Starting phenix.real_space_refine on Tue Sep 15 11:29:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5xtc_6772/09_2026/5xtc_6772.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xtc_6772/09_2026/5xtc_6772.map 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 { model { file = "/net/cci-nas-00/data/ceres_data/5xtc_6772/09_2026/5xtc_6772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xtc_6772/09_2026/5xtc_6772.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5xtc_6772/09_2026/5xtc_6772.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5xtc_6772/09_2026/5xtc_6772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xtc_6772/09_2026/5xtc_6772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xtc_6772/09_2026/5xtc_6772.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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, 'HIS:plan': 1, 'TYR: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: {'ASP:plan': 3, 'TRP:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} 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: {'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 2, 'TYR:plan': 1, 'PHE:plan': 1} 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: 7.90, per 1000 atoms: 0.20 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 1.8 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... Secondary structure from input PDB file: 226 helices and 4 sheets defined 70.3% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'Q' and resid 40 through 49 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 69 through 74 removed outlier: 3.920A pdb=" N LYS Q 73 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 79 Processing helix chain 'S' and resid 1 through 3 No H-bonds generated for 'chain 'S' and resid 1 through 3' Processing helix chain 'S' and resid 4 through 16 removed outlier: 4.608A pdb=" N GLY S 8 " --> pdb=" O GLU S 4 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU S 9 " --> pdb=" O ILE S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 31 removed outlier: 4.337A pdb=" N GLY S 20 " --> pdb=" O LEU S 16 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR S 25 " --> pdb=" O LEU S 21 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 56 removed outlier: 3.518A pdb=" N TRP S 45 " --> pdb=" O PHE S 41 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.764A pdb=" N ASP S 70 " --> pdb=" O GLU S 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 13 removed outlier: 3.917A pdb=" N PHE U 8 " --> pdb=" O ARG U 4 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 36 removed outlier: 3.519A pdb=" N VAL U 20 " --> pdb=" O GLU U 16 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 49 removed outlier: 3.550A pdb=" N THR U 49 " --> pdb=" O ILE U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 78 through 84 removed outlier: 3.747A pdb=" N LEU U 84 " --> pdb=" O TRP U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 11 removed outlier: 3.907A pdb=" N TRP V 10 " --> pdb=" O PHE V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 44 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 48 through 82 removed outlier: 3.514A pdb=" N GLY V 52 " --> pdb=" O THR V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 106 Processing helix chain 'V' and resid 107 through 132 removed outlier: 3.813A pdb=" N GLY V 111 " --> pdb=" O ASN V 107 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL V 116 " --> pdb=" O ALA V 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 34 through 70 removed outlier: 3.934A pdb=" N ILE W 38 " --> pdb=" O SER W 34 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR W 42 " --> pdb=" O ILE W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 99 removed outlier: 3.664A pdb=" N LEU W 75 " --> pdb=" O LEU W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 125 Processing helix chain 'W' and resid 129 through 139 Processing helix chain 'X' and resid 75 through 90 removed outlier: 3.811A pdb=" N ASP X 81 " --> pdb=" O GLU X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 110 through 127 removed outlier: 4.181A pdb=" N ASP X 114 " --> pdb=" O LEU X 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN X 115 " --> pdb=" O ASP X 111 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL X 116 " --> pdb=" O SER X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 136 Processing helix chain 'X' and resid 140 through 152 Processing helix chain 'Y' and resid 51 through 76 removed outlier: 3.755A pdb=" N VAL Y 55 " --> pdb=" O THR Y 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 22 Processing helix chain 'Z' and resid 27 through 39 removed outlier: 3.686A pdb=" N THR Z 31 " --> pdb=" O THR Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 54 removed outlier: 3.649A pdb=" N GLU Z 49 " --> pdb=" O TRP Z 45 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET Z 54 " --> pdb=" O ALA Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 68 removed outlier: 3.576A pdb=" N VAL Z 66 " --> pdb=" O SER Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 89 removed outlier: 3.667A pdb=" N GLU Z 89 " --> pdb=" O GLU Z 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 78 removed outlier: 3.781A pdb=" N LEU a 68 " --> pdb=" O ASP a 64 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR a 78 " --> pdb=" O TYR a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 92 Processing helix chain 'a' and resid 108 through 113 Processing helix chain 'a' and resid 115 through 125 Processing helix chain 'a' and resid 128 through 164 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 175 through 179 removed outlier: 3.752A pdb=" N LEU a 178 " --> pdb=" O ASP a 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 26 Processing helix chain 'b' and resid 40 through 48 removed outlier: 3.685A pdb=" N GLU b 44 " --> pdb=" O MET b 40 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP b 47 " --> pdb=" O MET b 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 53 removed outlier: 3.717A pdb=" N ASN b 53 " --> pdb=" O LYS b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 55 through 75 removed outlier: 3.748A pdb=" N LYS b 59 " --> pdb=" O SER b 55 " (cutoff:3.500A) 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 75 through 93 removed outlier: 4.749A pdb=" N SER b 91 " --> pdb=" O LYS b 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 82 through 86 Processing helix chain 'c' and resid 109 through 113 removed outlier: 3.559A pdb=" N ASN c 113 " --> pdb=" O ASP c 110 " (cutoff:3.500A) Processing helix chain 'c' and resid 125 through 150 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 161 through 167 removed outlier: 3.633A pdb=" N ASN c 165 " --> pdb=" O TYR c 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR c 167 " --> pdb=" O TYR c 163 " (cutoff:3.500A) Processing helix chain 'c' and resid 168 through 170 No H-bonds generated for 'chain 'c' and resid 168 through 170' Processing helix chain 'd' and resid 2 through 7 removed outlier: 3.506A pdb=" N LYS d 7 " --> pdb=" O SER d 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 35 removed outlier: 3.524A pdb=" N VAL d 25 " --> pdb=" O PRO d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 53 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 67 through 71 Processing helix chain 'd' and resid 76 through 111 removed outlier: 3.774A pdb=" N LYS d 91 " --> pdb=" O LYS d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 115 through 137 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 145 through 171 removed outlier: 3.616A pdb=" N THR d 171 " --> pdb=" O ALA d 167 " (cutoff:3.500A) Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.052A pdb=" N LYS e 69 " --> pdb=" O ASN e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 94 Processing helix chain 'e' and resid 97 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 114 through 133 Processing helix chain 'f' and resid 33 through 37 Processing helix chain 'f' and resid 41 through 73 removed outlier: 3.919A pdb=" N GLY f 45 " --> pdb=" O TRP f 41 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE f 46 " --> pdb=" O LEU f 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 14 through 20 Processing helix chain 'g' and resid 27 through 48 Processing helix chain 'g' and resid 56 through 96 removed outlier: 3.921A pdb=" N GLN g 60 " --> pdb=" O GLY g 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 100 Processing helix chain 'h' and resid 5 through 10 Processing helix chain 'h' and resid 15 through 19 Processing helix chain 'h' and resid 25 through 29 removed outlier: 3.522A pdb=" N MET h 29 " --> pdb=" O PRO h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 34 through 44 removed outlier: 3.749A pdb=" N ALA h 44 " --> pdb=" O TRP h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 56 Processing helix chain 'h' and resid 56 through 69 Processing helix chain 'h' and resid 69 through 85 Processing helix chain 'i' and resid 5 through 23 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 