> pdb=" O LYS U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 37 through 48 removed outlier: 3.865A pdb=" N LYS U 40 " --> pdb=" O PRO U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 3 through 10 removed outlier: 3.907A pdb=" N TRP V 10 " --> pdb=" O PHE V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 18 through 43 removed outlier: 4.562A pdb=" N SER V 24 " --> pdb=" O ARG V 20 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR V 25 " --> pdb=" O LYS V 21 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SER V 27 " --> pdb=" O TYR V 23 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA V 29 " --> pdb=" O THR V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 removed outlier: 4.007A pdb=" N VAL V 116 " --> pdb=" O ALA V 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 69 removed outlier: 3.673A pdb=" N THR W 42 " --> pdb=" O ILE W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 100 removed outlier: 5.218A pdb=" N ASP W 100 " --> pdb=" O ILE W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 124 No H-bonds generated for 'chain 'W' and resid 121 through 124' Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.278A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET W 141 " --> pdb=" O SER W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 89 removed outlier: 3.811A pdb=" N ASP X 81 " --> pdb=" O GLU X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 126 removed outlier: 3.528A pdb=" N VAL X 116 " --> pdb=" O SER X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 151 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 38 Processing helix chain 'Z' and resid 44 through 53 removed outlier: 4.492A pdb=" N ARG Z 47 " --> pdb=" O PRO Z 44 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG Z 52 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR Z 53 " --> pdb=" O ALA Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'a' and resid 62 through 77 removed outlier: 3.781A pdb=" N LEU a 68 " --> pdb=" O ASP a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 92 Processing helix chain 'a' and resid 109 through 112 Processing helix chain 'a' and resid 116 through 124 Processing helix chain 'a' and resid 129 through 163 removed outlier: 3.702A pdb=" N MET a 137 " --> pdb=" O TYR a 133 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL a 151 " --> pdb=" O ALA a 147 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 40 through 47 Processing helix chain 'b' and resid 49 through 52 No H-bonds generated for 'chain 'b' and resid 49 through 52' Processing helix chain 'b' and resid 56 through 74 removed outlier: 3.882A pdb=" N VAL b 61 " --> pdb=" O TRP b 57 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL b 64 " --> pdb=" O MET b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 92 removed outlier: 4.749A pdb=" N SER b 91 " --> pdb=" O LYS b 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 83 through 85 No H-bonds generated for 'chain 'c' and resid 83 through 85' Processing helix chain 'c' and resid 110 through 112 No H-bonds generated for 'chain 'c' and resid 110 through 112' Processing helix chain 'c' and resid 126 through 149 removed outlier: 3.539A pdb=" N ASP c 148 " --> pdb=" O CYS c 144 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL c 149 " --> pdb=" O TRP c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 169 removed outlier: 3.504A pdb=" N TYR c 167 " --> pdb=" O TYR c 163 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU c 168 " --> pdb=" O ASN c 164 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU c 169 " --> pdb=" O ASN c 165 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 6 Processing helix chain 'd' and resid 22 through 34 Processing helix chain 'd' and resid 36 through 52 removed outlier: 4.497A pdb=" N GLN d 49 " --> pdb=" O PHE d 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS d 50 " --> pdb=" O ILE d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 70 No H-bonds generated for 'chain 'd' and resid 68 through 70' Processing helix chain 'd' and resid 77 through 110 removed outlier: 3.774A pdb=" N LYS d 91 " --> pdb=" O LYS d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 136 removed outlier: 4.217A pdb=" N ILE d 120 " --> pdb=" O GLN d 116 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS d 121 " --> pdb=" O GLN d 117 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU d 122 " --> pdb=" O ASN d 118 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL d 123 " --> pdb=" O CYS d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 170 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 93 Processing helix chain 'e' and resid 98 through 108 removed outlier: 3.877A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 through 132 Processing helix chain 'f' and resid 29 through 38 Proline residue: f 34 - end of helix removed outlier: 4.008A pdb=" N ALA f 37 " --> pdb=" O GLU f 33 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 72 removed outlier: 4.223A pdb=" N PHE f 46 " --> pdb=" O LEU f 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 15 through 19 Processing helix chain 'g' and resid 28 through 47 Processing helix chain 'g' and resid 57 through 95 Processing helix chain 'g' and resid 97 through 99 No H-bonds generated for 'chain 'g' and resid 97 through 99' Processing helix chain 'h' and resid 6 through 9 No H-bonds generated for 'chain 'h' and resid 6 through 9' Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 35 through 43 Processing helix chain 'h' and resid 52 through 55 No H-bonds generated for 'chain 'h' and resid 52 through 55' Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 84 Processing helix chain 'h' and resid 94 through 96 No H-bonds generated for 'chain 'h' and resid 94 through 96' Processing helix chain 'i' and resid 3 through 22 Proline residue: i 7 - end of helix removed outlier: 3.559A pdb=" N THR i 12 " --> pdb=" O VAL i 8 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR i 20 " --> pdb=" O GLY i 16 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA i 21 " --> pdb=" O THR i 17 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.775A pdb=" N THR i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 80 removed outlier: 3.737A pdb=" N ALA i 56 " --> pdb=" O SER i 52 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE i 57 " --> pdb=" O THR i 53 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR i 62 " --> pdb=" O LYS i 58 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER i 67 " --> pdb=" O GLN i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 105 Processing helix chain 'i' and resid 112 through 121 Proline residue: i 116 - end of helix removed outlier: 3.740A pdb=" N THR i 119 " --> pdb=" O PRO i 116 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY i 121 " --> pdb=" O VAL i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 131 Processing helix chain 'i' and resid 133 through 144 removed outlier: 4.173A pdb=" N ALA i 137 " --> pdb=" O GLN i 134 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 170 removed outlier: 3.863A pdb=" N GLY i 169 " --> pdb=" O GLY i 165 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU i 170 " --> pdb=" O SER i 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 removed outlier: 3.608A pdb=" N MET i 191 " --> pdb=" O MET i 187 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 222 removed outlier: 3.500A pdb=" N ASN i 204 " --> pdb=" O THR i 201 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE i 207 " --> pdb=" O ASN i 204 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN i 222 " --> pdb=" O LEU i 219 " (cutoff:3.500A) Processing helix chain 'i' and resid 227 through 234 removed outlier: 4.217A pdb=" N ARG i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR i 233 " --> pdb=" O LEU i 229 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Proline residue: i 242 - end of helix Proline residue: i 245 - end of helix Processing helix chain 'i' and resid 259 through 273 removed outlier: 4.288A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 299 removed outlier: 4.277A pdb=" N LEU i 287 " --> pdb=" O ALA i 283 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU i 288 " --> pdb=" O THR i 284 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN i 289 " --> pdb=" O ILE i 285 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR i 293 " --> pdb=" O ASN i 289 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER i 299 " --> pdb=" O ARG i 295 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 314 Processing helix chain 'i' and resid 326 through 333 Processing helix chain 'i' and resid 335 through 346 Proline residue: i 338 - end of helix Proline residue: i 341 - end of helix removed outlier: 3.738A pdb=" N LEU i 344 " --> pdb=" O PRO i 341 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET i 345 " --> pdb=" O PHE i 342 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 23 removed outlier: 4.185A pdb=" N ASN j 10 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP j 23 " --> pdb=" O ILE j 19 " (cutoff:3.500A) Processing helix chain 'j' and resid 54 through 80 removed outlier: 4.350A pdb=" N VAL j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU j 72 " --> pdb=" O GLU j 68 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.836A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 removed outlier: 3.781A pdb=" N MET j 89 " --> pdb=" O PRO j 85 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU j 105 " --> pdb=" O SER j 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 21 Processing helix chain 'k' and resid 27 through 50 removed outlier: 4.104A pdb=" N MET k 47 " --> pdb=" O MET k 43 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR k 48 " --> pdb=" O ALA k 44 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 84 Proline residue: k 60 - end of helix removed outlier: 3.676A pdb=" N MET k 63 " --> pdb=" O PRO k 60 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR k 84 " --> pdb=" O ILE k 81 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 24 removed outlier: 3.771A pdb=" N LEU l 12 " --> pdb=" O ALA l 8 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) Proline residue: l 17 - end of helix Processing helix chain 'l' and resid 31 through 56 removed outlier: 3.741A pdb=" N LYS l 37 " --> pdb=" O PRO l 33 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE l 49 " --> pdb=" O ILE l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 removed outlier: 3.746A pdb=" N ILE l 90 " --> pdb=" O SER l 86 " (cutoff:3.500A) Proline residue: l 91 - end of helix removed outlier: 3.623A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 removed outlier: 4.198A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.737A pdb=" N ILE l 172 " --> pdb=" O ALA l 168 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 223 Processing helix chain 'l' and resid 227 through 236 Proline residue: l 231 - end of helix Proline residue: l 234 - end of helix Processing helix chain 'l' and resid 241 through 247 Processing helix chain 'l' and resid 253 through 262 removed outlier: 3.679A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.497A pdb=" N ASN l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 293 removed outlier: 3.679A pdb=" N LEU l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 removed outlier: 3.620A pdb=" N ILE l 317 " --> pdb=" O MET l 313 " (cutoff:3.500A) Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.735A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE l 335 " --> pdb=" O THR l 331 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS l 336 " --> pdb=" O HIS l 332 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE l 346 " --> pdb=" O CYS l 342 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 381 Processing helix chain 'l' and resid 392 through 401 Processing helix chain 'l' and resid 407 through 430 removed outlier: 3.924A pdb=" N SER l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 452 through 471 removed outlier: 5.597A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE l 466 " --> pdb=" O LEU l 462 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN l 470 " --> pdb=" O PHE l 466 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 508 removed outlier: 4.436A pdb=" N ALA l 490 " --> pdb=" O LEU l 486 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU l 491 " --> pdb=" O LYS l 487 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 529 through 546 removed outlier: 4.336A pdb=" N ARG l 535 " --> pdb=" O SER l 531 " (cutoff:3.500A) Proline residue: l 538 - end of helix removed outlier: 4.101A pdb=" N SER l 545 " --> pdb=" O GLY l 541 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 564 through 576 Processing helix chain 'l' and resid 584 through 599 removed outlier: 3.718A pdb=" N PHE l 588 " --> pdb=" O ILE l 584 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE l 592 " --> pdb=" O PHE l 588 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE l 593 " --> pdb=" O LEU l 589 " (cutoff:3.500A) Proline residue: l 594 - end of helix Processing helix chain 'm' and resid 4 through 21 removed outlier: 4.017A pdb=" N LEU m 8 " --> pdb=" O ALA m 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 46 removed outlier: 4.078A pdb=" N LEU m 30 " --> pdb=" O ILE m 26 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE m 46 " --> pdb=" O ILE m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 58 removed outlier: 3.651A pdb=" N VAL m 55 " --> pdb=" O MET m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 63 through 74 removed outlier: 3.535A pdb=" N ALA m 72 " --> pdb=" O GLY m 68 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N MET m 73 " --> pdb=" O TYR m 69 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA m 74 " --> pdb=" O THR m 70 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 112 removed outlier: 6.925A pdb=" N GLY m 111 " --> pdb=" O LYS m 107 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL m 112 " --> pdb=" O GLU m 108 " (cutoff:3.500A) Processing helix chain 'm' and resid 137 through 145 removed outlier: 4.040A pdb=" N LEU m 145 " --> pdb=" O GLY m 141 " (cutoff:3.500A) Processing helix chain 'm' and resid 150 through 173 removed outlier: 4.033A pdb=" N TYR m 165 " --> pdb=" O PHE m 161 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY m 173 " --> pdb=" O GLU m 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 