25 through 45 removed outlier: 3.633A pdb=" N THR i 29 " --> pdb=" O HIS i 25 " (cutoff:3.500A) 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 49 through 81 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 92 through 106 Processing helix chain 'i' and resid 111 through 113 No H-bonds generated for 'chain 'i' and resid 111 through 113' Processing helix chain 'i' and resid 114 through 122 removed outlier: 3.784A pdb=" N THR i 122 " --> pdb=" O VAL i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 132 Processing helix chain 'i' and resid 135 through 145 Processing helix chain 'i' and resid 146 through 149 Processing helix chain 'i' and resid 150 through 170 removed outlier: 3.691A pdb=" N LEU i 154 " --> pdb=" O ASN i 150 " (cutoff:3.500A) 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 174 through 194 removed outlier: 3.608A pdb=" N MET i 191 " --> pdb=" O MET i 187 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU i 194 " --> pdb=" O MET i 190 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 223 Processing helix chain 'i' and resid 226 through 231 Processing helix chain 'i' and resid 232 through 235 Processing helix chain 'i' and resid 237 through 241 Processing helix chain 'i' and resid 242 through 252 removed outlier: 3.721A pdb=" N LEU i 248 " --> pdb=" O ILE i 244 " (cutoff:3.500A) Processing helix chain 'i' and resid 259 through 272 removed outlier: 4.288A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (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 310 through 315 Processing helix chain 'i' and resid 325 through 334 removed outlier: 3.907A pdb=" N THR i 334 " --> pdb=" O ILE i 330 " (cutoff:3.500A) Processing helix chain 'i' and resid 336 through 338 No H-bonds generated for 'chain 'i' and resid 336 through 338' Processing helix chain 'i' and resid 339 through 347 removed outlier: 4.004A pdb=" N MET i 345 " --> pdb=" O PRO i 341 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE i 346 " --> pdb=" O PHE i 342 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU i 347 " --> pdb=" O MET i 343 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 23 removed outlier: 3.552A pdb=" N ILE j 6 " --> pdb=" O ASN j 2 " (cutoff:3.500A) 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 53 through 73 removed outlier: 3.616A pdb=" N LEU j 57 " --> pdb=" O MET j 53 " (cutoff:3.500A) 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) Processing helix chain 'j' and resid 74 through 79 Processing helix chain 'j' and resid 83 through 108 removed outlier: 3.554A pdb=" N MET j 87 " --> pdb=" O ASN j 83 " (cutoff:3.500A) 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 22 removed outlier: 3.835A pdb=" N TYR k 22 " --> pdb=" O GLY k 18 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 51 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 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 57 through 85 removed outlier: 3.999A pdb=" N ILE k 61 " --> pdb=" O ASN k 57 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU k 64 " --> pdb=" O PRO k 60 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL k 65 " --> pdb=" O ILE k 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU k 78 " --> pdb=" O GLY k 74 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN k 83 " --> pdb=" O VAL k 79 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 14 removed outlier: 3.771A pdb=" N LEU l 12 " --> pdb=" O ALA l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 25 Processing helix chain 'l' and resid 30 through 57 removed outlier: 4.402A pdb=" N HIS l 34 " --> pdb=" O ASN l 30 " (cutoff:3.500A) 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 83 through 108 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 113 through 134 Processing helix chain 'l' and resid 136 through 156 removed outlier: 4.198A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER l 156 " --> pdb=" O PHE l 152 " (cutoff:3.500A) Processing helix chain 'l' and resid 161 through 194 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 197 through 205 Processing helix chain 'l' and resid 209 through 224 removed outlier: 4.430A pdb=" N LEU l 213 " --> pdb=" O SER l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 Processing helix chain 'l' and resid 233 through 237 Processing helix chain 'l' and resid 240 through 248 removed outlier: 3.586A pdb=" N SER l 244 " --> pdb=" O PRO l 240 " (cutoff:3.500A) Processing helix chain 'l' and resid 254 through 263 removed outlier: 3.880A pdb=" N LEU l 260 " --> pdb=" O GLY l 256 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE l 261 " --> pdb=" O ILE l 257 " (cutoff:3.500A) Processing helix chain 'l' and resid 263 through 268 removed outlier: 3.935A pdb=" N ALA l 267 " --> pdb=" O PHE l 263 " (cutoff:3.500A) Processing helix chain 'l' and resid 270 through 293 removed outlier: 3.558A pdb=" N GLN l 274 " --> pdb=" O ASN l 270 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) Processing helix chain 'l' and resid 297 through 319 removed outlier: 3.620A pdb=" N ILE l 317 " --> pdb=" O MET l 313 " (cutoff:3.500A) Processing helix chain 'l' and resid 321 through 350 removed outlier: 3.554A pdb=" N ALA l 325 " --> pdb=" O GLN l 321 " (cutoff:3.500A) 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 355 through 359 removed outlier: 3.744A pdb=" N LYS l 358 " --> pdb=" O ASP l 355 " (cutoff:3.500A) Processing helix chain 'l' and resid 366 through 382 Processing helix chain 'l' and resid 391 through 402 Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.924A pdb=" N SER l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 451 through 472 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 483 through 509 removed outlier: 3.546A pdb=" N LYS l 487 " --> pdb=" O PRO l 483 " (cutoff:3.500A) 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) removed outlier: 3.695A pdb=" N ASN l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 517 through 525 removed outlier: 3.542A pdb=" N TYR l 521 " --> pdb=" O LEU l 517 " (cutoff:3.500A) Processing helix chain 'l' and resid 528 through 547 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 556 through 562 removed outlier: 3.644A pdb=" N LEU l 562 " --> pdb=" O LEU l 558 " (cutoff:3.500A) Processing helix chain 'l' and resid 563 through 577 Processing helix chain 'l' and resid 583 through 600 removed outlier: 4.311A pdb=" N TYR l 587 " --> pdb=" O MET l 583 " (cutoff:3.500A) 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 3 through 20 removed outlier: 3.983A pdb=" N LEU m 7 " --> pdb=" O TYR m 3 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU m 8 " --> pdb=" O ALA m 4 " (cutoff:3.500A) Processing helix chain 'm' and resid 24 through 45 removed outlier: 4.078A pdb=" N LEU m 30 " --> pdb=" O ILE m 26 " (cutoff:3.500A) Processing helix chain 'm' and resid 48 through 59 removed outlier: 3.651A pdb=" N VAL m 55 " --> pdb=" O MET m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 removed outlier: 3.696A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA m 72 " --> pdb=" O GLY m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 73 through 75 No H-bonds generated for 'chain 'm' and resid 73 through 75' Processing helix chain 'm' and resid 85 through 110 removed outlier: 3.895A pdb=" N LEU m 89 " --> pdb=" O GLY m 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 111 through 113 No H-bonds generated for 'chain 'm' and resid 111 through 113' Processing helix chain 'm' and resid 136 through 144 removed outlier: 4.403A pdb=" N ILE m 140 " --> pdb=" O ARG m 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 149 through 172 removed outlier: 4.033A pdb=" N TYR m 165 " --> pdb=" O PHE m 161 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 8 removed outlier: 3.725A pdb=" N VAL n 8 " --> pdb=" O LEU n 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 4 through 8' Processing helix chain 'n' and resid 9 through 14 removed outlier: 5.866A pdb=" N TRP n 12 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL n 13 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS n 14 " --> pdb=" O HIS n 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 9 through 14' Processing helix chain 'n' and resid 15 through 35 removed outlier: 3.927A pdb=" N GLY n 24 " --> pdb=" O GLY n 20 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG n 29 " --> pdb=" O CYS n 25 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU n 33 " --> pdb=" O ARG n 29 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG n 34 " --> pdb=" O LYS n 30 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 39 Processing helix chain 'o' and resid 15 through 23 Proline residue: o 20 - end of helix removed outlier: 3.579A pdb=" N TYR o 23 " --> pdb=" O PRO o 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 53 removed outlier: 3.598A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP o 53 " --> pdb=" O LEU o 49 " (cutoff:3.500A) Processing helix chain 'o' and resid 62 through 72 Processing helix chain 'o' and