9 removed outlier: 3.725A pdb=" N VAL n 8 " --> pdb=" O LEU n 4 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG n 9 " --> pdb=" O LEU n 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 4 through 9' Processing helix chain 'n' and resid 11 through 38 removed outlier: 3.682A pdb=" N HIS n 14 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL n 17 " --> pdb=" O HIS n 14 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.881A pdb=" N ILE n 23 " --> pdb=" O GLY n 20 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP n 28 " --> pdb=" O CYS n 25 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP n 32 " --> pdb=" O ARG n 29 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR n 36 " --> pdb=" O GLU n 33 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA n 37 " --> pdb=" O ARG n 34 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE n 38 " --> pdb=" O LEU n 35 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 52 removed outlier: 3.598A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 71 Processing helix chain 'o' and resid 74 through 79 Proline residue: o 78 - end of helix No H-bonds generated for 'chain 'o' and resid 74 through 79' Processing helix chain 'o' and resid 84 through 117 Proline residue: o 97 - end of helix removed outlier: 3.734A pdb=" N GLU o 108 " --> pdb=" O ILE o 104 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN o 117 " --> pdb=" O GLU o 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 12 through 31 Processing helix chain 'p' and resid 34 through 51 removed outlier: 3.623A pdb=" N GLU p 50 " --> pdb=" O ALA p 46 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 58 through 74 Processing helix chain 'p' and resid 101 through 106 removed outlier: 3.946A pdb=" N ASP p 105 " --> pdb=" O TRP p 102 " (cutoff:3.500A) Processing helix chain 'p' and resid 109 through 112 No H-bonds generated for 'chain 'p' and resid 109 through 112' Processing helix chain 'p' and resid 116 through 143 removed outlier: 4.403A pdb=" N GLU p 123 " --> pdb=" O PHE p 119 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN p 124 " --> pdb=" O ALA p 120 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP p 125 " --> pdb=" O LYS p 121 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 17 Proline residue: r 7 - end of helix removed outlier: 4.366A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 41 removed outlier: 3.906A pdb=" N THR r 29 " --> pdb=" O ILE r 25 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE r 36 " --> pdb=" O LEU r 32 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE r 37 " --> pdb=" O ILE r 33 " (cutoff:3.500A) Proline residue: r 38 - end of helix Processing helix chain 'r' and resid 60 through 83 Proline residue: r 64 - end of helix Proline residue: r 74 - end of helix removed outlier: 3.640A pdb=" N GLN r 81 " --> pdb=" O ILE r 77 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 109 removed outlier: 4.051A pdb=" N LEU r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.858A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 148 removed outlier: 4.397A pdb=" N GLY r 146 " --> pdb=" O LEU r 143 " (cutoff:3.500A) Processing helix chain 'r' and resid 150 through 170 removed outlier: 3.564A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.607A pdb=" N ILE r 165 " --> pdb=" O LEU r 161 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 removed outlier: 3.529A pdb=" N LEU r 181 " --> pdb=" O LEU r 177 " (cutoff:3.500A) Processing helix chain 'r' and resid 189 through 206 removed outlier: 3.660A pdb=" N ASN r 193 " --> pdb=" O SER r 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU r 194 " --> pdb=" O TRP r 190 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE r 203 " --> pdb=" O TYR r 199 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 210 through 212 No H-bonds generated for 'chain 'r' and resid 210 through 212' Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.143A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL r 221 " --> pdb=" O PRO r 217 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 248 removed outlier: 4.119A pdb=" N MET r 229 " --> pdb=" O ILE r 225 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL r 230 " --> pdb=" O ALA r 226 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL r 234 " --> pdb=" O VAL r 230 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU r 236 " --> pdb=" O ALA r 232 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS r 237 " --> pdb=" O ALA r 233 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET r 243 " --> pdb=" O GLY r 239 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 278 removed outlier: 4.120A pdb=" N ILE r 270 " --> pdb=" O LEU r 266 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 3.725A pdb=" N LEU r 296 " --> pdb=" O SER r 292 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL r 297 " --> pdb=" O HIS r 293 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.570A pdb=" N THR r 310 " --> pdb=" O PRO r 306 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER r 332 " --> pdb=" O CYS r 328 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 342 through 344 No H-bonds generated for 'chain 'r' and resid 342 through 344' Processing helix chain 'r' and resid 348 through 350 No H-bonds generated for 'chain 'r' and resid 348 through 350' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 414 removed outlier: 3.744A pdb=" N LEU r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR r 403 " --> pdb=" O MET r 400 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR r 406 " --> pdb=" O THR r 403 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N SER r 407 " --> pdb=" O ALA r 404 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR r 412 " --> pdb=" O TYR r 409 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 424 through 426 No H-bonds generated for 'chain 'r' and resid 424 through 426' Processing helix chain 'r' and resid 431 through 447 removed outlier: 3.706A pdb=" N HIS r 440 " --> pdb=" O LEU r 436 " (cutoff:3.500A) Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 451 through 455 removed outlier: 3.517A pdb=" N THR r 455 " --> pdb=" O ASP r 452 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 4.007A pdb=" N ARG s 25 " --> pdb=" O MET s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 87 Proline residue: s 75 - end of helix removed outlier: 4.308A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR s 87 " --> pdb=" O LEU s 83 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.543A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 157 removed outlier: 4.416A pdb=" N LEU s 133 " --> pdb=" O LEU s 129 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG s 134 " --> pdb=" O ILE s 130 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 162 through 169 removed outlier: 3.601A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN s 169 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 179 through 193 removed outlier: 3.885A pdb=" N ILE s 187 " --> pdb=" O MET s 183 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR s 193 " --> pdb=" O THR s 189 " (cutoff:3.500A) Processing helix chain 's' and resid 196 through 198 No H-bonds generated for 'chain 's' and resid 196 through 198' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 removed outlier: 4.090A pdb=" N THR s 275 " --> pdb=" O LEU s 271 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA s 276 " --> pdb=" O TRP s 272 " (cutoff:3.500A) Processing helix chain 's' and resid 282 through 289 removed outlier: 4.317A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS s 287 " --> pdb=" O ASP s 283 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU s 288 " --> pdb=" O GLN s 284 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU s 289 " --> pdb=" O LEU s 285 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 282 through 289' Processing helix chain 's' and resid 294 through 310 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 22 through 35 removed outlier: 3.884A pdb=" N ALA u 27 " --> pdb=" O ALA u 23 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA u 34 " --> pdb=" O HIS u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 48 removed outlier: 3.610A pdb=" N CYS u 46 " --> pdb=" O GLU u 42 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 75 removed outlier: 3.836A pdb=" N LEU u 57 " --> pdb=" O ARG u 54 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLU u 58 " --> pdb=" O ARG u 55 " (cutoff:3.500A) Processing helix chain 'u' and resid 80 through 90 removed outlier: 3.753A pdb=" N GLU u 84 " --> pdb=" O GLU u 80 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR u 85 " --> pdb=" O PRO u 81 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE u 89 " --> pdb=" O TYR u 85 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP u 90 " --> pdb=" O TRP u 86 " (cutoff:3.500A) Processing helix chain 'u' and resid 97 through 99 No H-bonds generated for 'chain 'u' and resid 97 through 99' Processing helix chain 'u' and resid 101 through 112 removed outlier: 3.800A pdb=" N LYS u 106 " --> pdb=" O GLN u 103 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU u 109 " --> pdb=" O LYS u 106 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 11 Processing helix chain 'v' and resid 44 through 49 Processing helix chain 'v' and resid 58 through 72 removed outlier: 4.422A pdb=" N HIS v 61 " --> pdb=" O TYR v 58 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS v 62 " --> pdb=" O CYS v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 122 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 72 through 80 removed outlier: 3.625A pdb=" N GLU w 76 " --> pdb=" O LYS w 72 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU w 79 " --> pdb=" O LYS w 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS w 80 " --> pdb=" O GLU w 76 " (cutoff:3.500A) Processing helix chain 'w' and resid 93 through 97 Processing helix chain 'w' and resid 106 through 109 No H-bonds generated for 'chain 'w' and resid 106 through 109' Processing helix chain 'w' and resid 114 through 118 Processing helix chain 'w' and resid 129 through 136 Processing helix chain 'w' and resid 139 through 153 Processing helix chain 'w' and resid 163 through 165 No H-bonds generated for 'chain 'w' and resid 163 through 165' Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.538A pdb=" N CYS w 196 " --> pdb=" O SER w 192 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASP w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 removed outlier: 3.928A pdb=" N GLN w 219 " --> pdb=" O GLN w 215 " (cutoff:3.500A) Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 251 Proline residue: w 247 - end of helix Processing helix chain 'w' and resid 263 through 269 removed outlier: 3.517A pdb=" N LYS w 268 " --> pdb=" O GLN w 264 " (cutoff:3.500A) Processing helix chain 'w' and resid 274 through 276 No H-bonds generated for 'chain 'w' and resid 274 through 276' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 323 through 333 removed outlier: 3.530A pdb=" N HIS w 329 " --> pdb=" O ASP w 325 " (cutoff:3.500A) Processing helix chain 'w' and resid 351 through 354 Processing sheet with id= A, first strand: chain 'w' and resid 61 through 63 removed outlier: 3.636A pdb=" N ILE w 205 " --> pdb=" O THR w 61 " (cutoff:3.500A) 1861 hydrogen bonds defined for protein. 5052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.32 Time building geometry restraints manager: 17.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5887 1.31 - 1.43: 10887 1.43 - 1.56: 22586 1.56 - 1.69: 56 1.69 - 1.82: 437 Bond restraints: 39853 Sorted by residual: bond pdb=" CB7 CDL l 704 " pdb=" OB8 CDL l 704 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" CB7 CDL l 703 " pdb=" OB8 CDL l 703 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CB7 CDL V 201 " pdb=" OB8 CDL V 201 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.10e-02 8.26e+03 1.12e+02 bond pdb=" CA7 CDL l 704 " pdb=" OA8 CDL l 704 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.10e-02 8.26e+03 1.11e+02 bond pdb=" CB7 CDL n 101 " pdb=" OB8 CDL n 101 " ideal model delta sigma weight residual 1.334 1.449 -0.115 1.10e-02 8.26e+03 1.10e+02 ... (remaining 39848 not shown) Histogram of bond angle deviations from ideal: 92.15 - 103.20: 693 103.20 - 114.25: 24339 114.25 - 125.30: 28105 125.30 - 136.35: 828 136.35 - 147.40: 9 Bond angle restraints: 53974 Sorted by residual: angle pdb=" C ILE s 314 " pdb=" N PRO s 315 " pdb=" CA PRO s 315 " ideal model delta sigma weight residual 119.66 126.77 -7.11 7.30e-01 1.88e+00 9.48e+01 angle pdb=" C THR i 323 " pdb=" N PRO i 324 " pdb=" CA PRO i 324 " ideal model delta sigma weight residual 127.00 147.40 -20.40 2.40e+00 1.74e-01 7.22e+01 angle pdb=" C TYR Y 86 " pdb=" N PRO Y 87 " pdb=" CD PRO Y 87 " ideal model delta sigma weight residual 120.60 139.15 -18.55 2.20e+00 2.07e-01 7.11e+01 angle pdb=" N TRP Y 92 " pdb=" CA TRP Y 92 " pdb=" C TRP Y 92 " ideal model delta sigma weight residual 107.75 92.15 15.60 1.86e+00 2.89e-01 7.04e+01 angle pdb=" C PHE Y 47 " pdb=" N PRO Y 48 " pdb=" CA PRO Y 48 " ideal model delta sigma weight residual 119.78 128.26 -8.48 1.03e+00 9.43e-01 6.78e+01 ... (remaining 53969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 23483 35.67 - 71.33: 454 71.33 - 107.00: 38 107.00 - 142.66: 10 142.66 - 178.33: 10 Dihedral angle restraints: 23995 sinusoidal: 10204 harmonic: 13791 Sorted by residual: dihedral pdb=" CA LYS w 338 " pdb=" C LYS w 338 " pdb=" N TYR w 339 " pdb=" CA TYR w 339 " ideal model delta harmonic sigma weight residual 180.00 -142.74 -37.26 0 5.00e+00 4.00e-02 5.55e+01 dihedral pdb=" CA PHE Y 84 " pdb=" C PHE Y 84 " pdb=" N PRO Y 85 " pdb=" CA PRO Y 85 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA MET l 383 " pdb=" C MET l 383 " pdb=" N PRO l 384 " pdb=" CA PRO l 384 " ideal model delta harmonic sigma weight residual -180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 23992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5004 0.095 - 0.191: 882 0.191 - 0.286: 41 0.286 - 0.382: 12 0.382 - 0.477: 1 Chirality restraints: 5940 Sorted by residual: chirality pdb=" CA ASN l 25 " pdb=" N ASN l 25 " pdb=" C ASN l 25 " pdb=" CB ASN l 25 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CA PRO Y 85 " pdb=" N PRO Y 85 " pdb=" C PRO Y 85 " pdb=" CB PRO Y 85 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA TRP Y 92 " pdb=" N TRP Y 92 " pdb=" C TRP Y 92 " pdb=" CB TRP Y 92 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 5937 not shown) Planarity restraints: 6610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP r 307 " -0.034 2.00e-02 2.50e+03 2.68e-02 1.80e+01 pdb=" CG TRP r 307 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP r 307 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP r 307 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP r 307 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP r 307 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP r 307 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP r 307 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP r 307 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP r 307 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP i 264 " 0.022 2.00e-02 2.50e+03 2.63e-02 1.73e+01 pdb=" CG TRP i 264 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP i 264 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP i 264 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP i 264 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP i 264 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP i 264 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP i 264 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP i 264 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP i 264 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN l 446 " -0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ASN l 446 " 0.071 2.00e-02 2.50e+03 pdb=" O ASN l 446 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN l 447 " -0.024 2.00e-02 2.50e+03 ... (remaining 6607 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 6 1.82 - 2.59: 686 2.59 - 3.36: 56890 3.36 - 4.13: 90787 4.13 - 4.90: 171437 Nonbonded interactions: 319806 Sorted by model distance: nonbonded pdb=" OD2 ASP b 108 " pdb=" CG1 VAL d 19 " model vdw 1.049 3.460 nonbonded pdb=" CE MET k 1 " pdb=" ND2 ASN k 50 " model vdw 1.336 3.540 nonbonded pdb=" O LEU l 186 " pdb=" CD1 ILE l 190 " model vdw 1.374 3.460 nonbonded pdb=" OD2 ASP b 108 " pdb=" CB VAL d 19 " model vdw 1.459 3.470 nonbonded pdb=" NH2 ARG Y 72 " pdb=" OH TYR l 390 " model vdw 1.758 2.520 ... (remaining 319801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 7.220 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: 0.040 Extract box with map and model: 23.210 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 95.800 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.014 0.122 39853 Z= 0.896 Angle : 1.549 20.398 53974 Z= 0.998 Chirality : 0.070 0.477 5940 Planarity : 0.008 0.101 6610 Dihedral : 13.902 178.326 15066 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 26.41 Ramachandran Plot: Outliers : 2.78 % Allowed : 6.36 % Favored : 90.86 % Rotamer: Outliers : 1.20 % Allowed : 1.59 % Favored : 97.21 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.64 (0.12), residues: 4641 helix: -1.65 (0.08), residues: 2861 sheet: -4.38 (1.10), residues: 10 loop : 0.35 (0.17), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRP r 307 HIS 0.022 0.003 HIS l 534 PHE 0.036 0.003 PHE i 28 TYR 0.044 0.003 TYR w 339 ARG 0.016 0.002 ARG c 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1329 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1280 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 34 LYS cc_start: 0.8018 (mtpp) cc_final: 0.6777 (mtpt) REVERT: S 36 LYS cc_start: 0.8768 (tptm) cc_final: 0.8493 (tppp) REVERT: V 19 HIS cc_start: 0.7954 (p-80) cc_final: 0.7527 (p-80) REVERT: V 21 LYS cc_start: 0.8294 (mttt) cc_final: 0.7727 (mttt) REVERT: V 82 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7453 (mm-30) REVERT: V 106 HIS cc_start: 0.7171 (p-80) cc_final: 0.6853 (t-170) REVERT: V 118 PHE cc_start: 0.8635 (m-80) cc_final: 0.8037 (m-80) REVERT: V 129 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8617 (tpp80) REVERT: X 77 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7991 (mm-30) REVERT: X 137 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8837 (mmmt) REVERT: Y 78 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6516 (pp20) REVERT: a 74 TYR cc_start: 0.8263 (m-80) cc_final: 0.7975 (m-80) REVERT: b 104 ILE cc_start: 0.8952 (mt) cc_final: 0.8192 (mm) REVERT: c 119 THR cc_start: 0.8624 (p) cc_final: 0.8410 (m) REVERT: c 131 MET cc_start: 0.7557 (mmt) cc_final: 0.7273 (ttt) REVERT: c 140 MET cc_start: 0.9140 (mmm) cc_final: 0.8928 (mmm) REVERT: d 28 MET cc_start: 0.7409 (mmt) cc_final: 0.6554 (mmt) REVERT: d 32 ASP cc_start: 0.8403 (m-30) cc_final: 0.8085 (m-30) REVERT: d 55 TYR cc_start: 0.6506 (OUTLIER) cc_final: 0.5850 (m-10) REVERT: d 61 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: d 107 CYS cc_start: 0.7370 (t) cc_final: 0.6909 (t) REVERT: g 38 TYR cc_start: 0.8535 (t80) cc_final: 0.8325 (t80) REVERT: g 99 ASP cc_start: 0.8468 (m-30) cc_final: 0.7708 (m-30) REVERT: h 15 ASP cc_start: 0.8657 (t0) cc_final: 0.8358 (t0) REVERT: i 36 ASN cc_start: 0.8348 (m-40) cc_final: 0.7768 (t0) REVERT: i 47 LYS cc_start: 0.8115 (mttt) cc_final: 0.7809 (mmtm) REVERT: i 72 MET cc_start: 0.8704 (tpt) cc_final: 0.8441 (tpt) REVERT: i 79 MET cc_start: 0.8018 (mtp) cc_final: 0.7754 (mtp) REVERT: i 86 MET cc_start: 0.8640 (mmm) cc_final: 0.8403 (mmt) REVERT: i 120 GLN cc_start: 0.8754 (tt0) cc_final: 0.8179 (tp-100) REVERT: j 1 MET cc_start: 0.3387 (ptp) cc_final: 0.1491 (mmp) REVERT: j 8 MET cc_start: 0.8234 (mmt) cc_final: 0.8019 (mmm) REVERT: j 56 PHE cc_start: 0.8438 (t80) cc_final: 0.8205 (t80) REVERT: j 90 SER cc_start: 0.8885 (p) cc_final: 0.8609 (t) REVERT: k 25 HIS cc_start: 0.8294 (p90) cc_final: 0.7298 (t70) REVERT: l 179 ASP cc_start: 0.8515 (m-30) cc_final: 0.7998 (m-30) REVERT: l 268 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7970 (mt-10) REVERT: l 503 ASP cc_start: 0.8069 (m-30) cc_final: 0.7741 (m-30) REVERT: l 510 LYS cc_start: 0.8030 (mttm) cc_final: 0.7215 (tptt) REVERT: l 583 MET cc_start: 0.6557 (tpt) cc_final: 0.6284 (mtp) REVERT: m 2 MET cc_start: 0.8487 (tpt) cc_final: 0.8008 (tpp) REVERT: m 3 TYR cc_start: 0.8302 (m-80) cc_final: 0.7786 (m-80) REVERT: m 82 TRP cc_start: 0.4255 (m100) cc_final: 0.3124 (m-90) REVERT: m 96 LEU cc_start: 0.7439 (mt) cc_final: 0.7190 (mt) REVERT: m 98 MET cc_start: 0.7646 (mmm) cc_final: 0.7355 (mtt) REVERT: m 100 VAL cc_start: 0.8604 (t) cc_final: 0.7845 (p) REVERT: m 123 SER cc_start: 0.8163 (m) cc_final: 0.7910 (m) REVERT: m 161 PHE cc_start: 0.9147 (t80) cc_final: 0.8815 (t80) REVERT: n 7 ILE cc_start: 0.7863 (mt) cc_final: 0.7644 (pt) REVERT: o 13 THR cc_start: 0.8629 (p) cc_final: 0.8361 (p) REVERT: o 86 ASN cc_start: 0.7593 (m-40) cc_final: 0.7188 (m-40) REVERT: o 89 MET cc_start: 0.7742 (tpt) cc_final: 0.7374 (tpt) REVERT: o 106 LYS cc_start: 0.8673 (tptt) cc_final: 0.8417 (ttmm) REVERT: o 112 LYS cc_start: 0.8712 (mttt) cc_final: 0.8286 (mtpp) REVERT: p 124 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: s 3 MET cc_start: 0.8502 (mmp) cc_final: 0.6894 (ptt) REVERT: s 34 ARG cc_start: 0.8488 (ptm160) cc_final: 0.7433 (mmt-90) REVERT: s 54 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7381 (mptt) REVERT: s 71 TYR cc_start: 0.7659 (m-80) cc_final: 0.6991 (m-80) REVERT: s 214 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7911 (mt-10) REVERT: s 277 TYR cc_start: 0.8715 (m-80) cc_final: 0.8426 (m-10) REVERT: s 281 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7437 (mtm180) REVERT: v 47 MET cc_start: 0.7896 (mmt) cc_final: 0.7657 (mmp) REVERT: v 84 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8092 (tpt90) REVERT: w 102 LYS cc_start: 0.8513 (mptt) cc_final: 0.8294 (ttpt) REVERT: w 287 ASP cc_start: 0.7346 (t0) cc_final: 0.6821 (t0) outliers start: 49 outliers final: 22 residues processed: 1319 average time/residue: 0.5513 time to fit residues: 1144.3194 Evaluate side-chains 855 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 829 time to evaluate : 4.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 78 GLU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 87 PRO Chi-restraints excluded: chain Y residue 95 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain b residue 112 GLU Chi-restraints excluded: chain d residue 55 TYR Chi-restraints excluded: chain d residue 57 TYR Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain d residue 61 GLN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain l residue 87 MET Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 191 LEU Chi-restraints excluded: chain l residue 195 SER Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 217 LEU Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 223 LYS Chi-restraints excluded: chain l residue 226 GLN Chi-restraints excluded: chain l residue 450 LEU Chi-restraints excluded: chain l residue 452 ASN Chi-restraints excluded: chain p residue 124 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 0.9980 chunk 345 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 chunk 184 optimal weight: 0.7980 chunk 357 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 414 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 38 GLN Q 60 HIS S 44 HIS V 89 ASN W 47 HIS ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 112 HIS W 135 HIS Z 21 GLN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 GLN ** d 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 153 GLN g 96 HIS h 25 GLN i 88 ASN i 92 GLN i 150 ASN i 204 ASN ** i 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 83 ASN j 108 GLN k 25 HIS ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 199 GLN l 205 ASN l 207 ASN l 248 HIS l 269 ASN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 348 HIS ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 505 ASN l 524 ASN ** l 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 568 GLN l 569 HIS ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 45 ASN n 40 ASN o 52 ASN ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 HIS p 75 GLN p 141 GLN r 30 HIS r 48 ASN r 168 HIS r 184 GLN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 366 ASN r 390 ASN r 415 GLN s 93 ASN s 138 GLN s 169 GLN s 235 ASN u 30 HIS ** u 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN u 95 GLN u 99 HIS u 104 GLN u 143 HIS v 61 HIS v 85 HIS ** v 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 124 ASN w 132 GLN w 182 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 39853 Z= 0.288 Angle : 0.840 11.118 53974 Z= 0.430 Chirality : 0.047 0.255 5940 Planarity : 0.007 0.090 6610 Dihedral : 16.222 177.739 6000 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 1.01 % Allowed : 5.67 % Favored : 93.32 % Rotamer: Outliers : 3.40 % Allowed : 10.52 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: -0.62 (0.12), residues: 4641 helix: -0.15 (0.09), residues: 2896 sheet: -4.03 (1.07), residues: 12 loop : -0.60 (0.16), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP r 307 HIS 0.012 0.002 HIS l 192 PHE 0.032 0.002 PHE s 293 TYR 0.041 0.002 TYR w 339 ARG 0.008 0.001 ARG V 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1051 time to evaluate : 4.602 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: S 36 LYS cc_start: 0.8902 (tptm) cc_final: 0.8375 (tppp) REVERT: U 16 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7592 (pt0) REVERT: V 104 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7435 (ttm-80) REVERT: V 118 PHE cc_start: 0.8514 (m-80) cc_final: 0.7980 (m-80) REVERT: V 129 ARG cc_start: 0.8813 (tpp80) cc_final: 0.8415 (tpp80) REVERT: W 33 TYR cc_start: 0.7441 (t80) cc_final: 0.7026 (t80) REVERT: Z 23 LYS cc_start: 0.8285 (mmmm) cc_final: 0.8017 (mmmm) REVERT: a 74 TYR cc_start: 0.8207 (m-80) cc_final: 0.7769 (m-80) REVERT: b 104 ILE cc_start: 0.8807 (mt) cc_final: 0.8169 (mm) REVERT: c 119 THR cc_start: 0.8379 (p) cc_final: 0.8085 (m) REVERT: c 132 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8270 (mp10) REVERT: c 140 MET cc_start: 0.9255 (mmm) cc_final: 0.9052 (mmm) REVERT: c 168 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8310 (pp) REVERT: e 68 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7667 (mt-10) REVERT: g 8 GLU cc_start: 0.7217 (tp30) cc_final: 0.6930 (tm-30) REVERT: g 11 ARG cc_start: 0.7504 (tpt90) cc_final: 0.7300 (tpp-160) REVERT: g 105 LYS cc_start: 0.8751 (mttm) cc_final: 0.8482 (mtpp) REVERT: h 15 ASP cc_start: 0.8633 (t0) cc_final: 0.8327 (t0) REVERT: h 27 TYR cc_start: 0.8896 (m-80) cc_final: 0.8601 (m-80) REVERT: i 1 MET cc_start: 0.7495 (mmm) cc_final: 0.6514 (mmm) REVERT: i 72 MET cc_start: 0.8621 (tpt) cc_final: 0.8328 (tpt) REVERT: i 120 GLN cc_start: 0.8702 (tt0) cc_final: 0.8245 (tp-100) REVERT: i 149 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8765 (mt) REVERT: j 1 MET cc_start: 0.3431 (ptp) cc_final: 0.1566 (mmp) REVERT: j 37 TYR cc_start: 0.4857 (p90) cc_final: 0.4305 (m-10) REVERT: j 87 MET cc_start: 0.8809 (tmm) cc_final: 0.8499 (tmm) REVERT: k 7 ASN cc_start: 0.8734 (t0) cc_final: 0.8401 (t0) REVERT: k 9 MET cc_start: 0.8198 (mtm) cc_final: 0.7981 (mtm) REVERT: k 25 HIS cc_start: 0.8271 (p-80) cc_final: 0.7293 (t70) REVERT: l 58 ASP cc_start: 0.8084 (t70) cc_final: 0.7581 (t70) REVERT: l 87 MET cc_start: 0.8583 (tpp) cc_final: 0.7735 (mpp) REVERT: l 338 MET cc_start: 0.8692 (tpp) cc_final: 0.8305 (tpp) REVERT: l 510 LYS cc_start: 0.8195 (mttm) cc_final: 0.7489 (tptt) REVERT: l 583 MET cc_start: 0.6225 (tpt) cc_final: 0.5687 (tpp) REVERT: m 32 LEU cc_start: 0.9171 (mt) cc_final: 0.8730 (tt) REVERT: m 69 TYR cc_start: 0.8493 (t80) cc_final: 0.8274 (t80) REVERT: m 82 TRP cc_start: 0.3891 (m100) cc_final: 0.2952 (m-90) REVERT: m 105 TRP cc_start: 0.8137 (t60) cc_final: 0.7612 (t60) REVERT: m 161 PHE cc_start: 0.9069 (t80) cc_final: 0.8711 (t80) REVERT: m 172 ARG cc_start: 0.6564 (ttp80) cc_final: 0.6161 (ttp80) REVERT: o 13 THR cc_start: 0.8347 (p) cc_final: 0.7902 (p) REVERT: o 86 ASN cc_start: 0.7551 (m-40) cc_final: 0.7291 (m-40) REVERT: o 108 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7638 (tm-30) REVERT: o 112 LYS cc_start: 0.8645 (mttt) cc_final: 0.8411 (mtpp) REVERT: p 124 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: r 117 MET cc_start: 0.8495 (tpp) cc_final: 0.8294 (ttp) REVERT: r 264 LEU cc_start: 0.9246 (pp) cc_final: 0.8472 (tt) REVERT: r 415 GLN cc_start: 0.8460 (mm110) cc_final: 0.8202 (mm110) REVERT: r 454 ILE cc_start: 