resid 75 through 80 removed outlier: 3.597A pdb=" N ASN o 79 " --> pdb=" O ASN o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 83 through 118 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 11 through 32 removed outlier: 3.522A pdb=" N VAL p 32 " --> pdb=" O GLU p 28 " (cutoff:3.500A) Processing helix chain 'p' and resid 33 through 50 removed outlier: 3.623A pdb=" N GLU p 50 " --> pdb=" O ALA p 46 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 100 through 107 removed outlier: 3.946A pdb=" N ASP p 105 " --> pdb=" O TRP p 102 " (cutoff:3.500A) Processing helix chain 'p' and resid 108 through 113 Processing helix chain 'p' and resid 115 through 144 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 167 through 172 Processing helix chain 'r' and resid 2 through 18 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 22 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 61 through 81 removed outlier: 4.135A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 3.640A pdb=" N GLN r 81 " --> pdb=" O ILE r 77 " (cutoff:3.500A) Processing helix chain 'r' and resid 82 through 84 No H-bonds generated for 'chain 'r' and resid 82 through 84' Processing helix chain 'r' and resid 88 through 110 removed outlier: 4.051A pdb=" N LEU r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 125 through 137 removed outlier: 3.687A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 171 removed outlier: 4.622A pdb=" N THR r 147 " --> pdb=" O LEU r 143 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU r 150 " --> pdb=" O GLY r 146 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR r 152 " --> pdb=" O TYR r 148 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) 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 175 through 182 removed outlier: 3.529A pdb=" N LEU r 181 " --> pdb=" O LEU r 177 " (cutoff:3.500A) Processing helix chain 'r' and resid 188 through 207 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 209 through 213 removed outlier: 4.045A pdb=" N HIS r 213 " --> pdb=" O TYR r 210 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 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 224 through 247 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) Processing helix chain 'r' and resid 252 through 258 removed outlier: 4.099A pdb=" N HIS r 256 " --> pdb=" O PRO r 252 " (cutoff:3.500A) Processing helix chain 'r' and resid 258 through 277 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) Processing helix chain 'r' and resid 281 through 304 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) removed outlier: 3.866A pdb=" N GLN r 304 " --> pdb=" O ALA r 300 " (cutoff:3.500A) Processing helix chain 'r' and resid 305 through 338 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 341 through 345 Processing helix chain 'r' and resid 347 through 351 removed outlier: 3.829A pdb=" N THR r 350 " --> pdb=" O GLY r 347 " (cutoff:3.500A) Processing helix chain 'r' and resid 352 through 367 Processing helix chain 'r' and resid 372 through 389 Processing helix chain 'r' and resid 392 through 413 removed outlier: 3.904A pdb=" N ALA r 404 " --> pdb=" O MET r 400 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER r 407 " --> pdb=" O THR r 403 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU r 408 " --> pdb=" O ALA r 404 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR r 413 " --> pdb=" O TYR r 409 " (cutoff:3.500A) Processing helix chain 'r' and resid 423 through 427 removed outlier: 4.215A pdb=" N MET r 426 " --> pdb=" O ILE r 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS r 427 " --> pdb=" O ASN r 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 423 through 427' Processing helix chain 'r' and resid 430 through 448 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 '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 46 through 58 Processing helix chain 's' and resid 67 through 85 removed outlier: 3.886A pdb=" N TYR s 71 " --> pdb=" O THR s 67 " (cutoff:3.500A) Proline residue: s 75 - end of helix Processing helix chain 's' and resid 100 through 112 Processing helix chain 's' and resid 112 through 124 removed outlier: 4.023A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN s 124 " --> pdb=" O GLY s 120 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 158 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 161 through 168 removed outlier: 3.617A pdb=" N LEU s 165 " --> pdb=" O ASN s 161 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 178 through 194 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 195 through 199 removed outlier: 3.976A pdb=" N ASP s 199 " --> pdb=" O ALA s 196 " (cutoff:3.500A) Processing helix chain 's' and resid 209 through 213 removed outlier: 3.719A pdb=" N ILE s 213 " --> pdb=" O GLY s 210 " (cutoff:3.500A) Processing helix chain 's' and resid 217 through 243 Processing helix chain 's' and resid 251 through 277 removed outlier: 4.119A pdb=" N TYR s 255 " --> pdb=" O SER s 251 " (cutoff:3.500A) 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) removed outlier: 3.903A pdb=" N TYR s 277 " --> pdb=" O ILE s 273 " (cutoff:3.500A) Processing helix chain 's' and resid 281 through 290 removed outlier: 3.519A pdb=" N LEU s 285 " --> pdb=" O ARG s 281 " (cutoff:3.500A) 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) Processing helix chain 's' and resid 293 through 312 removed outlier: 3.542A pdb=" N THR s 297 " --> pdb=" O PHE s 293 " (cutoff:3.500A) Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 21 through 36 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 36 through 49 removed outlier: 3.610A pdb=" N CYS u 46 " --> pdb=" O GLU u 42 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 56 through 76 Processing helix chain 'u' and resid 79 through 91 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 96 through 100 removed outlier: 4.105A pdb=" N HIS u 99 " --> pdb=" O LEU u 96 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 113 removed outlier: 4.011A pdb=" N ALA u 105 " --> pdb=" O ARG u 101 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS u 106 " --> pdb=" O LYS u 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE u 107 " --> pdb=" O GLN u 103 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS u 110 " --> pdb=" O LYS u 106 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 12 removed outlier: 3.766A pdb=" N ARG v 8 " --> pdb=" O HIS v 4 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY v 11 " --> pdb=" O ARG v 7 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 50 Processing helix chain 'v' and resid 57 through 59 No H-bonds generated for 'chain 'v' and resid 57 through 59' Processing helix chain 'v' and resid 60 through 73 removed outlier: 3.614A pdb=" N ILE v 64 " --> pdb=" O ALA v 60 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG v 65 " --> pdb=" O HIS v 61 " (cutoff:3.500A) Processing helix chain 'v' and resid 80 through 123 Processing helix chain 'w' and resid 39 through 46 Processing helix chain 'w' and resid 49 through 53 removed outlier: 4.363A pdb=" N LEU w 53 " --> pdb=" O SER w 50 " (cutoff:3.500A) Processing helix chain 'w' and resid 71 through 81 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 92 through 98 Processing helix chain 'w' and resid 105 through 110 removed outlier: 3.821A pdb=" N ASN w 109 " --> pdb=" O ALA w 105 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 119 removed outlier: 3.887A pdb=" N ASP w 119 " --> pdb=" O GLU w 115 " (cutoff:3.500A) Processing helix chain 'w' and resid 128 through 137 Processing helix chain 'w' and resid 139 through 154 Processing helix chain 'w' and resid 162 through 165 Processing helix chain 'w' and resid 166 through 176 Processing helix chain 'w' and resid 180 through 195 Processing helix chain 'w' and resid 196 through 198 No H-bonds generated for 'chain 'w' and resid 196 through 198' Processing helix chain 'w' and resid 210 through 222 removed outlier: 3.928A pdb=" N GLN w 219 " --> pdb=" O GLN w 215 " (cutoff:3.500A) Processing helix chain 'w' and resid 225 through 229 removed outlier: 3.531A pdb=" N LYS w 228 " --> pdb=" O HIS w 225 " (cutoff:3.500A) Processing helix chain 'w' and resid 230 through 252 Proline residue: w 247 - end of helix Processing helix chain 'w' and resid 262 through 270 removed outlier: 3.517A pdb=" N LYS w 268 " --> pdb=" O GLN w 264 " (cutoff:3.500A) Processing helix chain 'w' and resid 273 through 277 Processing helix chain 'w' and resid 287 through 299 removed outlier: 3.527A pdb=" N GLN w 299 " --> pdb=" O ARG w 295 " (cutoff:3.500A) Processing helix chain 'w' and resid 300 through 306 removed outlier: 3.711A pdb=" N LEU w 305 " --> pdb=" O LYS w 301 " (cutoff:3.500A) Processing helix chain 'w' and resid 322 through 334 removed outlier: 3.530A pdb=" N HIS w 329 " --> pdb=" O ASP w 325 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU w 334 " --> pdb=" O GLN w 330 " (cutoff:3.500A) Processing helix chain 'w' and resid 350 through 355 removed outlier: 4.100A pdb=" N TRP w 353 " --> pdb=" O LYS w 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 57 through 58 removed outlier: 6.739A pdb=" N VAL U 57 " --> pdb=" O VAL u 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'b' and resid 97 through 99 removed outlier: 3.829A pdb=" N VAL b 98 " --> pdb=" O ILE l 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'i' and resid 307 through 308 Processing sheet with id=AA4, first strand: chain 'w' and resid 84 through 85 removed outlier: 6.257A pdb=" N LYS w 84 " --> pdb=" O VAL w 158 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE w 60 " --> pdb=" O LEU w 159 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE w 205 " --> pdb=" O THR w 61 " (cutoff:3.500A) 2104 hydrogen bonds defined for protein. 