0.9347 (mt) cc_final: 0.9117 (mt) REVERT: s 3 MET cc_start: 0.8329 (mmp) cc_final: 0.7026 (ptt) REVERT: s 34 ARG cc_start: 0.8472 (ptm160) cc_final: 0.7514 (mmt-90) REVERT: s 134 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7788 (mmt90) REVERT: s 206 GLU cc_start: 0.7889 (tp30) cc_final: 0.7153 (mp0) REVERT: s 281 ARG cc_start: 0.7951 (ttt180) cc_final: 0.7407 (mtm180) REVERT: v 72 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7952 (p0) REVERT: v 91 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8161 (mm-30) REVERT: v 100 LYS cc_start: 0.8560 (mttt) cc_final: 0.7208 (tttt) REVERT: v 101 GLU cc_start: 0.7890 (mp0) cc_final: 0.7646 (mp0) REVERT: v 117 LYS cc_start: 0.8008 (tppt) cc_final: 0.7717 (tppp) REVERT: w 85 HIS cc_start: 0.6601 (t70) cc_final: 0.6357 (t70) REVERT: w 115 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6613 (mm-30) REVERT: w 287 ASP cc_start: 0.7338 (t0) cc_final: 0.6777 (t0) REVERT: w 289 ARG cc_start: 0.8463 (ptt90) cc_final: 0.8167 (tmm160) outliers start: 139 outliers final: 64 residues processed: 1127 average time/residue: 0.5019 time to fit residues: 923.5969 Evaluate side-chains 928 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 858 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 15 CYS Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 189 ASN Chi-restraints excluded: chain b residue 25 ASP Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain c residue 132 GLN Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 99 ILE Chi-restraints excluded: chain e residue 73 SER Chi-restraints excluded: chain e residue 90 VAL Chi-restraints excluded: chain g residue 26 THR Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 149 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 79 VAL Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 217 LEU Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 429 LEU Chi-restraints excluded: chain l residue 450 LEU Chi-restraints excluded: chain l residue 452 ASN Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 30 LEU Chi-restraints excluded: chain m residue 40 CYS Chi-restraints excluded: chain m residue 63 MET Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain o residue 55 ASN Chi-restraints excluded: chain p residue 124 GLN Chi-restraints excluded: chain p residue 137 VAL Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 317 ILE Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 172 LEU Chi-restraints excluded: chain s residue 188 SER Chi-restraints excluded: chain s residue 229 THR Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain u residue 30 HIS Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 72 ASP Chi-restraints excluded: chain w residue 98 THR Chi-restraints excluded: chain w residue 211 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 344 optimal weight: 0.8980 chunk 281 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 414 optimal weight: 20.0000 chunk 448 optimal weight: 20.0000 chunk 369 optimal weight: 4.9990 chunk 411 optimal weight: 0.3980 chunk 141 optimal weight: 0.8980 chunk 332 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 47 HIS ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 138 HIS ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 48 ASN ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 83 HIS c 56 ASN c 83 GLN ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 63 GLN i 222 ASN ** i 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 GLN k 50 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 199 GLN l 207 ASN l 269 ASN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 296 ASN ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 40 ASN o 33 GLN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 26 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 279 GLN ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 39853 Z= 0.263 Angle : 0.764 10.749 53974 Z= 0.386 Chirality : 0.045 0.312 5940 Planarity : 0.006 0.069 6610 Dihedral : 14.924 175.700 5959 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.40 % Favored : 92.74 % Rotamer: Outliers : 3.84 % Allowed : 12.79 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.18 (0.12), residues: 4641 helix: 0.40 (0.09), residues: 2907 sheet: -3.63 (1.22), residues: 12 loop : -0.85 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP s 185 HIS 0.009 0.001 HIS d 50 PHE 0.038 0.002 PHE b 46 TYR 0.049 0.002 TYR S 61 ARG 0.010 0.001 ARG v 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 958 time to evaluate : 4.702 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: S 36 LYS cc_start: 0.8819 (tptm) cc_final: 0.8405 (tppp) REVERT: U 16 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7626 (pt0) REVERT: V 81 ARG cc_start: 0.8669 (ttm170) cc_final: 0.8417 (ttm-80) REVERT: V 118 PHE cc_start: 0.8503 (m-80) cc_final: 0.7987 (m-80) REVERT: X 115 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8711 (tm-30) REVERT: X 116 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8617 (p) REVERT: c 56 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8382 (t0) REVERT: c 119 THR cc_start: 0.8441 (p) cc_final: 0.8196 (m) REVERT: c 132 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: d 36 ASP cc_start: 0.7764 (t0) cc_final: 0.7523 (t0) REVERT: e 68 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7665 (mt-10) REVERT: e 79 ASP cc_start: 0.7201 (t0) cc_final: 0.6995 (m-30) REVERT: g 8 GLU cc_start: 0.7155 (tp30) cc_final: 0.6780 (tm-30) REVERT: g 11 ARG cc_start: 0.7475 (tpt90) cc_final: 0.7185 (tpp-160) REVERT: g 44 ASP cc_start: 0.8544 (t0) cc_final: 0.8318 (t0) REVERT: g 98 GLU cc_start: 0.8504 (pm20) cc_final: 0.8046 (pm20) REVERT: g 99 ASP cc_start: 0.8543 (m-30) cc_final: 0.7577 (m-30) REVERT: h 15 ASP cc_start: 0.8616 (t0) cc_final: 0.8292 (t0) REVERT: i 54 GLU cc_start: 0.8601 (pp20) cc_final: 0.8232 (pt0) REVERT: i 72 MET cc_start: 0.8627 (tpt) cc_final: 0.8405 (tpt) REVERT: i 120 GLN cc_start: 0.8746 (tt0) cc_final: 0.7900 (tp-100) REVERT: i 142 MET cc_start: 0.8482 (mmm) cc_final: 0.8235 (mtp) REVERT: i 269 GLU cc_start: 0.8444 (tp30) cc_final: 0.7981 (tp30) REVERT: i 339 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8862 (mt) REVERT: j 1 MET cc_start: 0.3415 (ptp) cc_final: 0.1567 (mmp) REVERT: j 8 MET cc_start: 0.8483 (mmm) cc_final: 0.7519 (mtm) REVERT: j 37 TYR cc_start: 0.4942 (p90) cc_final: 0.4465 (m-10) REVERT: k 6 MET cc_start: 0.8204 (mtp) cc_final: 0.7691 (tpt) REVERT: k 7 ASN cc_start: 0.8891 (t0) cc_final: 0.8454 (t0) REVERT: k 25 HIS cc_start: 0.8162 (p-80) cc_final: 0.7123 (t70) REVERT: l 50 PRO cc_start: 0.8620 (Cg_exo) cc_final: 0.8404 (Cg_endo) REVERT: l 179 ASP cc_start: 0.8405 (m-30) cc_final: 0.8198 (m-30) REVERT: l 217 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8912 (tt) REVERT: l 310 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8862 (mm) REVERT: l 503 ASP cc_start: 0.7432 (m-30) cc_final: 0.7224 (m-30) REVERT: l 510 LYS cc_start: 0.8012 (mttm) cc_final: 0.7380 (tptt) REVERT: l 583 MET cc_start: 0.6225 (tpt) cc_final: 0.5998 (tpp) REVERT: m 2 MET cc_start: 0.8742 (tpt) cc_final: 0.8416 (tpt) REVERT: m 54 MET cc_start: 0.8500 (mmp) cc_final: 0.8232 (tpp) REVERT: m 76 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6763 (mp0) REVERT: m 82 TRP cc_start: 0.3779 (m100) cc_final: 0.2810 (m-90) REVERT: m 105 TRP cc_start: 0.8036 (t60) cc_final: 0.7572 (t60) REVERT: m 161 PHE cc_start: 0.8986 (t80) cc_final: 0.8657 (t80) REVERT: n 40 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8715 (t0) REVERT: o 16 GLU cc_start: 0.7617 (pm20) cc_final: 0.7143 (pm20) REVERT: o 102 TYR cc_start: 0.8905 (t80) cc_final: 0.8559 (t80) REVERT: o 106 LYS cc_start: 0.8492 (tttt) cc_final: 0.7867 (ttpp) REVERT: p 124 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: r 238 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8847 (tp) REVERT: r 244 MET cc_start: 0.8354 (mtp) cc_final: 0.8120 (ttm) REVERT: r 264 LEU cc_start: 0.9208 (pp) cc_final: 0.8608 (tp) REVERT: s 3 MET cc_start: 0.8324 (mmp) cc_final: 0.6975 (ptt) REVERT: s 34 ARG cc_start: 0.8491 (ptm160) cc_final: 0.7475 (mmt-90) REVERT: s 59 GLU cc_start: 0.8707 (tt0) cc_final: 0.7972 (pm20) REVERT: s 134 ARG cc_start: 0.8093 (mmt90) cc_final: 0.7770 (mmt90) REVERT: s 185 TRP cc_start: 0.8846 (t-100) cc_final: 0.8552 (t-100) REVERT: s 206 GLU cc_start: 0.7898 (tp30) cc_final: 0.7211 (mp0) REVERT: s 277 TYR cc_start: 0.8528 (m-10) cc_final: 0.8298 (m-10) REVERT: s 281 ARG cc_start: 0.7851 (ttt180) cc_final: 0.7371 (mtm180) REVERT: s 286 MET cc_start: 0.8823 (mmm) cc_final: 0.8337 (mpp) REVERT: u 30 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8176 (m-70) REVERT: u 44 MET cc_start: 0.8380 (mmt) cc_final: 0.7565 (tpt) REVERT: v 72 ASP cc_start: 0.8594 (m-30) cc_final: 0.7979 (p0) REVERT: v 91 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8113 (mm-30) REVERT: v 100 LYS cc_start: 0.8410 (mttt) cc_final: 0.7379 (tttt) REVERT: w 85 HIS cc_start: 0.6555 (t70) cc_final: 0.6213 (t70) REVERT: w 115 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6722 (mm-30) REVERT: w 127 ASN cc_start: 0.7347 (m-40) cc_final: 0.6922 (m-40) outliers start: 157 outliers final: 84 residues processed: 1045 average time/residue: 0.5006 time to fit residues: 861.2377 Evaluate side-chains 939 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 844 time to evaluate : 4.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 95 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 55 PHE Chi-restraints excluded: chain a residue 86 ILE Chi-restraints excluded: chain a residue 189 ASN Chi-restraints excluded: chain b residue 25 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 131 MET Chi-restraints excluded: chain c residue 132 GLN Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain d residue 99 ILE Chi-restraints excluded: chain d residue 107 CYS Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 147 ILE Chi-restraints excluded: chain f residue 43 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 93 TYR Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain i residue 221 LEU Chi-restraints excluded: chain i residue 339 ILE Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 217 LEU Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 310 LEU Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain l residue 429 LEU Chi-restraints excluded: chain l residue 450 LEU Chi-restraints excluded: chain l residue 452 ASN Chi-restraints excluded: chain l residue 489 THR Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 30 LEU Chi-restraints excluded: chain m residue 40 CYS Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 106 VAL Chi-restraints excluded: chain m residue 110 ASP Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 40 ASN Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain o residue 55 ASN Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 124 GLN Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 150 LEU Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 238 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 317 ILE Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 172 LEU Chi-restraints excluded: chain s residue 229 THR Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 30 HIS Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 118 LYS Chi-restraints excluded: chain w residue 98 THR Chi-restraints excluded: chain w residue 150 LEU Chi-restraints excluded: chain w residue 211 VAL Chi-restraints excluded: chain w residue 328 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 6.9990 chunk 311 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 197 optimal weight: 0.0770 chunk 278 optimal weight: 0.0470 chunk 416 optimal weight: 0.6980 chunk 440 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 394 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 GLN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 161 HIS ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 48 ASN ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 63 GLN i 204 ASN ** i 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 207 ASN l 269 ASN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 309 GLN ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 174 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 12 HIS p 141 GLN r 192 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 415 GLN ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 161 ASN s 235 ASN u 31 HIS ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN w 330 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39853 Z= 0.216 Angle : 0.724 13.591 53974 Z= 0.362 Chirality : 0.043 0.235 5940 Planarity : 0.005 0.062 6610 Dihedral : 14.121 176.739 5956 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.80 % Favored : 93.43 % Rotamer: Outliers : 3.60 % Allowed : 14.46 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.10 (0.12), residues: 4641 helix: 0.71 (0.10), residues: 2907 sheet: None (None), residues: 0 loop : -0.95 (0.16), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP u 86 HIS 0.007 0.001 HIS d 50 PHE 0.034 0.002 PHE b 46 TYR 0.047 0.002 TYR S 61 ARG 0.007 0.001 ARG v 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 934 time to evaluate : 4.359 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: S 36 LYS cc_start: 0.8759 (tptm) cc_final: 0.8361 (tppp) REVERT: S 43 TYR cc_start: 0.8946 (t80) cc_final: 0.8606 (t80) REVERT: V 118 PHE cc_start: 0.8434 (m-80) cc_final: 0.7956 (m-80) REVERT: X 116 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8400 (p) REVERT: Y 97 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6333 (mm) REVERT: Z 41 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7664 (mp) REVERT: c 56 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8577 (t0) REVERT: c 119 THR cc_start: 0.8431 (p) cc_final: 0.8042 (m) REVERT: c 132 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: g 8 GLU cc_start: 0.6984 (tp30) cc_final: 0.6288 (tm-30) REVERT: g 11 ARG cc_start: 0.7441 (tpt90) cc_final: 0.7152 (tpp-160) REVERT: g 44 ASP cc_start: 0.8752 (t0) cc_final: 0.8451 (t0) REVERT: g 98 GLU cc_start: 0.8447 (pm20) cc_final: 0.8046 (pm20) REVERT: g 99 ASP cc_start: 0.8558 (m-30) cc_final: 0.7610 (m-30) REVERT: i 1 MET cc_start: 0.7034 (mpp) cc_final: 0.6630 (mpp) REVERT: i 54 GLU cc_start: 0.8502 (pp20) cc_final: 0.8130 (pt0) REVERT: i 108 