6126 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: 7.30 Time building geometry restraints manager: 5.36 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: 0.00 - 4.08: 52593 4.08 - 8.16: 1252 8.16 - 12.24: 108 12.24 - 16.32: 14 16.32 - 20.40: 7 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 - 35.58: 23506 35.58 - 71.16: 450 71.16 - 106.73: 36 106.73 - 142.31: 14 142.31 - 177.89: 9 Dihedral angle restraints: 24015 sinusoidal: 10224 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 24012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4995 0.095 - 0.191: 882 0.191 - 0.286: 43 0.286 - 0.382: 19 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: 5 1.82 - 2.59: 670 2.59 - 3.36: 56683 3.36 - 4.13: 90425 4.13 - 4.90: 171048 Nonbonded interactions: 318831 Sorted by model distance: nonbonded pdb=" OD2 ASP b 108 " pdb=" CG1 VAL d 19 " model vdw 1.049 3.460 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 3.120 nonbonded pdb=" CE2 PHE a 55 " pdb=" CE2 TYR p 118 " model vdw 1.817 3.640 ... (remaining 318826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 7.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.320 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.015 0.858 39865 Z= 1.051 Angle : 1.634 62.009 53988 Z= 1.025 Chirality : 0.071 0.477 5940 Planarity : 0.008 0.101 6610 Dihedral : 13.929 177.891 15086 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 26.43 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (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 ARG 0.016 0.002 ARG c 116 TYR 0.044 0.003 TYR w 339 PHE 0.036 0.003 PHE i 28 TRP 0.073 0.004 TRP r 307 HIS 0.022 0.003 HIS l 534 Details of bonding type rmsd/Z covalent geometry : bond 0.01373 / 0.82 (39853) covalent geometry : angle 1.56904 / 1.00 (53974) SS BOND : bond 0.03578 / 1.13 ( 7) SS BOND : angle 28.42473 / 16.09 ( 14) hydrogen bonds : bond 0.15370 / 10.50 ( 2104) hydrogen bonds : angle 8.74516 / 6.26 ( 6126) Misc. bond : bond 0.58705 / 32.35 ( 5) *********************** 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 to be fit. rotamer outliers: 49 poor density : 1280 time to evaluate : 1.593 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: S 34 LYS cc_start: 0.8018 (mtpp) cc_final: 0.6780 (mtpt) REVERT: S 36 LYS cc_start: 0.8768 (tptm) cc_final: 0.8491 (tppp) REVERT: V 19 HIS cc_start: 0.7954 (p-80) cc_final: 0.7522 (p-80) REVERT: V 21 LYS cc_start: 0.8294 (mttt) cc_final: 0.7726 (mttt) REVERT: V 82 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7451 (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: 0.8036 (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: 0.6518 (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: 0.8190 (mm) REVERT: c 119 THR cc_start: 0.8624 (p) cc_final: 0.8411 (m) REVERT: c 131 MET cc_start: 0.7557 (mmt) cc_final: 0.7270 (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: 0.6178 (mmt) REVERT: d 32 ASP cc_start: 0.8403 (m-30) cc_final: 0.8018 (m-30) REVERT: d 55 TYR cc_start: 0.6506 (OUTLIER) cc_final: 0.5847 (m-10) REVERT: d 107 CYS cc_start: 0.7370 (t) cc_final: 0.6918 (t) REVERT: g 38 TYR cc_start: 0.8535 (t80) cc_final: 0.8326 (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: h 60 TYR cc_start: 0.9214 (t80) cc_final: 0.8896 (t80) REVERT: i 36 ASN cc_start: 0.8348 (m-40) cc_final: 0.7765 (t0) REVERT: i 47 LYS cc_start: 0.8115 (mttt) cc_final: 0.7811 (mmtm) REVERT: i 72 MET cc_start: 0.8704 (tpt) cc_final: 0.8445 (tpt) REVERT: i 79 MET cc_start: 0.8018 (mtp) cc_final: 0.7746 (mtp) REVERT: i 86 MET cc_start: 0.8640 (mmm) cc_final: 0.8406 (mmt) REVERT: i 120 GLN cc_start: 0.8754 (tt0) cc_final: 0.8178 (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: 0.8020 (mmm) REVERT: j 56 PHE cc_start: 0.8438 (t80) cc_final: 0.8201 (t80) REVERT: j 90 SER cc_start: 0.8885 (p) cc_final: 0.8608 (t) REVERT: k 25 HIS cc_start: 0.8294 (p90) cc_final: 0.7299 (t70) REVERT: l 179 ASP cc_start: 0.8515 (m-30) cc_final: 0.8003 (m-30) REVERT: l 268 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7974 (mt-10) REVERT: l 503 ASP cc_start: 0.8069 (m-30) cc_final: 0.7742 (m-30) REVERT: l 510 LYS cc_start: 0.8030 (mttm) cc_final: 0.7217 (tptt) REVERT: l 583 MET cc_start: 0.6557 (tpt) cc_final: 0.6278 (mtp) REVERT: m 2 MET cc_start: 0.8487 (tpt) cc_final: 0.8009 (tpp) REVERT: m 3 TYR cc_start: 0.8302 (m-80) cc_final: 0.7792 (m-80) REVERT: m 82 TRP cc_start: 0.4255 (m100) cc_final: 0.3123 (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: 0.7349 (mtt) REVERT: m 100 VAL cc_start: 0.8604 (t) cc_final: 0.7848 (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: 0.7645 (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: 0.8414 (ttmm) REVERT: o 112 LYS cc_start: 0.8712 (mttt) cc_final: 0.7997 (mtpp) REVERT: p 14 GLN cc_start: 0.8129 (mt0) cc_final: 0.7857 (mt0) REVERT: p 124 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: s 3 MET cc_start: 0.8502 (mmp) cc_final: 0.6896 (ptt) REVERT: s 34 ARG cc_start: 0.8488 (ptm160) cc_final: 0.7434 (mmt-90) REVERT: s 54 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7379 (mptt) REVERT: s 71 TYR cc_start: 0.7659 (m-80) cc_final: 0.6995 (m-80) REVERT: s 214 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7909 (mt-10) REVERT: s 277 TYR cc_start: 0.8715 (m-80) cc_final: 0.8425 (m-10) REVERT: s 281 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7436 (mtm180) REVERT: v 47 MET cc_start: 0.7896 (mmt) cc_final: 0.7655 (mmp) REVERT: v 84 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8095 (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: 0.6814 (t0) outliers start: 49 outliers final: 22 residues processed: 1319 average time/residue: 0.2612 time to fit residues: 547.9127 Evaluate side-chains 850 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 825 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 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 432 optimal weight: 0.8980 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 0.0670 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 85 GLN d 98 ASN d 108 GLN ** d 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 HIS ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 GLN i 150 ASN 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 248 HIS ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 348 HIS l 400 ASN 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** ** n 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 40 ASN o 52 ASN ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 12 HIS p 26 HIS p 51 HIS p 75 GLN p 141 GLN r 30 HIS r 43 ASN r 48 ASN r 168 HIS r 184 GLN r 192 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 319 HIS r 366 ASN r 390 ASN r 415 GLN s 93 ASN s 138 GLN s 169 GLN s 171 HIS s 235 ASN ** 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: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.107205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.085467 restraints weight = 90000.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.088148 restraints weight = 46600.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089325 restraints weight = 26725.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.089545 restraints weight = 25420.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.089630 restraints weight = 21876.424| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 39865 Z= 0.203 Angle : 0.876 10.857 53988 Z= 0.452 Chirality : 0.049 0.251 5940 Planarity : 0.007 0.085 6610 Dihedral : 15.970 170.988 6017 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 1.03 % Allowed : 5.52 % Favored : 93.45 % Rotamer: Outliers : 3.23 % Allowed : 10.10 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 4641 helix: -0.02 (0.09), residues: 2925 sheet: -3.96 (1.14), residues: 12 loop : -0.69 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 59 TYR 0.042 0.002 TYR w 339 PHE 0.032 0.002 PHE s 293 TRP 0.027 0.002 TRP s 272 HIS 0.015 0.002 HIS l 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (39853) covalent geometry : angle 0.87533 / 0.45 (53974) SS BOND : bond 0.00717 / 0.30 ( 7) SS BOND : angle 2.43227 / 1.35 ( 14) hydrogen bonds : bond 0.06045 / 4.05 ( 2104) hydrogen bonds : angle 5.49615 / 3.93 ( 6126) Misc. bond : bond 0.00863 / 0.49 ( 5) *********************** 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 1218 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1086 time to evaluate : 1.564 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: S 36 LYS cc_start: 0.8723 (tptm) cc_final: 0.8174 (tppp) REVERT: U 16 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7525 (pt0) REVERT: V 118 PHE cc_start: 0.8543 (m-80) cc_final: 0.7973 (m-80) REVERT: V 129 ARG cc_start: 0.8869 (tpp80) cc_final: 0.8475 (tpp80) REVERT: V 138 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8323 (ttmt) REVERT: X 115 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8714 (tm-30) REVERT: X 147 TYR cc_start: 0.8802 (t80) cc_final: 0.8551 (t80) REVERT: X 151 LYS cc_start: 0.9125 (tppp) cc_final: 0.8784 (tppp) REVERT: b 104 ILE cc_start: 0.8800 (mt) cc_final: 0.8139 (mm) REVERT: c 119 THR cc_start: 0.8387 (p) cc_final: 0.7975 (m) REVERT: c 132 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8281 (mp10) REVERT: c 140 MET cc_start: 0.9266 (mmm) cc_final: 0.9025 (mmm) REVERT: c 166 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8830 (mm) REVERT: d 56 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.8249 (m-10) REVERT: g 11 ARG cc_start: 0.7395 (tpt90) cc_final: 0.6086 (tpm170) REVERT: g 79 ASP cc_start: 0.8728 (m-30) cc_final: 0.8343 (m-30) REVERT: g 105 LYS cc_start: 0.8721 (mttm) cc_final: 0.8506 (mtpp) REVERT: h 27 TYR cc_start: 0.8963 (m-80) cc_final: 0.8747 (m-80) REVERT: h 60 TYR cc_start: 0.8990 (t80) cc_final: 0.8719 (t80) REVERT: i 1 MET cc_start: 0.7066 (mmm) cc_final: 0.6052 (mmm) REVERT: i 72 MET cc_start: 0.8643 (tpt) cc_final: 0.8316 (tpt) REVERT: i 120 GLN cc_start: 0.8906 (tt0) cc_final: 0.7958 (tp-100) REVERT: i 142 MET cc_start: 0.8754 (mmm) cc_final: 0.8459 (mtp) REVERT: j 1 MET cc_start: 0.3084 (ptp) cc_final: 0.1129 (mmp) REVERT: j 37 TYR cc_start: 0.5210 (p90) cc_final: 0.4374 (m-10) REVERT: j 93 LEU cc_start: 0.9260 (tt) cc_final: 0.9040 (tp) REVERT: k 6 MET cc_start: 0.8404 (mtp) cc_final: 0.8178 (mtp) REVERT: k 7 ASN cc_start: 0.8773 (t0) cc_final: 0.8398 (t0) REVERT: k 9 MET cc_start: 0.8238 (mtm) cc_final: 0.8009 (mtm) REVERT: k 25 HIS cc_start: 0.8121 (p-80) cc_final: 0.7219 (t70) REVERT: l 199 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: l 338 MET cc_start: 0.8757 (tpp) cc_final: 0.8318 (tpp) REVERT: l 353 GLU cc_start: 0.8369 (tp30) cc_final: 0.7804 (tp30) REVERT: l 503 ASP cc_start: 0.7582 (m-30) cc_final: 0.7363 (m-30) REVERT: l 510 LYS cc_start: 0.8152 (mttm) cc_final: 0.7429 (tptt) REVERT: m 32 LEU cc_start: 0.9165 (mt) cc_final: 0.8667 (tt) REVERT: m 54 MET cc_start: 0.8423 (mmp) cc_final: 0.8217 (mmp) REVERT: m 69 TYR cc_start: 0.8505 (t80) cc_final: 0.8232 (t80) REVERT: m 82 TRP cc_start: 0.4016 (m100) cc_final: 0.2908 (m-90) REVERT: m 105 TRP cc_start: 0.8142 (t60) cc_final: 0.7482 (t60) REVERT: m 110 ASP cc_start: 0.7910 (t70) cc_final: 0.7652 (m-30) REVERT: m 161 PHE cc_start: 0.9112 (t80) cc_final: 0.8772 (t80) REVERT: m 172 ARG cc_start: 0.6521 (ttp80) cc_final: 0.6078 (ttp80) REVERT: n 38 PHE cc_start: 0.8564 (t80) cc_final: 0.8141 (t80) REVERT: o 13 THR cc_start: 0.8424 (p) cc_final: 0.8082 (p) REVERT: o 108 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7525 (tm-30) REVERT: p 124 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: r 117 MET cc_start: 0.8754 (tpp) cc_final: 0.8469 (ttp) REVERT: r 264 LEU cc_start: 0.9217 (pp) cc_final: 0.8495 (tt) REVERT: r 454 ILE cc_start: 0.9325 (mt) cc_final: 0.9113 (mt) REVERT: s 3 MET cc_start: 0.8244 (mmp) cc_final: 0.6992 (ptt) REVERT: s 21 MET cc_start: 0.8724 (tmm) cc_final: 0.8355 (tmm) REVERT: s 34 ARG cc_start: 0.8471 (ptm160) cc_final: 0.7505 (mmt-90) REVERT: s 206 GLU cc_start: 0.7662 (tp30) cc_final: 0.7024 (mp0) REVERT: s 230 ASN cc_start: 0.9252 (m-40) cc_final: 0.9038 (t0) REVERT: s 281 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7401 (mtm180) REVERT: s 286 MET cc_start: 0.8785 (mmm) cc_final: 0.8001 (mpp) REVERT: u 30 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.7710 (m90) REVERT: u 44 MET cc_start: 0.8520 (mmt) cc_final: 0.7652 (tpt) REVERT: v 7 ARG cc_start: 0.6495 (ptt90) cc_final: 0.6173 (ptm160) REVERT: v 47 MET cc_start: 0.7688 (mmt) cc_final: 0.7455 (mmp) REVERT: v 72 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7889 (p0) REVERT: v 91 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8275 (mm-30) REVERT: v 100 LYS cc_start: 0.8390 (mttt) cc_final: 0.7308 (tmmt) REVERT: v 101 GLU cc_start: 0.7957 (mp0) cc_final: 0.7740 (mp0) REVERT: v 117 LYS cc_start: 0.8009 (tppt) cc_final: 0.7683 (tppp) REVERT: w 60 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7712 (mm) REVERT: w 85 HIS cc_start: 0.6571 (t70) cc_final: 0.6351 (t70) REVERT: w 115 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6631 (mm-30) REVERT: w 249 MET cc_start: 0.4211 (mtt) cc_final: 0.3997 (mtm) REVERT: w 287 ASP cc_start: 0.7138 (t0) cc_final: 0.6790 (t0) REVERT: w 289 ARG cc_start: 0.8314 (ptt90) cc_final: 0.8038 (tmm160) REVERT: w 303 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7170 (tm-30) outliers start: 132 outliers final: 55 residues processed: 1160 average time/residue: 0.2351 time to fit residues: 449.6924 Evaluate side-chains 936 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 872 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 U residue 36 SER Chi-restraints excluded: chain V residue 53 VAL 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 148 ILE Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain c residue 132 GLN Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 166 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 99 ILE Chi-restraints excluded: chain e residue 73 SER Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 19 ILE Chi-restraints excluded: chain i residue 244 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 31 LEU 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 199 GLN 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 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 p residue 11 THR 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 r residue 350 THR 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 62 LYS Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 172 LEU Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain u residue 30 HIS Chi-restraints excluded: chain v residue 72 ASP Chi-restraints excluded: chain w residue 60 ILE 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 12 optimal weight: 1.9990 chunk 452 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 345 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 47 HIS ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 138 HIS X 103 HIS ** 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** b 83 HIS c 56 ASN ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 ASN d 153 GLN ** h 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 88 ASN j 10 ASN j 108 GLN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 199 GLN l 296 ASN ** l 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 40 ASN o 33 GLN o 50 GLN o 75 ASN ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 26 ASN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 279 GLN ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 31 HIS w 176 GLN ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 330 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.082606 restraints weight = 91150.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.085118 restraints weight = 47872.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.086359 restraints weight = 28529.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.087190 restraints weight = 23113.