MET cc_start: 0.8166 (mtm) cc_final: 0.7796 (mtp) REVERT: i 120 GLN cc_start: 0.8815 (tt0) cc_final: 0.7909 (tp-100) REVERT: i 201 THR cc_start: 0.9177 (p) cc_final: 0.8943 (p) REVERT: i 269 GLU cc_start: 0.8531 (tp30) cc_final: 0.8281 (tp30) REVERT: i 339 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8830 (mt) REVERT: j 1 MET cc_start: 0.3372 (ptp) cc_final: 0.1541 (mmp) REVERT: j 8 MET cc_start: 0.8328 (mmm) cc_final: 0.7430 (mtm) REVERT: j 37 TYR cc_start: 0.4834 (p90) cc_final: 0.4163 (m-10) REVERT: j 56 PHE cc_start: 0.7968 (t80) cc_final: 0.7742 (t80) REVERT: k 6 MET cc_start: 0.8140 (mtp) cc_final: 0.7543 (tpt) REVERT: k 7 ASN cc_start: 0.8844 (t0) cc_final: 0.8385 (t0) REVERT: k 25 HIS cc_start: 0.8094 (p-80) cc_final: 0.7128 (t70) REVERT: l 50 PRO cc_start: 0.8915 (Cg_exo) cc_final: 0.8708 (Cg_endo) REVERT: l 113 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7087 (m110) REVERT: l 145 GLU cc_start: 0.8268 (mp0) cc_final: 0.7592 (mp0) REVERT: l 310 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8771 (mm) REVERT: l 510 LYS cc_start: 0.7951 (mttm) cc_final: 0.7367 (tptt) REVERT: l 583 MET cc_start: 0.6123 (tpt) cc_final: 0.5809 (tpp) REVERT: m 2 MET cc_start: 0.8744 (tpt) cc_final: 0.8416 (tpt) REVERT: m 54 MET cc_start: 0.8527 (mmp) cc_final: 0.8294 (tpp) REVERT: m 76 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6655 (mp0) REVERT: m 82 TRP cc_start: 0.4011 (m100) cc_final: 0.2986 (m-90) REVERT: m 105 TRP cc_start: 0.8028 (t60) cc_final: 0.7594 (t60) REVERT: m 161 PHE cc_start: 0.8942 (t80) cc_final: 0.8581 (t80) REVERT: n 7 ILE cc_start: 0.7851 (mt) cc_final: 0.7585 (pt) REVERT: o 13 THR cc_start: 0.8277 (p) cc_final: 0.7878 (p) REVERT: o 70 TYR cc_start: 0.9252 (t80) cc_final: 0.8883 (t80) REVERT: o 79 ASN cc_start: 0.8891 (m-40) cc_final: 0.8480 (m-40) REVERT: o 102 TYR cc_start: 0.8859 (t80) cc_final: 0.8620 (t80) REVERT: o 106 LYS cc_start: 0.8483 (tttt) cc_final: 0.7778 (ttpp) REVERT: r 26 ASN cc_start: 0.8217 (m-40) cc_final: 0.7972 (m110) REVERT: r 135 ARG cc_start: 0.8227 (tpt90) cc_final: 0.7990 (ttm-80) REVERT: r 238 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8779 (tp) REVERT: r 244 MET cc_start: 0.8239 (mtp) cc_final: 0.8018 (ttm) REVERT: r 264 LEU cc_start: 0.9115 (pp) cc_final: 0.8661 (tp) REVERT: r 271 MET cc_start: 0.7633 (tpp) cc_final: 0.7314 (mmt) REVERT: r 439 MET cc_start: 0.8539 (mmm) cc_final: 0.8229 (mtp) REVERT: s 3 MET cc_start: 0.8299 (mmp) cc_final: 0.7017 (ptt) REVERT: s 34 ARG cc_start: 0.8515 (ptm160) cc_final: 0.7485 (mmt-90) REVERT: s 59 GLU cc_start: 0.8726 (tt0) cc_final: 0.7991 (pm20) REVERT: s 184 MET cc_start: 0.8188 (mtm) cc_final: 0.7981 (mtm) REVERT: s 185 TRP cc_start: 0.8947 (t-100) cc_final: 0.8625 (t-100) REVERT: s 206 GLU cc_start: 0.7916 (tp30) cc_final: 0.7307 (mp0) REVERT: s 281 ARG cc_start: 0.7795 (ttt180) cc_final: 0.7370 (mtm180) REVERT: s 286 MET cc_start: 0.8786 (mmm) cc_final: 0.8345 (mpp) REVERT: u 30 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8305 (m-70) REVERT: u 44 MET cc_start: 0.8475 (mmt) cc_final: 0.7990 (mmt) REVERT: u 101 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8187 (tpp-160) REVERT: v 72 ASP cc_start: 0.8649 (m-30) cc_final: 0.7920 (p0) REVERT: v 100 LYS cc_start: 0.8368 (mttt) cc_final: 0.7301 (tttt) REVERT: w 85 HIS cc_start: 0.6440 (t70) cc_final: 0.6132 (t70) REVERT: w 115 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6612 (mm-30) REVERT: w 127 ASN cc_start: 0.7352 (m-40) cc_final: 0.6871 (m-40) REVERT: w 353 TRP cc_start: 0.4899 (p90) cc_final: 0.4693 (p90) outliers start: 147 outliers final: 78 residues processed: 1023 average time/residue: 0.4849 time to fit residues: 818.7162 Evaluate side-chains 931 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 843 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 95 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 55 PHE Chi-restraints excluded: chain a residue 86 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 189 ASN Chi-restraints excluded: chain b residue 25 ASP Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 132 GLN Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 107 CYS Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain e residue 147 ILE Chi-restraints excluded: chain f residue 43 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 93 TYR Chi-restraints excluded: chain i residue 141 ILE Chi-restraints excluded: chain i residue 218 LEU Chi-restraints excluded: chain i residue 221 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 307 MET Chi-restraints excluded: chain i residue 339 ILE Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 30 LEU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 113 ASN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 310 LEU Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain l residue 429 LEU Chi-restraints excluded: chain l residue 452 ASN Chi-restraints excluded: chain l residue 489 THR Chi-restraints excluded: chain l residue 571 ILE Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 30 LEU Chi-restraints excluded: chain m residue 40 CYS Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 106 VAL Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 150 LEU Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 238 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 172 LEU Chi-restraints excluded: chain s residue 229 THR Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain u residue 30 HIS Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 118 LYS Chi-restraints excluded: chain w residue 98 THR Chi-restraints excluded: chain w residue 150 LEU Chi-restraints excluded: chain w residue 157 VAL Chi-restraints excluded: chain w residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 328 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 376 optimal weight: 0.4980 chunk 304 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 225 optimal weight: 0.2980 chunk 395 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 90 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 204 ASN ** i 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 83 ASN j 108 GLN l 30 ASN l 207 ASN l 269 ASN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39853 Z= 0.227 Angle : 0.719 12.835 53974 Z= 0.357 Chirality : 0.043 0.252 5940 Planarity : 0.005 0.082 6610 Dihedral : 13.497 176.063 5949 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.80 % Allowed : 5.80 % Favored : 93.41 % Rotamer: Outliers : 3.69 % Allowed : 15.92 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.20 (0.12), residues: 4641 helix: 0.85 (0.10), residues: 2910 sheet: None (None), residues: 0 loop : -1.05 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP u 86 HIS 0.007 0.001 HIS d 50 PHE 0.036 0.002 PHE b 46 TYR 0.042 0.002 TYR S 61 ARG 0.011 0.001 ARG V 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 901 time to evaluate : 4.391 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: S 36 LYS cc_start: 0.8784 (tptm) cc_final: 0.8349 (tppp) REVERT: V 99 LEU cc_start: 0.8557 (mm) cc_final: 0.8348 (mm) REVERT: V 118 PHE cc_start: 0.8423 (m-80) cc_final: 0.7997 (m-80) REVERT: Y 97 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6484 (mm) REVERT: Z 41 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7714 (mp) REVERT: c 119 THR cc_start: 0.8475 (p) cc_final: 0.8078 (m) REVERT: c 132 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: d 56 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7928 (m-10) REVERT: d 116 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: g 8 GLU cc_start: 0.6786 (tp30) cc_final: 0.5891 (tm-30) REVERT: g 11 ARG cc_start: 0.7429 (tpt90) cc_final: 0.7084 (tpp-160) REVERT: g 44 ASP cc_start: 0.8898 (t0) cc_final: 0.8550 (t0) REVERT: g 98 GLU cc_start: 0.8455 (pm20) cc_final: 0.8102 (pm20) REVERT: g 99 ASP cc_start: 0.8557 (m-30) cc_final: 0.7620 (m-30) REVERT: h 15 ASP cc_start: 0.8480 (t0) cc_final: 0.8202 (t0) REVERT: i 1 MET cc_start: 0.7093 (mpp) cc_final: 0.6696 (mpp) REVERT: i 54 GLU cc_start: 0.8448 (pp20) cc_final: 0.8137 (pt0) REVERT: i 120 GLN cc_start: 0.8804 (tt0) cc_final: 0.7836 (tp-100) REVERT: i 201 THR cc_start: 0.9144 (p) cc_final: 0.8846 (p) REVERT: i 339 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8900 (mt) REVERT: j 1 MET cc_start: 0.3240 (ptp) cc_final: 0.1383 (mmp) REVERT: j 8 MET cc_start: 0.8368 (mmm) cc_final: 0.7468 (mtm) REVERT: j 37 TYR cc_start: 0.4944 (p90) cc_final: 0.4172 (m-10) REVERT: j 56 PHE cc_start: 0.7870 (t80) cc_final: 0.7656 (t80) REVERT: k 6 MET cc_start: 0.8163 (mtp) cc_final: 0.7575 (tpt) REVERT: k 7 ASN cc_start: 0.8798 (t0) cc_final: 0.8261 (t0) REVERT: k 25 HIS cc_start: 0.8032 (p-80) cc_final: 0.7141 (t70) REVERT: l 50 PRO cc_start: 0.8960 (Cg_exo) cc_final: 0.8714 (Cg_endo) REVERT: l 145 GLU cc_start: 0.8196 (mp0) cc_final: 0.7414 (mp0) REVERT: l 310 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8833 (mm) REVERT: l 510 LYS cc_start: 0.7892 (mttm) cc_final: 0.7370 (tptt) REVERT: l 583 MET cc_start: 0.6191 (tpt) cc_final: 0.5806 (tpp) REVERT: m 2 MET cc_start: 0.8724 (tpt) cc_final: 0.8406 (tpt) REVERT: m 3 TYR cc_start: 0.8375 (m-80) cc_final: 0.8066 (m-80) REVERT: m 54 MET cc_start: 0.8547 (mmp) cc_final: 0.8323 (tpp) REVERT: m 76 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6718 (mp0) REVERT: m 82 TRP cc_start: 0.4061 (m100) cc_final: 0.2955 (m-90) REVERT: m 105 TRP cc_start: 0.7979 (t60) cc_final: 0.7575 (t60) REVERT: m 161 PHE cc_start: 0.8884 (t80) cc_final: 0.8502 (t80) REVERT: n 7 ILE cc_start: 0.7922 (mt) cc_final: 0.7654 (pt) REVERT: o 13 THR cc_start: 0.8234 (p) cc_final: 0.7909 (p) REVERT: o 79 ASN cc_start: 0.8838 (m-40) cc_final: 0.8530 (m-40) REVERT: o 83 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.7992 (p) REVERT: o 106 LYS cc_start: 0.8342 (tttt) cc_final: 0.7577 (ttmm) REVERT: p 49 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: r 238 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8749 (tp) REVERT: r 264 LEU cc_start: 0.9192 (pp) cc_final: 0.8687 (tp) REVERT: r 439 MET cc_start: 0.8503 (mmm) cc_final: 0.8293 (mtp) REVERT: s 3 MET cc_start: 0.8328 (mmp) cc_final: 0.6932 (ptt) REVERT: s 34 ARG cc_start: 0.8472 (ptm160) cc_final: 0.7590 (mmt90) REVERT: s 59 GLU cc_start: 0.8731 (tt0) cc_final: 0.7980 (pm20) REVERT: s 185 TRP cc_start: 0.8993 (OUTLIER) cc_final: 0.8622 (t-100) REVERT: s 206 GLU cc_start: 0.7928 (tp30) cc_final: 0.7309 (mp0) REVERT: s 224 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8538 (m-80) REVERT: s 279 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7306 (mpp-170) REVERT: s 281 ARG cc_start: 0.7825 (ttt180) cc_final: 0.7417 (mtm180) REVERT: s 286 MET cc_start: 0.8774 (mmm) cc_final: 0.8351 (mpp) REVERT: u 44 MET cc_start: 0.8492 (mmt) cc_final: 0.8073 (mmt) REVERT: u 101 ARG cc_start: 0.8444 (mmm160) cc_final: 0.7952 (tpp-160) REVERT: v 72 ASP cc_start: 0.8607 (m-30) cc_final: 0.7874 (p0) REVERT: v 91 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7588 (mm-30) REVERT: v 100 LYS cc_start: 0.8273 (mttt) cc_final: 0.7329 (tttt) REVERT: w 85 HIS cc_start: 0.6563 (t70) cc_final: 0.6244 (t70) REVERT: w 115 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6736 (mm-30) REVERT: w 127 ASN cc_start: 0.7275 (m-40) cc_final: 0.6762 (m-40) outliers start: 151 outliers final: 91 residues processed: 993 average time/residue: 0.4911 time to fit residues: 805.2102 Evaluate side-chains 932 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 829 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 95 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 55 PHE Chi-restraints excluded: chain a residue 86 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 189 ASN Chi-restraints excluded: chain b residue 25 ASP Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain c residue 132 GLN Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 107 CYS Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain e residue 73 SER Chi-restraints excluded: chain f residue 43 LYS Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 93 TYR Chi-restraints excluded: chain i residue 221 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 307 MET Chi-restraints excluded: chain i residue 339 ILE Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 30 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 113 ASN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 254 VAL Chi-restraints excluded: chain l residue 257 ILE Chi-restraints excluded: chain l residue 279 CYS Chi-restraints excluded: chain l residue 310 LEU Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain l residue 450 LEU Chi-restraints excluded: chain l residue 452 ASN Chi-restraints excluded: chain l residue 489 THR Chi-restraints excluded: chain l residue 571 ILE Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 30 LEU Chi-restraints excluded: chain m residue 40 CYS Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 106 VAL Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 86 ASN Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 238 LEU Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 172 LEU Chi-restraints excluded: chain s residue 185 TRP Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 229 THR Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain w residue 98 THR Chi-restraints excluded: chain w residue 150 LEU Chi-restraints excluded: chain w residue 157 VAL Chi-restraints excluded: chain w residue 328 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 1.9990 chunk 396 optimal weight: 1.9990 chunk 87 optimal weight: 0.0000 chunk 258 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 441 optimal weight: 5.9990 chunk 366 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 231 optimal weight: 0.9980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 90 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 ASN ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 321 GLN ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 ASN ** m 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 21 HIS r 26 ASN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 415 GLN ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 61 HIS ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39853 Z= 0.240 Angle : 0.716 12.510 53974 Z= 0.353 Chirality : 0.043 0.246 5940 Planarity : 0.005 0.083 6610 Dihedral : 13.166 