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.087323 restraints weight = 21669.495| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 39865 Z= 0.226 Angle : 0.827 11.127 53988 Z= 0.421 Chirality : 0.048 0.225 5940 Planarity : 0.006 0.068 6610 Dihedral : 14.790 174.412 5977 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.03 % Favored : 93.08 % Rotamer: Outliers : 3.84 % Allowed : 12.57 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.12), residues: 4641 helix: 0.50 (0.09), residues: 2928 sheet: -3.32 (0.97), residues: 22 loop : -0.94 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG v 98 TYR 0.044 0.002 TYR S 61 PHE 0.043 0.002 PHE b 46 TRP 0.029 0.002 TRP s 185 HIS 0.013 0.002 HIS h 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 (39853) covalent geometry : angle 0.82600 / 0.42 (53974) SS BOND : bond 0.02434 / 1.21 ( 7) SS BOND : angle 2.88116 / 1.63 ( 14) hydrogen bonds : bond 0.05486 / 3.67 ( 2104) hydrogen bonds : angle 5.08821 / 3.65 ( 6126) Misc. bond : bond 0.01316 / 0.66 ( 5) *********************** 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 1111 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 954 time to evaluate : 1.496 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: S 36 LYS cc_start: 0.8694 (tptm) cc_final: 0.8258 (tppp) REVERT: U 16 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7738 (pt0) REVERT: U 36 SER cc_start: 0.8769 (m) cc_final: 0.8526 (p) REVERT: V 108 TYR cc_start: 0.8244 (m-80) cc_final: 0.8024 (m-80) REVERT: V 118 PHE cc_start: 0.8593 (m-80) cc_final: 0.8049 (m-80) REVERT: X 115 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8860 (tm-30) REVERT: b 104 ILE cc_start: 0.8835 (mt) cc_final: 0.8458 (pt) REVERT: c 56 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8332 (t0) REVERT: c 119 THR cc_start: 0.8528 (p) cc_final: 0.8307 (m) REVERT: d 28 MET cc_start: 0.7455 (mmt) cc_final: 0.7177 (mmt) REVERT: d 56 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8147 (m-10) REVERT: e 125 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8996 (mp) REVERT: g 8 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7626 (tm-30) REVERT: g 11 ARG cc_start: 0.7010 (tpt90) cc_final: 0.6184 (tpm170) REVERT: g 98 GLU cc_start: 0.8140 (pm20) cc_final: 0.7910 (pm20) REVERT: g 105 LYS cc_start: 0.8700 (mttm) cc_final: 0.8491 (mtpp) REVERT: h 15 ASP cc_start: 0.8935 (t0) cc_final: 0.8717 (t0) REVERT: h 21 GLN cc_start: 0.8194 (mp10) cc_final: 0.7985 (mp10) REVERT: i 72 MET cc_start: 0.8662 (tpt) cc_final: 0.8388 (tpt) REVERT: i 120 GLN cc_start: 0.8975 (tt0) cc_final: 0.7962 (tp-100) REVERT: i 142 MET cc_start: 0.8706 (mmm) cc_final: 0.8467 (mtp) REVERT: i 269 GLU cc_start: 0.8525 (tp30) cc_final: 0.8045 (tp30) REVERT: i 339 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8629 (mt) REVERT: j 1 MET cc_start: 0.3022 (ptp) cc_final: 0.1145 (mmp) REVERT: j 8 MET cc_start: 0.8364 (mmm) cc_final: 0.7510 (mtm) REVERT: j 37 TYR cc_start: 0.5001 (p90) cc_final: 0.4258 (m-10) REVERT: j 89 MET cc_start: 0.7634 (tmm) cc_final: 0.7271 (tmm) REVERT: j 90 SER cc_start: 0.8485 (p) cc_final: 0.8095 (t) REVERT: k 7 ASN cc_start: 0.8845 (t0) cc_final: 0.8375 (t0) REVERT: k 25 HIS cc_start: 0.7972 (p-80) cc_final: 0.7026 (t70) REVERT: l 70 THR cc_start: 0.8551 (m) cc_final: 0.8340 (t) REVERT: l 310 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8962 (mm) REVERT: l 392 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8582 (ttmm) REVERT: l 510 LYS cc_start: 0.8049 (mttm) cc_final: 0.7391 (tptt) REVERT: m 2 MET cc_start: 0.8717 (tpt) cc_final: 0.8354 (tpt) REVERT: m 76 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6807 (mp0) REVERT: m 82 TRP cc_start: 0.3622 (m100) cc_final: 0.2800 (m-90) REVERT: m 105 TRP cc_start: 0.8108 (t60) cc_final: 0.7639 (t60) REVERT: m 110 ASP cc_start: 0.7876 (t70) cc_final: 0.7667 (m-30) REVERT: m 161 PHE cc_start: 0.9065 (t80) cc_final: 0.8730 (t80) REVERT: n 40 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8766 (t0) REVERT: o 28 GLU cc_start: 0.8457 (pm20) cc_final: 0.8157 (pm20) REVERT: o 102 TYR cc_start: 0.8992 (t80) cc_final: 0.8473 (t80) REVERT: o 106 LYS cc_start: 0.8521 (tttt) cc_final: 0.8032 (ttmt) REVERT: p 14 GLN cc_start: 0.8449 (mt0) cc_final: 0.8140 (mt0) REVERT: p 124 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: r 264 LEU cc_start: 0.9208 (pp) cc_final: 0.8503 (tt) REVERT: r 454 ILE cc_start: 0.9356 (mt) cc_final: 0.9126 (mt) REVERT: s 3 MET cc_start: 0.8288 (mmp) cc_final: 0.6940 (ptt) REVERT: s 34 ARG cc_start: 0.8488 (ptm160) cc_final: 0.7448 (mmt-90) REVERT: s 134 ARG cc_start: 0.8083 (mmt90) cc_final: 0.7765 (mmt90) REVERT: s 185 TRP cc_start: 0.8954 (t-100) cc_final: 0.8596 (t-100) REVERT: s 206 GLU cc_start: 0.7695 (tp30) cc_final: 0.7118 (mp0) REVERT: s 277 TYR cc_start: 0.8504 (m-10) cc_final: 0.8259 (m-10) REVERT: s 281 ARG cc_start: 0.7797 (ttt180) cc_final: 0.7392 (mtm180) REVERT: s 286 MET cc_start: 0.8724 (mmm) cc_final: 0.8209 (mpp) REVERT: u 30 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7896 (m90) REVERT: u 101 ARG cc_start: 0.8372 (mmm160) cc_final: 0.8171 (tpp-160) REVERT: v 7 ARG cc_start: 0.6527 (ptt90) cc_final: 0.6212 (ptm160) REVERT: v 48 ASP cc_start: 0.8091 (p0) cc_final: 0.7887 (p0) REVERT: v 72 ASP cc_start: 0.8314 (m-30) cc_final: 0.7941 (p0) REVERT: v 91 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8213 (mm-30) REVERT: v 100 LYS cc_start: 0.8583 (mttt) cc_final: 0.7446 (tttt) REVERT: v 101 GLU cc_start: 0.8065 (mp0) cc_final: 0.7861 (mp0) REVERT: w 85 HIS cc_start: 0.6611 (t70) cc_final: 0.6345 (t70) REVERT: w 115 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6738 (mm-30) REVERT: w 289 ARG cc_start: 0.8303 (ptt90) cc_final: 0.8032 (tmm160) REVERT: w 303 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7397 (tm-30) outliers start: 157 outliers final: 84 residues processed: 1042 average time/residue: 0.2275 time to fit residues: 394.8557 Evaluate side-chains 933 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 840 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 15 CYS 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 U residue 46 ASN Chi-restraints excluded: chain V residue 27 SER 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 80 ASP Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 115 GLN Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain X residue 150 ASP 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 186 THR Chi-restraints excluded: chain b residue 25 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 76 ILE Chi-restraints excluded: chain d residue 99 ILE Chi-restraints excluded: chain d residue 107 CYS Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain e residue 73 SER Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 147 ILE Chi-restraints excluded: chain f residue 43 LYS 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 88 LYS Chi-restraints excluded: chain i residue 41 ILE Chi-restraints excluded: chain i residue 141 ILE Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 237 LEU Chi-restraints excluded: chain i residue 244 ILE 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 51 THR 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 94 LEU 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 489 THR 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 63 MET Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 40 ASN Chi-restraints excluded: chain o residue 17 THR 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 58 SER Chi-restraints excluded: chain r residue 167 THR 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 28 LEU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 62 LYS Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 172 LEU 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 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 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 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 415 optimal weight: 6.9990 chunk 253 optimal weight: 0.4980 chunk 142 optimal weight: 0.6980 chunk 211 optimal weight: 0.0670 chunk 444 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 61 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 i 63 GLN l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** 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 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 415 GLN s 235 ASN ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 110 GLN ** w 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085785 restraints weight = 90294.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087995 restraints weight = 45411.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.089047 restraints weight = 27319.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.089317 restraints weight = 24339.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.089461 restraints weight = 22222.183| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39865 Z= 0.154 Angle : 0.757 10.492 53988 Z= 0.381 Chirality : 0.045 0.254 5940 Planarity : 0.006 0.059 6610 Dihedral : 13.818 176.288 5972 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.75 % Allowed : 5.47 % Favored : 93.77 % Rotamer: Outliers : 3.47 % Allowed : 14.24 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.12), residues: 4641 helix: 0.83 (0.09), residues: 2949 sheet: None (None), residues: 0 loop : -1.09 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 81 TYR 0.046 0.002 TYR S 61 PHE 0.027 0.002 PHE i 292 TRP 0.027 0.001 TRP u 86 HIS 0.011 0.001 HIS h 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (39853) covalent geometry : angle 0.75662 / 0.38 (53974) SS BOND : bond 0.00372 / 0.17 ( 7) SS BOND : angle 2.00523 / 1.13 ( 14) hydrogen bonds : bond 0.04811 / 3.22 ( 2104) hydrogen bonds : angle 4.72337 / 3.38 ( 6126) Misc. bond : bond 0.00175 / 0.08 ( 5) *********************** 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 1110 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 968 time to evaluate : 1.617 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: Q 53 TYR cc_start: 0.6647 (m-80) cc_final: 0.6441 (m-80) REVERT: S 36 LYS cc_start: 0.8641 (tptm) cc_final: 0.8199 (tppp) REVERT: U 16 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7930 (pt0) REVERT: U 36 SER cc_start: 0.8705 (m) cc_final: 0.8484 (p) REVERT: V 21 LYS cc_start: 0.8322 (mttm) cc_final: 0.8039 (mttt) REVERT: V 118 PHE cc_start: 0.8555 (m-80) cc_final: 0.8051 (m-80) REVERT: X 116 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8474 (p) REVERT: Y 97 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6590 (mm) REVERT: b 25 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8400 (t0) REVERT: b 40 MET cc_start: 0.4151 (ptm) cc_final: 0.3935 (ptm) REVERT: b 60 MET cc_start: 0.6204 (mtp) cc_final: 0.5796 (mtp) REVERT: d 56 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.8049 (m-10) REVERT: e 113 ARG cc_start: 0.8536 (mtp180) cc_final: 0.8280 (mtt180) REVERT: f 43 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6755 (mtmm) REVERT: g 8 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7490 (tm-30) REVERT: g 11 ARG cc_start: 0.6937 (tpt90) cc_final: 0.6065 (tpm170) REVERT: g 44 ASP cc_start: 0.8859 (t0) cc_final: 0.8647 (t0) REVERT: g 105 LYS cc_start: 0.8734 (mttm) cc_final: 0.8523 (mtpp) REVERT: h 15 ASP cc_start: 0.8916 (t0) cc_final: 0.8669 (t0) REVERT: i 1 MET cc_start: 0.6952 (mpp) cc_final: 0.6718 (mpp) REVERT: i 108 MET cc_start: 0.8154 (mtm) cc_final: 0.7865 (mtp) REVERT: i 120 GLN cc_start: 0.8897 (tt0) cc_final: 0.8093 (tp-100) REVERT: i 269 GLU cc_start: 0.8512 (tp30) cc_final: 0.8271 (tp30) REVERT: i 339 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8718 (mm) REVERT: j 1 MET cc_start: 0.3061 (ptp) cc_final: 0.1186 (mmp) REVERT: j 8 MET cc_start: 0.8348 (mmm) cc_final: 0.7454 (mtm) REVERT: j 37 TYR cc_start: 0.4846 (p90) cc_final: 0.4215 (m-10) REVERT: j 87 MET cc_start: 0.8553 (tmm) cc_final: 0.8268 (tmm) REVERT: k 6 MET cc_start: 0.8234 (mtp) cc_final: 0.7480 (tpt) REVERT: k 7 ASN cc_start: 0.8876 (t0) cc_final: 0.8360 (t0) REVERT: k 25 HIS cc_start: 0.7824 (p-80) cc_final: 0.6915 (t70) REVERT: l 58 ASP cc_start: 0.8139 (t70) cc_final: 0.7653 (t70) REVERT: l 70 THR cc_start: 0.8328 (m) cc_final: 0.7833 (p) REVERT: l 145 GLU cc_start: 0.8242 (mp0) cc_final: 0.7375 (mp0) REVERT: l 310 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8828 (mm) REVERT: l 392 LYS cc_start: 0.8905 (mtpp) cc_final: 0.8646 (ttmm) REVERT: l 510 LYS cc_start: 0.8006 (mttm) cc_final: 0.7393 (tptt) REVERT: m 2 MET cc_start: 0.8696 (tpt) cc_final: 0.8363 (tpp) REVERT: m 76 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6756 (mp0) REVERT: m 82 TRP cc_start: 0.3901 (m100) cc_final: 0.2906 (m-90) REVERT: m 105 TRP cc_start: 0.8110 (t60) cc_final: 0.7635 (t60) REVERT: m 161 PHE cc_start: 0.8944 (t80) cc_final: 0.8649 (t80) REVERT: o 102 TYR cc_start: 0.8898 (t80) cc_final: 0.8455 (t80) REVERT: o 106 LYS cc_start: 0.8438 (tttt) cc_final: 0.7609 (ttmm) REVERT: p 14 GLN cc_start: 0.8468 (mt0) cc_final: 0.8176 (mt0) REVERT: p 49 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: r 76 THR cc_start: 0.9551 (p) cc_final: 0.9288 (t) REVERT: r 264 LEU cc_start: 0.9124 (pp) cc_final: 0.8511 (tt) REVERT: r 439 MET cc_start: 0.8612 (mmm) cc_final: 0.8403 (mtp) REVERT: r 454 ILE cc_start: 0.9375 (mt) cc_final: 0.9087 (mt) REVERT: s 3 MET cc_start: 0.8275 (mmp) cc_final: 0.6848 (ptt) REVERT: s 34 ARG cc_start: 0.8518 (ptm160) cc_final: 0.7563 (mmt90) REVERT: s 185 TRP cc_start: 0.8990 (t-100) cc_final: 0.8664 (t-100) REVERT: s 206 GLU cc_start: 0.7807 (tp30) cc_final: 0.7320 (mp0) REVERT: s 230 ASN cc_start: 0.9264 (m-40) cc_final: 0.9048 (t0) REVERT: s 279 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7226 (mpp-170) REVERT: s 281 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7395 (mtm180) REVERT: s 286 MET cc_start: 0.8663 (mmm) cc_final: 0.8268 (mpp) REVERT: u 101 ARG cc_start: 0.8394 (mmm160) cc_final: 0.8183 (tpp-160) REVERT: v 7 ARG cc_start: 0.6455 (ptt90) cc_final: 0.6131 (ptm160) REVERT: v 72 ASP cc_start: 0.8294 (m-30) cc_final: 0.7976 (p0) REVERT: v 81 LYS cc_start: 0.8897 (mmtp) cc_final: 0.8556 (mmtt) REVERT: v 100 LYS cc_start: 0.8383 (mttt) cc_final: 0.7339 (tttt) REVERT: v 101 GLU cc_start: 0.8101 (mp0) cc_final: 0.7840 (mp0) REVERT: w 60 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7771 (mm) REVERT: w 115 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6763 (mm-30) outliers start: 142 outliers final: 63 residues processed: 1046 average time/residue: 0.2389 time to fit residues: 416.2274 Evaluate side-chains 931 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 859 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 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 69 ILE Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 86 ILE Chi-restraints excluded: chain b residue 25 ASP Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 76 ILE 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 e residue 65 ASN Chi-restraints excluded: chain e residue 147 ILE 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 88 LYS Chi-restraints excluded: chain i residue 201 THR Chi-restraints excluded: chain i residue 339 ILE Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain j residue 51 PHE Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 80 SER Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 243 VAL 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 482 ILE 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 n residue 13 VAL Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 83 THR 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 247 THR Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 172 LEU 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 w residue 60 ILE 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 195 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 440 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 417 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 361 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 46 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** d 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 174 ASN ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN r 415 GLN s 138 GLN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 99 HIS ** w 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083674 restraints weight = 90897.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085650 restraints weight = 47148.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.086547 restraints weight = 28673.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.086781 restraints weight = 25480.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.087031 restraints weight = 23672.047| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 39865 Z= 0.194 Angle : 0.774 15.310 53988 Z= 0.386 Chirality : 0.046 0.253 5940 Planarity : 0.006 0.064 6610 Dihedral : 13.427 177.410 5964 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.73 % Allowed : 5.86 % Favored : 93.41 % Rotamer: Outliers : 3.42 % Allowed : 16.12 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.12), residues: 4641 helix: 0.99 (0.09), residues: 2941 sheet: -2.04 (1.41), residues: 10 loop : -1.14 (0.16), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 82 TYR 0.037 0.002 TYR S 61 PHE 0.046 0.002 PHE i 292 TRP 0.029 0.001 TRP u 86 HIS 0.009 0.001 HIS h 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (39853) covalent geometry : angle 0.77307 / 0.39 (53974) SS BOND : bond 0.00668 / 0.31 ( 7) SS BOND : angle 2.01413 / 1.15 ( 14) hydrogen bonds : bond 0.04838 / 3.24 ( 2104) hydrogen bonds : angle 4.70525 / 3.37 ( 6126) Misc. bond : bond 0.00325 / 0.16 ( 5) *********************** 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 1023 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 883 time to evaluate : 1.593 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: S 36 LYS cc_start: 0.8682 (tptm) cc_final: 0.8215 (tppp) REVERT: U 16 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7933 (pt0) REVERT: U 36 SER cc_start: 0.8743 (m) cc_final: 0.8515 (p) REVERT: V 21 LYS cc_start: 0.8242 (mttm) cc_final: 0.7929 (mttt) REVERT: V 99 LEU cc_start: 0.8641 (mm) cc_final: 0.8433 (mm) REVERT: V 118 PHE cc_start: 0.8589 (m-80) cc_final: 0.8123 (m-80) REVERT: X 106 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8487 (ptmm) REVERT: X 115 GLN cc_start: 0.9227 (tm-30) cc_final: 0.9001 (tm-30) REVERT: Y 97 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6518 (mm) REVERT: b 25 ASP cc_start: 0.8755 (t70) cc_final: 0.8442 (t0) REVERT: b 40 MET cc_start: 0.4271 (ptm) cc_final: 0.3936 (ptm) REVERT: d 56 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.8131 (m-10) REVERT: d 134 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8715 (mm-40) REVERT: e 113 ARG cc_start: 0.8550 (mtp180) cc_final: 0.8298 (mtt180) REVERT: e 121 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7200 (mm-30) REVERT: g 11 ARG cc_start: 0.7070 (tpt90) cc_final: 0.6153 (tpm170) REVERT: g 105 LYS cc_start: 0.8737 (mttm) cc_final: 0.8518 (mtpp) REVERT: h 60 TYR cc_start: 0.8866 (t80) cc_final: 