178.940 5949 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.88 % Favored : 93.34 % Rotamer: Outliers : 3.57 % Allowed : 16.93 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.27 (0.13), residues: 4641 helix: 0.94 (0.10), residues: 2912 sheet: None (None), residues: 0 loop : -1.09 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP u 86 HIS 0.007 0.001 HIS h 34 PHE 0.035 0.001 PHE b 46 TYR 0.037 0.002 TYR S 61 ARG 0.007 0.000 ARG W 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 881 time to evaluate : 4.487 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: S 36 LYS cc_start: 0.8792 (tptm) cc_final: 0.8364 (tppp) REVERT: V 99 LEU cc_start: 0.8537 (mm) cc_final: 0.8184 (mm) REVERT: V 118 PHE cc_start: 0.8492 (m-80) cc_final: 0.8081 (m-80) REVERT: Y 97 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6534 (mm) REVERT: Z 41 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7678 (mp) REVERT: a 53 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7902 (ptp-170) REVERT: c 56 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8338 (t0) REVERT: c 119 THR cc_start: 0.8499 (p) cc_final: 0.8110 (m) REVERT: c 132 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: d 56 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7984 (m-10) REVERT: d 116 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: g 11 ARG cc_start: 0.7450 (tpt90) cc_final: 0.6691 (tpm170) REVERT: g 44 ASP cc_start: 0.8864 (t0) cc_final: 0.8641 (t0) REVERT: g 98 GLU cc_start: 0.8455 (pm20) cc_final: 0.8111 (pm20) REVERT: g 99 ASP cc_start: 0.8564 (m-30) cc_final: 0.7635 (m-30) REVERT: h 15 ASP cc_start: 0.8541 (t0) cc_final: 0.8299 (t0) REVERT: i 1 MET cc_start: 0.7082 (mpp) cc_final: 0.6797 (mpp) REVERT: i 54 GLU cc_start: 0.8446 (pp20) cc_final: 0.8072 (pt0) REVERT: i 120 GLN cc_start: 0.8804 (tt0) cc_final: 0.7795 (tp-100) REVERT: i 190 MET cc_start: 0.8244 (mmm) cc_final: 0.7803 (mtt) REVERT: i 339 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8868 (mt) REVERT: j 1 MET cc_start: 0.3315 (ptp) cc_final: 0.1342 (mmp) REVERT: j 8 MET cc_start: 0.8364 (mmm) cc_final: 0.7446 (mtm) REVERT: j 37 TYR cc_start: 0.4956 (p90) cc_final: 0.4180 (m-10) REVERT: j 56 PHE cc_start: 0.7831 (t80) cc_final: 0.7494 (t80) REVERT: j 89 MET cc_start: 0.7795 (tmm) cc_final: 0.7462 (tmm) REVERT: k 6 MET cc_start: 0.8167 (mtp) cc_final: 0.7594 (tpt) REVERT: k 7 ASN cc_start: 0.8582 (t0) cc_final: 0.8236 (t0) REVERT: k 25 HIS cc_start: 0.8185 (p-80) cc_final: 0.7149 (t70) REVERT: k 31 LEU cc_start: 0.8793 (mm) cc_final: 0.8563 (mm) REVERT: l 50 PRO cc_start: 0.8897 (Cg_exo) cc_final: 0.8675 (Cg_endo) REVERT: l 145 GLU cc_start: 0.8189 (mp0) cc_final: 0.7435 (mp0) REVERT: l 510 LYS cc_start: 0.7955 (mttm) cc_final: 0.7325 (tptt) REVERT: l 583 MET cc_start: 0.6111 (tpt) cc_final: 0.5699 (tpp) REVERT: m 2 MET cc_start: 0.8727 (tpt) cc_final: 0.8453 (tpt) REVERT: m 3 TYR cc_start: 0.8381 (m-80) cc_final: 0.8130 (m-80) REVERT: m 76 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6861 (mp0) REVERT: m 82 TRP cc_start: 0.4283 (m100) cc_final: 0.3172 (m-90) REVERT: m 105 TRP cc_start: 0.8044 (t60) cc_final: 0.7639 (t60) REVERT: m 161 PHE cc_start: 0.8823 (t80) cc_final: 0.8450 (t80) REVERT: n 7 ILE cc_start: 0.7901 (mt) cc_final: 0.7629 (pt) REVERT: o 13 THR cc_start: 0.8203 (p) cc_final: 0.7898 (p) REVERT: o 79 ASN cc_start: 0.8774 (m-40) cc_final: 0.8510 (m-40) REVERT: o 83 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8007 (p) REVERT: o 102 TYR cc_start: 0.8756 (t80) cc_final: 0.8060 (t80) REVERT: o 106 LYS cc_start: 0.8392 (tttt) cc_final: 0.7830 (ttmm) REVERT: p 49 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: r 23 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8596 (mt) REVERT: r 238 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8743 (tp) REVERT: r 244 MET cc_start: 0.8179 (mtp) cc_final: 0.7914 (ttm) REVERT: r 264 LEU cc_start: 0.9173 (pp) cc_final: 0.8740 (tp) REVERT: s 3 MET cc_start: 0.8352 (mmp) cc_final: 0.6974 (ptt) REVERT: s 34 ARG cc_start: 0.8474 (ptm160) cc_final: 0.7612 (mmt90) REVERT: s 47 GLN cc_start: 0.8490 (tp40) cc_final: 0.8273 (tp-100) REVERT: s 80 THR cc_start: 0.9307 (p) cc_final: 0.9031 (t) REVERT: s 185 TRP cc_start: 0.8949 (OUTLIER) cc_final: 0.8518 (t-100) REVERT: s 206 GLU cc_start: 0.8017 (tp30) cc_final: 0.7402 (mp0) REVERT: s 224 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8524 (m-80) REVERT: s 279 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7363 (mpp-170) REVERT: s 281 ARG cc_start: 0.7837 (ttt180) cc_final: 0.7420 (mtm180) REVERT: s 286 MET cc_start: 0.8751 (mmm) cc_final: 0.8238 (mpp) REVERT: u 20 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7846 (mm) REVERT: u 44 MET cc_start: 0.8525 (mmt) cc_final: 0.8101 (mmt) REVERT: u 101 ARG cc_start: 0.8430 (mmm160) cc_final: 0.8026 (tpp-160) REVERT: v 47 MET cc_start: 0.8033 (mmp) cc_final: 0.7784 (mmt) REVERT: v 72 ASP cc_start: 0.8647 (m-30) cc_final: 0.7926 (p0) REVERT: v 81 LYS cc_start: 0.8975 (mmtp) cc_final: 0.8689 (mmtm) REVERT: v 91 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8153 (mm-30) REVERT: v 100 LYS cc_start: 0.8324 (mttt) cc_final: 0.7447 (tttt) REVERT: w 85 HIS cc_start: 0.6360 (t70) cc_final: 0.6054 (t70) REVERT: w 115 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6821 (mm-30) outliers start: 146 outliers final: 98 residues processed: 975 average time/residue: 0.4818 time to fit residues: 775.7112 Evaluate side-chains 937 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 824 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 95 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 55 PHE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 189 ASN Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 132 GLN Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 98 ASN Chi-restraints excluded: chain d residue 99 ILE Chi-restraints excluded: chain d residue 107 CYS Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 73 SER Chi-restraints excluded: chain e residue 147 ILE Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 93 TYR Chi-restraints excluded: chain i residue 221 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 244 ILE Chi-restraints excluded: chain i residue 307 MET Chi-restraints excluded: chain i residue 326 LEU Chi-restraints excluded: chain i residue 339 ILE Chi-restraints excluded: chain j residue 3 PHE Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 30 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 113 ASN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 254 VAL Chi-restraints excluded: chain l residue 257 ILE Chi-restraints excluded: chain l residue 279 CYS Chi-restraints excluded: chain l residue 310 LEU Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain l residue 450 LEU Chi-restraints excluded: chain l residue 452 ASN Chi-restraints excluded: chain l residue 571 ILE Chi-restraints excluded: chain m residue 30 LEU Chi-restraints excluded: chain m residue 40 CYS Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 106 VAL Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain m residue 138 ASP Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 86 ASN Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 238 LEU Chi-restraints excluded: chain r residue 442 SER Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 172 LEU Chi-restraints excluded: chain s residue 185 TRP Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 229 THR Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain u residue 20 ILE Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 48 ASP Chi-restraints excluded: chain w residue 98 THR Chi-restraints excluded: chain w residue 173 MET Chi-restraints excluded: chain w residue 328 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 251 optimal weight: 0.6980 chunk 322 optimal weight: 0.4980 chunk 249 optimal weight: 0.9990 chunk 371 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 439 optimal weight: 1.9990 chunk 275 optimal weight: 0.5980 chunk 267 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 8 GLN a 90 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 204 ASN ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 524 ASN ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 26 ASN r 103 GLN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 39853 Z= 0.238 Angle : 0.731 15.989 53974 Z= 0.357 Chirality : 0.043 0.219 5940 Planarity : 0.005 0.070 6610 Dihedral : 12.928 177.003 5947 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.16 % Favored : 93.10 % Rotamer: Outliers : 3.94 % Allowed : 17.32 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.32 (0.13), residues: 4641 helix: 1.00 (0.10), residues: 2903 sheet: None (None), residues: 0 loop : -1.11 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP u 86 HIS 0.008 0.001 HIS h 34 PHE 0.035 0.001 PHE b 46 TYR 0.041 0.002 TYR S 61 ARG 0.012 0.001 ARG W 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 869 time to evaluate : 4.607 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: S 36 LYS cc_start: 0.8765 (tptm) cc_final: 0.8340 (tppp) REVERT: V 99 LEU cc_start: 0.8653 (mm) cc_final: 0.8361 (mm) REVERT: V 118 PHE cc_start: 0.8526 (m-80) cc_final: 0.8113 (m-80) REVERT: Y 97 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6582 (mm) REVERT: Z 41 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7701 (mp) REVERT: a 53 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7882 (ptp-170) REVERT: c 119 THR cc_start: 0.8515 (p) cc_final: 0.8128 (m) REVERT: d 56 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7954 (m-10) REVERT: d 116 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: e 124 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7574 (ttp-170) REVERT: g 11 ARG cc_start: 0.7408 (tpt90) cc_final: 0.6138 (tpm170) REVERT: g 44 ASP cc_start: 0.8839 (t0) cc_final: 0.8610 (t0) REVERT: g 98 GLU cc_start: 0.8467 (pm20) cc_final: 0.8171 (pm20) REVERT: g 99 ASP cc_start: 0.8583 (m-30) cc_final: 0.7648 (m-30) REVERT: i 54 GLU cc_start: 0.8445 (pp20) cc_final: 0.8062 (pt0) REVERT: i 120 GLN cc_start: 0.8770 (tt0) cc_final: 0.7769 (tp-100) REVERT: i 339 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8787 (mt) REVERT: j 1 MET cc_start: 0.3173 (ptp) cc_final: 0.1339 (mmp) REVERT: j 8 MET cc_start: 0.8305 (mmm) cc_final: 0.7408 (mtm) REVERT: j 37 TYR cc_start: 0.4965 (p90) cc_final: 0.4184 (m-10) REVERT: k 6 MET cc_start: 0.8171 (mtp) cc_final: 0.7579 (tpt) REVERT: k 7 ASN cc_start: 0.8672 (t0) cc_final: 0.8186 (t0) REVERT: k 25 HIS cc_start: 0.8143 (p-80) cc_final: 0.7107 (t70) REVERT: k 31 LEU cc_start: 0.8760 (mm) cc_final: 0.8526 (mm) REVERT: l 50 PRO cc_start: 0.9046 (Cg_exo) cc_final: 0.8775 (Cg_endo) REVERT: l 145 GLU cc_start: 0.8274 (mp0) cc_final: 0.7500 (mp0) REVERT: l 510 LYS cc_start: 0.7937 (mttm) cc_final: 0.7298 (tptt) REVERT: l 583 MET cc_start: 0.6172 (tpt) cc_final: 0.5701 (tpp) REVERT: m 2 MET cc_start: 0.8697 (tpt) cc_final: 0.8456 (tpt) REVERT: m 3 TYR cc_start: 0.8345 (m-80) cc_final: 0.8116 (m-80) REVERT: m 76 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6839 (mp0) REVERT: m 82 TRP cc_start: 0.4248 (m100) cc_final: 0.3331 (m-90) REVERT: m 105 TRP cc_start: 0.8008 (t60) cc_final: 0.7672 (t60) REVERT: m 150 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7617 (mtp180) REVERT: m 161 PHE cc_start: 0.8765 (t80) cc_final: 0.8393 (t80) REVERT: n 7 ILE cc_start: 0.7894 (mt) cc_final: 0.7642 (pt) REVERT: n 38 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.7557 (t80) REVERT: o 13 THR cc_start: 0.8248 (p) cc_final: 0.7962 (p) REVERT: o 35 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7826 (tm-30) REVERT: o 79 ASN cc_start: 0.8756 (m-40) cc_final: 0.8547 (m-40) REVERT: o 83 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.7979 (p) REVERT: o 106 LYS cc_start: 0.8382 (tttt) cc_final: 0.7839 (ttmm) REVERT: p 49 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: r 23 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8609 (mt) REVERT: r 238 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8690 (tp) REVERT: r 244 MET cc_start: 0.8158 (mtp) cc_final: 0.7915 (ttm) REVERT: r 264 LEU cc_start: 0.9158 (pp) cc_final: 0.8790 (tp) REVERT: s 3 MET cc_start: 0.8349 (mmp) cc_final: 0.6942 (ptt) REVERT: s 34 ARG cc_start: 0.8546 (ptm160) cc_final: 0.7564 (mmt90) REVERT: s 47 GLN cc_start: 0.8515 (tp40) cc_final: 0.8292 (tp-100) REVERT: s 59 GLU cc_start: 0.8762 (tt0) cc_final: 0.7959 (pm20) REVERT: s 134 ARG cc_start: 0.8126 (mmt90) cc_final: 0.7925 (mmt90) REVERT: s 184 MET cc_start: 0.8188 (mtm) cc_final: 0.7689 (mtm) REVERT: s 185 TRP cc_start: 0.8973 (OUTLIER) cc_final: 0.8505 (t-100) REVERT: s 206 GLU cc_start: 0.7854 (tp30) cc_final: 0.7279 (mp0) REVERT: s 224 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: s 279 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7346 (mpp-170) REVERT: s 281 ARG cc_start: 0.7787 (ttt180) cc_final: 0.7369 (mtm180) REVERT: s 286 MET cc_start: 0.8673 (mmm) cc_final: 0.8110 (mpp) REVERT: s 293 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: u 44 MET cc_start: 0.8545 (mmt) cc_final: 0.8122 (mmt) REVERT: u 101 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8031 (tpp-160) REVERT: v 47 MET cc_start: 0.8026 (mmp) cc_final: 0.7743 (mmt) REVERT: v 72 ASP cc_start: 0.8643 (m-30) cc_final: 0.7933 (p0) REVERT: v 91 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7886 (mm-30) REVERT: v 100 LYS cc_start: 0.8443 (mttt) cc_final: 0.7415 (tttt) REVERT: w 115 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6827 (mm-30) outliers start: 161 outliers final: 115 residues processed: 967 average time/residue: 0.4945 time to fit residues: 793.2352 Evaluate side-chains 946 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 816 time to evaluate : 4.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 95 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 55 PHE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 189 ASN Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 98 ASN Chi-restraints excluded: chain d residue 107 CYS Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 73 SER Chi-restraints excluded: chain e residue 147 ILE Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 93 TYR Chi-restraints excluded: chain i residue 221 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 307 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 326 LEU Chi-restraints excluded: chain i residue 339 ILE Chi-restraints excluded: chain j residue 3 PHE Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 30 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 113 ASN Chi-restraints excluded: chain l residue 115 ASN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 254 VAL Chi-restraints excluded: chain l residue 257 ILE Chi-restraints excluded: chain l residue 279 CYS Chi-restraints excluded: chain l residue 310 LEU Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain l residue 450 LEU Chi-restraints excluded: chain l residue 452 ASN Chi-restraints excluded: chain l residue 571 ILE Chi-restraints excluded: chain m residue 19 PHE Chi-restraints excluded: chain m residue 30 LEU Chi-restraints excluded: chain m residue 40 CYS Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 106 VAL Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain m residue 138 ASP Chi-restraints excluded: chain m residue 150 ARG Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 86 ASN Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 238 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 442 SER Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 139 THR Chi-restraints excluded: chain s residue 172 LEU Chi-restraints excluded: chain s residue 185 TRP Chi-restraints excluded: chain s residue 188 SER Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 293 PHE Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain u residue 154 ILE Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 48 ASP Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain w residue 98 THR Chi-restraints excluded: chain w residue 150 LEU Chi-restraints excluded: chain w residue 173 MET Chi-restraints excluded: chain w residue 250 SER Chi-restraints excluded: chain w residue 304 VAL Chi-restraints excluded: chain w residue 328 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 chunk 132 optimal weight: 0.0670 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 299 optimal weight: 0.7980 chunk 217 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 345 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 8 GLN a 90 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 ASN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 ASN ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 26 ASN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 104 GLN ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39853 Z= 0.223 Angle : 0.733 15.179 53974 Z= 0.357 Chirality : 0.044 0.343 5940 Planarity : 0.005 0.069 6610 Dihedral : 12.667 175.721 5947 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.99 % Favored : 93.30 % Rotamer: Outliers : 3.74 % Allowed : 17.91 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.13), residues: 4641 helix: 1.06 (0.10), residues: 2904 sheet: None (None), residues: 0 loop : -1.16 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP W 48 HIS 0.008 0.001 HIS h 34 PHE 0.040 0.002 PHE l 326 TYR 0.037 0.002 TYR S 61 ARG 0.011 0.000 ARG W 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 864 time to evaluate : 4.406 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: S 36 LYS cc_start: 0.8728 (tptm) cc_final: 0.8315 (tppp) REVERT: V 7 ARG cc_start: 0.7468 (mtt-85) cc_final: 0.7032 (tmm160) REVERT: V 99 LEU cc_start: 0.8622 (mm) cc_final: 0.8227 (mm) REVERT: V 118 PHE cc_start: 0.8558 (m-80) cc_final: 0.8189 (m-80) REVERT: W 51 MET cc_start: 0.8557 (tmm) cc_final: 0.7611 (tmm) REVERT: Y 97 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6571 (mm) REVERT: Z 41 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7683 (mp) REVERT: a 53 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7871 (ptp-170) REVERT: b 60 MET cc_start: 0.6182 (mtp) cc_final: 0.5846 (mtp) REVERT: c 80 ASP cc_start: 0.8358 (p0) cc_final: 0.8119 (p0) REVERT: c 119 THR cc_start: 0.8546 (p) cc_final: 0.8198 (m) REVERT: d 36 ASP cc_start: 0.7716 (t70) cc_final: 0.7500 (t0) REVERT: d 56 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7956 (m-10) REVERT: d 116 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: e 121 GLU cc_start: 0.7747 (mm-30) cc_final: 0.6822 (mm-30) REVERT: g 98 GLU cc_start: 0.8453 (pm20) cc_final: 0.8159 (pm20) REVERT: g 99 ASP cc_start: 0.8589 (m-30) cc_final: 0.7691 (m-30) REVERT: i 54 GLU cc_start: 0.8408 (pp20) cc_final: 0.8051 (pt0) REVERT: i 120 GLN cc_start: 0.8735 (tt0) cc_final: 0.7716 (tp-100) REVERT: j 1 MET cc_start: 0.2938 (ptp) cc_final: 0.1013 (mmp) REVERT: j 8 MET cc_start: 0.8255 (mmm) cc_final: 0.7409 (mtm) REVERT: j 37 TYR cc_start: 0.4988 (p90) cc_final: 0.4212 (m-10) REVERT: j 108 GLN cc_start: 0.8123 (mp10) cc_final: 0.7870 (mp10) REVERT: k 6 MET cc_start: 0.8152 (mtp) cc_final: 0.7562 (tpt) REVERT: k 7 ASN cc_start: 0.8654 (t0) cc_final: 0.8244 (t0) REVERT: k 25 HIS cc_start: 0.8009 (p-80) cc_final: 0.7134 (t70) REVERT: k 31 LEU cc_start: 0.8811 (mm) cc_final: 0.8585 (mm) REVERT: k 33 LEU cc_start: 0.8926 (mt) cc_final: 0.8542 (mp) REVERT: l 50 PRO cc_start: 0.9056 (Cg_exo) cc_final: 0.8778 (Cg_endo) REVERT: l 310 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8912 (mm) REVERT: l 510 LYS cc_start: 0.7912 (mttm) cc_final: 0.7303 (tptt) REVERT: l 583 MET cc_start: 0.6031 (tpt) cc_final: 0.5437 (tpp) REVERT: m 2 MET cc_start: 0.8682 (tpt) cc_final: 0.8445 (tpt) REVERT: m 76 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6794 (mp0) REVERT: m 82 TRP cc_start: 0.4272 (m100) cc_final: 0.3320 (m-90) REVERT: m 105 TRP cc_start: 0.8077 (t60) cc_final: 0.7797 (t60) REVERT: m 150 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7583 (mtp180) REVERT: m 161 PHE cc_start: 0.8723 (t80) cc_final: 0.8354 (t80) REVERT: m 172 ARG cc_start: 0.7302 (ttp80) cc_final: 0.7078 (ttp80) REVERT: n 7 ILE cc_start: 0.7934 (mt) cc_final: 0.7670 (pt) REVERT: n 38 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7490 (t80) REVERT: o 13 THR cc_start: 0.8301 (p) cc_final: 0.7988 (p) REVERT: o 28 GLU cc_start: 0.8491 (pm20) cc_final: 0.8221 (pm20) REVERT: o 79 ASN cc_start: 0.8761 (m-40) cc_final: 0.8527 (m-40) REVERT: o 83 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8008 (p) REVERT: o 106 LYS cc_start: 0.8329 (tttt) cc_final: 0.7971 (ttmm) REVERT: p 49 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: r 23 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8615 (mt) REVERT: r 238 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8664 (tp) REVERT: r 264 LEU cc_start: 0.9145 (pp) cc_final: 0.8860 (tp) REVERT: s 3 MET cc_start: 0.8371 (mmp) cc_final: 0.6952 (ptt) REVERT: s 34 ARG cc_start: 0.8549 (ptm160) cc_final: 0.7567 (mmt90) REVERT: s 47 GLN cc_start: 0.8511 (tp40) cc_final: 0.8286 (tp-100) REVERT: s 184 MET cc_start: 0.8207 (mtm) cc_final: 0.7744 (mtm) REVERT: s 185 TRP cc_start: 0.8969 (OUTLIER) cc_final: 0.8542 (t-100) REVERT: s 206 GLU cc_start: 0.7932 (tp30) cc_final: 0.7300 (mp0) REVERT: s 224 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8485 (m-80) REVERT: s 279 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7360 (mpp-170) REVERT: s 281 ARG cc_start: 0.7768 (ttt180) cc_final: 0.7358 (mtm180) REVERT: s 286 MET cc_start: 0.8626 (mmm) cc_final: 0.8027 (mpp) REVERT: s 293 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: u 44 MET cc_start: 0.8559 (mmt) cc_final: 0.8106 (mmt) REVERT: u 101 ARG cc_start: 0.8488 (mmm160) cc_final: 0.8011 (tpp-160) REVERT: v 47 MET cc_start: 0.8003 (mmp) cc_final: 0.7763 (mmt) REVERT: v 72 ASP cc_start: 0.8597 (m-30) cc_final: 0.7886 (p0) REVERT: v 100 LYS cc_start: 0.8440 (mttt) cc_final: 0.7424 (tttt) REVERT: w 115 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6836 (mm-30) outliers start: 153 outliers final: 104 residues processed: 956 average time/residue: 0.5017 time to fit residues: 795.9205 Evaluate side-chains 940 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 821 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 95 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 55 PHE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 189 ASN Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 98 ASN Chi-restraints excluded: chain d residue 107 CYS Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 73 SER Chi-restraints excluded: chain e residue 147 ILE Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 93 TYR Chi-restraints excluded: chain i residue 221 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 307 MET Chi-restraints excluded: chain i residue 326 LEU Chi-restraints excluded: chain j residue 3 PHE Chi-restraints excluded: chain j residue 51 PHE Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 113 ASN Chi-restraints excluded: chain l residue 115 ASN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 254 VAL Chi-restraints excluded: chain l residue 257 ILE Chi-restraints excluded: chain l residue 279 CYS Chi-restraints excluded: chain l residue 310 LEU Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain l residue 450 LEU Chi-restraints excluded: chain l residue 452 ASN Chi-restraints excluded: chain l residue 571 ILE Chi-restraints excluded: chain m residue 19 PHE Chi-restraints excluded: chain m residue 30 LEU Chi-restraints excluded: chain m residue 40 CYS Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 106 VAL Chi-restraints excluded: chain m residue 117 ASN Chi-restraints excluded: chain m residue 138 ASP Chi-restraints excluded: chain m residue 150 ARG Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 ASP Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 86 ASN Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 238 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 442 SER Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 185 TRP Chi-restraints excluded: chain s residue 188 SER Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 293 PHE Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain u residue 25 LEU Chi-restraints excluded: chain u residue 104 GLN Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 48 ASP Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain w residue 98 THR Chi-restraints excluded: chain w residue 150 LEU Chi-restraints excluded: chain w residue 173 MET Chi-restraints excluded: chain w residue 250 SER Chi-restraints excluded: chain w residue 304 VAL Chi-restraints excluded: chain w residue 328 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 0.8980 chunk 421 optimal weight: 0.9980 chunk 384 optimal weight: 0.7980 chunk 409 optimal weight: 3.9990 chunk 420 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 321 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 370 optimal weight: 0.0270 chunk 387 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 90 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 48 ASN ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 ASN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39853 Z= 0.233 Angle : 0.754 15.268 53974 Z= 0.366 Chirality : 0.044 0.346 5940 Planarity : 0.005 0.072 6610 Dihedral : 12.523 175.458 5945 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.23 % Favored : 93.06 % Rotamer: Outliers : 3.52 % Allowed : 18.47 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.36 (0.13), residues: 4641 helix: 1.08 (0.10), residues: 2896 sheet: None (None), residues: 0 loop : -1.19 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP u 86 HIS 0.008 0.001 HIS h 34 PHE 0.040 0.001 PHE l 326 TYR 0.036 0.002 TYR S 61 ARG 0.008 0.000 ARG s 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 836 time to evaluate : 4.894 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: S 36 LYS cc_start: 0.8721 (tptm) cc_final: 0.8307 (tppp) REVERT: V 7 ARG cc_start: 0.7435 (mtt-85) cc_final: 0.7125 (tmm160) REVERT: V 8 GLN cc_start: 0.5689 (pt0) cc_final: 0.5032 (pt0) REVERT: V 99 LEU cc_start: 0.8633 (mm) cc_final: 0.8308 (mm) REVERT: V 118 PHE cc_start: 0.8568 (m-80) cc_final: 0.8207 (m-80) REVERT: W 51 MET cc_start: 0.8290 (tmm) cc_final: 0.7664 (tmm) REVERT: W 55 ARG cc_start: 0.8326 (mtt180) cc_final: 0.8066 (mtt180) REVERT: W 140 PHE cc_start: 0.8867 (t80) cc_final: 0.8541 (t80) REVERT: Y 41 GLU cc_start: 0.6192 (tp30) cc_final: 0.5691 (tp30) REVERT: Y 97 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6593 (mm) REVERT: Z 33 GLN cc_start: 0.8787 (tp-100) cc_final: 0.8525 (tp-100) REVERT: Z 41 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7652 (mp) REVERT: a 53 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7874 (ptp-170) REVERT: b 60 MET cc_start: 0.6247 (mtp) cc_final: 0.5811 (mtp) REVERT: c 80 ASP cc_start: 0.8350 (p0) cc_final: 0.8106 (p0) REVERT: c 119 THR cc_start: 0.8594 (p) cc_final: 0.8220 (m) REVERT: d 29 LYS cc_start: 0.9066 (tppt) cc_final: 0.8814 (ptmt) REVERT: d 36 ASP cc_start: 0.7720 (t70) cc_final: 0.7477 (t0) REVERT: d 56 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.8001 (m-10) REVERT: d 116 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: e 121 GLU cc_start: 0.7743 (mm-30) cc_final: 0.6834 (mm-30) REVERT: g 98 GLU cc_start: 0.8430 (pm20) cc_final: 0.8140 (pm20) REVERT: g 99 ASP cc_start: 0.8597 (m-30) cc_final: 0.7692 (m-30) REVERT: h 99 ILE cc_start: 0.7389 (mm) cc_final: 0.7088 (mp) REVERT: i 54 GLU cc_start: 0.8309 (pp20) cc_final: 0.7974 (pt0) REVERT: i 120 GLN cc_start: 0.8740 (tt0) cc_final: 0.7675 (tp-100) REVERT: j 1 MET cc_start: 0.2815 (ptp) cc_final: 0.0905 (mmm) REVERT: j 8 MET cc_start: 0.8201 (mmm) cc_final: 0.7336 (mtm) REVERT: j 37 TYR cc_start: 0.4966 (p90) cc_final: 0.4173 (m-10) REVERT: k 6 MET cc_start: 0.8192 (mtp) cc_final: 0.7493 (tpt) REVERT: k 7 ASN cc_start: 0.8695 (t0) cc_final: 0.8303 (t0) REVERT: k 25 HIS cc_start: 0.7998 (p-80) cc_final: 0.7126 (t70) REVERT: k 31 LEU cc_start: 0.8832 (mm) cc_final: 0.8617 (mm) REVERT: l 50 PRO cc_start: 0.9056 (Cg_exo) cc_final: 0.8765 (Cg_endo) REVERT: l 145 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7415 (mp0) REVERT: l 338 MET cc_start: 0.8577 (mmm) cc_final: 0.7959 (tmm) REVERT: l 510 LYS cc_start: 0.7915 (mttm) cc_final: 0.7321 (tptt) REVERT: l 583 MET cc_start: 0.5969 (tpt) cc_final: 0.5402 (tpp) REVERT: m 2 MET cc_start: 0.8630 (tpt) cc_final: 0.8232 (tpp) REVERT: m 76 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6765 (mp0) REVERT: m 82 TRP cc_start: 0.4347 (m100) cc_final: 0.3362 (m-90) REVERT: m 105 TRP cc_start: 0.8119 (t60) cc_final: 0.7840 (t60) REVERT: m 150 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7609 (mtp180) REVERT: m 161 PHE cc_start: 0.8714 (t80) cc_final: 0.8374 (t80) REVERT: n 7 ILE cc_start: 0.7951 (mt) cc_final: 0.7679 (pt) REVERT: n 38 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7445 (t80) REVERT: o 13 THR cc_start: 0.8328 (p) cc_final: 0.8029 (p) REVERT: o 83 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8010 (p) REVERT: o 106 LYS cc_start: 0.8312 (tttt) cc_final: 0.7922 (ttmm) REVERT: p 49 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: r 10 MET cc_start: 0.8692 (tpp) cc_final: 0.8479 (tpp) REVERT: r 23 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8610 (mt) REVERT: r 238 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8680 (tp) REVERT: r 264 LEU cc_start: 0.9122 (pp) cc_final: 0.8870 (tp) REVERT: s 3 MET cc_start: 0.8413 (mmp) cc_final: 0.6939 (ptt) REVERT: s 34 ARG cc_start: 0.8534 (ptm160) cc_final: 0.7566 (mmt90) REVERT: s 47 GLN cc_start: 0.8563 (tp40) cc_final: 0.8344 (tp-100) REVERT: s 59 GLU cc_start: 0.8769 (tt0) cc_final: 0.7990 (pm20) REVERT: s 184 MET cc_start: 0.8269 (mtm) cc_final: 0.8056 (mtm) REVERT: s 185 TRP cc_start: 0.8959 (OUTLIER) cc_final: 0.8531 (t-100) REVERT: s 224 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: s 281 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7383 (mtm180) REVERT: s 286 MET cc_start: 0.8646 (mmm) cc_final: 0.7970 (mpp) REVERT: u 44 MET cc_start: 0.8569 (mmt) cc_final: 0.8116 (mmt) REVERT: u 101 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8248 (tpp-160) REVERT: v 47 MET cc_start: 0.7981 (mmp) cc_final: 0.7762 (mmt) REVERT: v 72 ASP cc_start: 0.8609 (m-30) cc_final: 0.7891 (p0) REVERT: v 91 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8060 (mm-30) REVERT: v 100 LYS cc_start: 0.8483 (mttt) cc_final: 0.7472 (tttt) REVERT: w 115 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6845 (mm-30) outliers start: 144 outliers final: 109 residues processed: 922 average time/residue: 0.4917 time to fit residues: 751.6261 Evaluate side-chains 937 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 815 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 95 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 55 PHE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 189 ASN Chi-restraints excluded: chain b residue 18 LEU Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 107 CYS Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 73 SER Chi-restraints excluded: chain e residue 147 ILE Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 221 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 307 MET Chi-restraints excluded: chain i residue 326 LEU Chi-restraints excluded: chain j residue 3 PHE Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 113 ASN Chi-restraints excluded: chain l residue 115 ASN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 254 VAL Chi-restraints excluded: chain l residue 257 ILE Chi-restraints excluded: chain l residue 279 CYS Chi-restraints excluded: chain l residue 310 LEU Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain l residue 450 LEU Chi-restraints excluded: chain l residue 452 ASN Chi-restraints excluded: chain l residue 571 ILE Chi-restraints excluded: chain m residue 19 PHE Chi-restraints excluded: chain m residue 30 LEU Chi-restraints excluded: chain m residue 40 CYS Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 150 ARG Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 86 ASN Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 238 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 442 SER Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 172 LEU Chi-restraints excluded: chain s residue 185 TRP Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 245 THR Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain u residue 25 LEU Chi-restraints excluded: chain u residue 154 ILE Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 48 ASP Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain w residue 98 THR Chi-restraints excluded: chain w residue 150 LEU Chi-restraints excluded: chain w residue 173 MET Chi-restraints excluded: chain w residue 250 SER Chi-restraints excluded: chain w residue 304 VAL Chi-restraints excluded: chain w residue 328 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 2.9990 chunk 268 optimal weight: 0.0970 chunk 433 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 301 optimal weight: 0.9990 chunk 454 optimal weight: 2.9990 chunk 418 optimal weight: 0.6980 chunk 361 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 279 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 67 ASN V 8 GLN a 90 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 48 ASN ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 ASN ** m 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 104 GLN ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 142 GLN ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39853 Z= 0.228 Angle : 0.761 15.257 53974 Z= 0.368 Chirality : 0.044 0.332 5940 Planarity : 0.005 0.070 6610 Dihedral : 12.360 176.701 5945 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.10 % Favored : 93.23 % Rotamer: Outliers : 3.40 % Allowed : 18.74 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.37 (0.13), residues: 4641 helix: 1.09 (0.10), residues: 2903 sheet: None (None), residues: 0 loop : -1.20 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP u 86 HIS 0.008 0.001 HIS h 34 PHE 0.037 0.001 PHE l 326 TYR 0.034 0.002 TYR S 61 ARG 0.016 0.000 ARG W 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 850 time to evaluate : 4.385 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: S 36 LYS cc_start: 0.8691 (tptm) cc_final: 0.8301 (tppp) REVERT: S 43 TYR cc_start: 0.8849 (t80) cc_final: 0.8578 (t80) REVERT: S 52 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7991 (ttt-90) REVERT: V 7 ARG cc_start: 0.7439 (mtt-85) cc_final: 0.7081 (tmm160) REVERT: V 20 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7344 (mtm-85) REVERT: V 99 LEU cc_start: 0.8566 (mm) cc_final: 0.8246 (mm) REVERT: V 118 PHE cc_start: 0.8584 (m-80) cc_final: 0.8219 (m-80) REVERT: W 51 MET cc_start: 0.8227 (tmm) cc_final: 0.7633 (tmm) REVERT: W 140 PHE cc_start: 0.8869 (t80) cc_final: 0.8516 (t80) REVERT: Y 95 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.4948 (tp30) REVERT: Z 41 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7846 (mp) REVERT: a 53 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7895 (ptp-170) REVERT: b 60 MET cc_start: 0.6204 (mtp) cc_final: 0.5856 (mtp) REVERT: c 80 ASP cc_start: 0.8342 (p0) cc_final: 0.8105 (p0) REVERT: c 119 THR cc_start: 0.8598 (p) cc_final: 0.8217 (m) REVERT: d 28 MET cc_start: 0.7208 (mmt) cc_final: 0.6634 (mmt) REVERT: d 36 ASP cc_start: 0.7713 (t70) cc_final: 0.7496 (t0) REVERT: d 56 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7995 (m-10) REVERT: d 116 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: e 121 GLU cc_start: 0.7746 (mm-30) cc_final: 0.6835 (mm-30) REVERT: g 89 MET cc_start: 0.8541 (ttp) cc_final: 0.8276 (ttm) REVERT: g 98 GLU cc_start: 0.8408 (pm20) cc_final: 0.8163 (pm20) REVERT: g 99 ASP cc_start: 0.8596 (m-30) cc_final: 0.7712 (m-30) REVERT: i 1 MET cc_start: 0.6825 (mpp) cc_final: 0.6256 (mpp) REVERT: i 54 GLU cc_start: 0.8300 (pp20) cc_final: 0.7960 (pt0) REVERT: i 120 GLN cc_start: 0.8742 (tt0) cc_final: 0.7661 (tp-100) REVERT: j 1 MET cc_start: 0.2809 (ptp) cc_final: 0.0958 (mmm) REVERT: j 8 MET cc_start: 0.8196 (mmm) cc_final: 0.7362 (mtm) REVERT: j 37 TYR cc_start: 0.4983 (p90) cc_final: 0.4139 (m-10) REVERT: j 43 PRO cc_start: 0.6035 (Cg_endo) cc_final: 0.5833 (Cg_exo) REVERT: k 6 MET cc_start: 0.8194 (mtp) cc_final: 0.7528 (tpt) REVERT: k 7 ASN cc_start: 0.8688 (t0) cc_final: 0.8270 (t0) REVERT: k 25 HIS cc_start: 0.8004 (p-80) cc_final: 0.7145 (t70) REVERT: k 31 LEU cc_start: 0.8796 (mm) cc_final: 0.8532 (mm) REVERT: l 50 PRO cc_start: 0.9042 (Cg_exo) cc_final: 0.8749 (Cg_endo) REVERT: l 145 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7339 (mp0) REVERT: l 310 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8920 (mm) REVERT: l 338 MET cc_start: 0.8566 (mmm) cc_final: 0.7831 (tmm) REVERT: l 510 LYS cc_start: 0.7936 (mttm) cc_final: 0.7352 (tptt) REVERT: l 583 MET cc_start: 0.5965 (tpt) cc_final: 0.5380 (tpp) REVERT: m 2 MET cc_start: 0.8621 (tpt) cc_final: 0.8253 (tpp) REVERT: m 69 TYR cc_start: 0.8440 (t80) cc_final: 0.8097 (m-80) REVERT: m 76 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6726 (mp0) REVERT: m 82 TRP cc_start: 0.4370 (m100) cc_final: 0.3388 (m-90) REVERT: m 105 TRP cc_start: 0.8123 (t60) cc_final: 0.7854 (t60) REVERT: m 150 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7636 (mtp180) REVERT: m 161 PHE cc_start: 0.8727 (t80) cc_final: 0.8401 (t80) REVERT: n 7 ILE cc_start: 0.7940 (mt) cc_final: 0.7670 (pt) REVERT: n 38 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7446 (t80) REVERT: o 13 THR cc_start: 0.8347 (p) cc_final: 0.8054 (p) REVERT: o 83 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8007 (p) REVERT: o 106 LYS cc_start: 0.8264 (tttt) cc_final: 0.7836 (ttmm) REVERT: p 49 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: r 23 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8611 (mt) REVERT: r 238 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8704 (tp) REVERT: r 264 LEU cc_start: 0.9108 (pp) cc_final: 0.8863 (tp) REVERT: s 3 MET cc_start: 0.8483 (mmp) cc_final: 0.6985 (ptt) REVERT: s 34 ARG cc_start: 0.8465 (ptm160) cc_final: 0.7487 (mmt90) REVERT: s 47 GLN cc_start: 0.8593 (tp40) cc_final: 0.8381 (tp-100) REVERT: s 59 GLU cc_start: 0.8767 (tt0) cc_final: 0.7988 (pm20) REVERT: s 184 MET cc_start: 0.8293 (mtm) cc_final: 0.8082 (mtm) REVERT: s 185 TRP cc_start: 0.8956 (OUTLIER) cc_final: 0.8560 (t-100) REVERT: s 281 ARG cc_start: 0.7765 (ttt180) cc_final: 0.7392 (mtm180) REVERT: s 286 MET cc_start: 0.8658 (mmm) cc_final: 0.7946 (mpp) REVERT: u 44 MET cc_start: 0.8584 (mmt) cc_final: 0.8335 (tpp) REVERT: u 101 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8005 (tpp-160) REVERT: v 72 ASP cc_start: 0.8577 (m-30) cc_final: 0.7847 (p0) REVERT: v 91 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7945 (mm-30) REVERT: v 100 LYS cc_start: 0.8416 (mttt) cc_final: 0.7329 (tttt) REVERT: w 115 GLU cc_start: 0.7455 (tm-30) cc_final: 0.6854 (mm-30) outliers start: 139 outliers final: 103 residues processed: 931 average time/residue: 0.5189 time to fit residues: 805.4217 Evaluate side-chains 930 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 814 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 8 GLN Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 95 GLU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 55 PHE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 189 ASN Chi-restraints excluded: chain b residue 18 LEU Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 107 CYS Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 73 SER Chi-restraints excluded: chain e residue 147 ILE Chi-restraints excluded: chain g residue 26 THR Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 221 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 307 MET Chi-restraints excluded: chain i residue 326 LEU Chi-restraints excluded: chain j residue 3 PHE Chi-restraints excluded: chain j residue 51 PHE Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 113 ASN Chi-restraints excluded: chain l residue 115 ASN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 254 VAL Chi-restraints excluded: chain l residue 257 ILE Chi-restraints excluded: chain l residue 279 CYS Chi-restraints excluded: chain l residue 310 LEU Chi-restraints excluded: chain l residue 356 ILE Chi-restraints excluded: chain l residue 452 ASN Chi-restraints excluded: chain l residue 571 ILE Chi-restraints excluded: chain m residue 19 PHE Chi-restraints excluded: chain m residue 30 LEU Chi-restraints excluded: chain m residue 40 CYS Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 150 ARG Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 86 ASN Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 238 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 442 SER Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 185 TRP Chi-restraints excluded: chain s residue 188 SER Chi-restraints excluded: chain s residue 245 THR Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain u residue 25 LEU Chi-restraints excluded: chain u residue 104 GLN Chi-restraints excluded: chain u residue 154 ILE Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 48 ASP Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain w residue 150 LEU Chi-restraints excluded: chain w residue 173 MET Chi-restraints excluded: chain w residue 250 SER Chi-restraints excluded: chain w residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 2.9990 chunk 287 optimal weight: 0.0000 chunk 385 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 333 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 362 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 372 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 67 ASN a 90 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 48 ASN ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 88 ASN ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.106526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.085047 restraints weight = 91453.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.087443 restraints weight = 46241.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088976 restraints weight = 29946.839| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39853 Z= 0.228 Angle : 0.769 15.269 53974 Z= 0.372 Chirality : 0.045 0.370 5940 Planarity : 0.005 0.069 6610 Dihedral : 12.263 177.912 5945 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.29 % Favored : 93.06 % Rotamer: Outliers : 3.18 % Allowed : 19.03 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.13), residues: 4641 helix: 1.08 (0.10), residues: 2907 sheet: None (None), residues: 0 loop : -1.21 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP u 86 HIS 0.008 0.001 HIS h 34 PHE 0.035 0.001 PHE l 326 TYR 0.034 0.002 TYR S 61 ARG 0.010 0.000 ARG V 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12535.39 seconds wall clock time: 225 minutes 43.23 seconds (13543.23 seconds total)