0.8605 (t80) REVERT: i 1 MET cc_start: 0.7203 (mpp) cc_final: 0.6959 (mpp) REVERT: i 54 GLU cc_start: 0.8766 (pp20) cc_final: 0.8559 (pt0) REVERT: i 90 THR cc_start: 0.8736 (p) cc_final: 0.8518 (p) REVERT: i 120 GLN cc_start: 0.8763 (tt0) cc_final: 0.8114 (tp-100) REVERT: i 218 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9148 (mm) REVERT: j 1 MET cc_start: 0.3037 (ptp) cc_final: 0.1149 (mmp) REVERT: j 8 MET cc_start: 0.8373 (mmm) cc_final: 0.7450 (mtm) REVERT: j 37 TYR cc_start: 0.4886 (p90) cc_final: 0.4220 (m-10) REVERT: j 101 SER cc_start: 0.9151 (t) cc_final: 0.8863 (p) REVERT: k 6 MET cc_start: 0.8239 (mtp) cc_final: 0.7596 (tpt) REVERT: k 7 ASN cc_start: 0.8837 (t0) cc_final: 0.8279 (t0) REVERT: k 25 HIS cc_start: 0.7864 (p-80) cc_final: 0.6874 (t70) REVERT: l 62 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9155 (mt) REVERT: l 70 THR cc_start: 0.8423 (m) cc_final: 0.7946 (p) REVERT: l 145 GLU cc_start: 0.8240 (mp0) cc_final: 0.7381 (mp0) REVERT: l 392 LYS cc_start: 0.8922 (mtpp) cc_final: 0.8699 (ttmm) REVERT: l 510 LYS cc_start: 0.8062 (mttm) cc_final: 0.7413 (tptt) REVERT: m 2 MET cc_start: 0.8734 (tpt) cc_final: 0.8376 (tpt) REVERT: m 76 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6885 (mp0) REVERT: m 82 TRP cc_start: 0.4031 (m100) cc_final: 0.3026 (m-90) REVERT: m 105 TRP cc_start: 0.8147 (t60) cc_final: 0.7750 (t60) REVERT: m 161 PHE cc_start: 0.8944 (t80) cc_final: 0.8579 (t80) REVERT: o 106 LYS cc_start: 0.8453 (tttt) cc_final: 0.7641 (ttmm) REVERT: p 14 GLN cc_start: 0.8537 (mt0) cc_final: 0.8227 (mt0) REVERT: p 49 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: r 264 LEU cc_start: 0.9239 (pp) cc_final: 0.8708 (tp) REVERT: r 454 ILE cc_start: 0.9407 (mt) cc_final: 0.9098 (mt) REVERT: s 3 MET cc_start: 0.8348 (mmp) cc_final: 0.6850 (ptt) REVERT: s 34 ARG cc_start: 0.8446 (ptm160) cc_final: 0.7556 (mmt90) REVERT: s 59 GLU cc_start: 0.8778 (tt0) cc_final: 0.8108 (mp0) REVERT: s 185 TRP cc_start: 0.9111 (OUTLIER) cc_final: 0.8653 (t-100) REVERT: s 206 GLU cc_start: 0.7922 (tp30) cc_final: 0.7384 (mp0) REVERT: s 230 ASN cc_start: 0.9270 (m-40) cc_final: 0.9014 (t0) REVERT: s 277 TYR cc_start: 0.8436 (m-10) cc_final: 0.8218 (m-10) REVERT: s 279 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7297 (mpp-170) REVERT: s 281 ARG cc_start: 0.7821 (ttt180) cc_final: 0.7396 (mtm180) REVERT: s 282 TYR cc_start: 0.8104 (t80) cc_final: 0.7830 (t80) REVERT: s 286 MET cc_start: 0.8666 (mmm) cc_final: 0.8280 (mpp) REVERT: u 101 ARG cc_start: 0.8394 (mmm160) cc_final: 0.8139 (tpp-160) REVERT: u 168 TYR cc_start: 0.8426 (m-80) cc_final: 0.7999 (m-80) REVERT: v 7 ARG cc_start: 0.6576 (ptt90) cc_final: 0.6258 (ptm160) REVERT: v 72 ASP cc_start: 0.8207 (m-30) cc_final: 0.7984 (p0) REVERT: v 82 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8354 (tp-100) REVERT: v 94 ASP cc_start: 0.8187 (p0) cc_final: 0.7927 (p0) REVERT: v 100 LYS cc_start: 0.8591 (mttt) cc_final: 0.7445 (tttt) REVERT: v 101 GLU cc_start: 0.8137 (mp0) cc_final: 0.7860 (mp0) REVERT: w 115 GLU cc_start: 0.7594 (tm-30) cc_final: 0.6763 (mm-30) outliers start: 140 outliers final: 84 residues processed: 975 average time/residue: 0.2299 time to fit residues: 374.6279 Evaluate side-chains 917 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 826 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain U residue 46 ASN Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 43 LEU 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 69 ILE Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 55 PHE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 82 SER Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 76 ILE Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain d residue 134 GLN Chi-restraints excluded: chain d residue 145 SER 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 218 LEU Chi-restraints excluded: chain i residue 326 LEU Chi-restraints excluded: chain j residue 3 PHE Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 30 LEU Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 80 SER Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 243 VAL 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 489 THR 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 66 VAL Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 117 ASN Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 44 LEU Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 344 LEU Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 172 LEU Chi-restraints excluded: chain s residue 185 TRP Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain s residue 306 SER 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 150 LEU Chi-restraints excluded: chain w residue 157 VAL Chi-restraints excluded: chain w residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 130 optimal weight: 0.9980 chunk 418 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 351 optimal weight: 0.9980 chunk 416 optimal weight: 2.9990 chunk 312 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 237 optimal weight: 0.6980 chunk 211 optimal weight: 0.0870 chunk 78 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 46 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 138 GLN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 99 HIS ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.084253 restraints weight = 90744.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.086815 restraints weight = 47088.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.087956 restraints weight = 27991.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.087869 restraints weight = 23290.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.087984 restraints weight = 23535.968| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 39865 Z= 0.165 Angle : 0.755 14.726 53988 Z= 0.375 Chirality : 0.045 0.248 5940 Planarity : 0.005 0.089 6610 Dihedral : 12.961 179.316 5964 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.60 % Favored : 93.71 % Rotamer: Outliers : 3.60 % Allowed : 17.03 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.12), residues: 4641 helix: 1.12 (0.09), residues: 2935 sheet: -0.87 (1.81), residues: 10 loop : -1.15 (0.16), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 81 TYR 0.037 0.002 TYR S 61 PHE 0.037 0.002 PHE i 292 TRP 0.028 0.001 TRP u 86 HIS 0.010 0.001 HIS h 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (39853) covalent geometry : angle 0.75463 / 0.37 (53974) SS BOND : bond 0.00385 / 0.16 ( 7) SS BOND : angle 1.79595 / 1.04 ( 14) hydrogen bonds : bond 0.04627 / 3.11 ( 2104) hydrogen bonds : angle 4.58319 / 3.28 ( 6126) Misc. bond : bond 0.00188 / 0.09 ( 5) *********************** 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 1042 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 895 time to evaluate : 1.548 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: Q 53 TYR cc_start: 0.6952 (m-80) cc_final: 0.6730 (m-80) REVERT: S 36 LYS cc_start: 0.8662 (tptm) cc_final: 0.8247 (tppp) REVERT: U 16 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7934 (pt0) REVERT: U 36 SER cc_start: 0.8757 (m) cc_final: 0.8516 (p) REVERT: V 20 ARG cc_start: 0.7535 (mtm-85) cc_final: 0.7269 (mtm-85) REVERT: V 21 LYS cc_start: 0.8225 (mttm) cc_final: 0.7982 (mttm) REVERT: V 99 LEU cc_start: 0.8660 (mm) cc_final: 0.8296 (mm) REVERT: V 118 PHE cc_start: 0.8591 (m-80) cc_final: 0.8125 (m-80) REVERT: V 130 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8948 (mp) REVERT: Y 97 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6508 (mm) REVERT: a 53 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7954 (ptp-170) REVERT: b 25 ASP cc_start: 0.8714 (t70) cc_final: 0.8395 (t0) REVERT: b 40 MET cc_start: 0.4440 (ptm) cc_final: 0.4191 (ptm) REVERT: c 56 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8183 (t0) REVERT: d 28 MET cc_start: 0.7241 (mmt) cc_final: 0.6579 (mmt) REVERT: d 56 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.8047 (m-10) REVERT: e 113 ARG cc_start: 0.8572 (mtp180) cc_final: 0.8347 (mtt180) REVERT: e 121 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7243 (mm-30) REVERT: g 105 LYS cc_start: 0.8736 (mttm) cc_final: 0.8501 (mtpp) REVERT: h 60 TYR cc_start: 0.8804 (t80) cc_final: 0.8569 (t80) REVERT: i 54 GLU cc_start: 0.8720 (pp20) cc_final: 0.8390 (pt0) REVERT: i 120 GLN cc_start: 0.8754 (tt0) cc_final: 0.8027 (tp-100) REVERT: i 218 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9119 (mm) REVERT: j 1 MET cc_start: 0.3005 (ptp) cc_final: 0.1172 (mmp) REVERT: j 8 MET cc_start: 0.8292 (mmm) cc_final: 0.7542 (mtm) REVERT: j 37 TYR cc_start: 0.4888 (p90) cc_final: 0.4214 (m-10) REVERT: j 101 SER cc_start: 0.9141 (t) cc_final: 0.8917 (p) REVERT: k 6 MET cc_start: 0.8240 (mtp) cc_final: 0.7578 (tpt) REVERT: k 7 ASN cc_start: 0.8789 (t0) cc_final: 0.8252 (t0) REVERT: k 25 HIS cc_start: 0.7726 (p-80) cc_final: 0.6932 (t70) REVERT: k 27 MET cc_start: 0.8770 (tpp) cc_final: 0.8490 (tpp) REVERT: k 31 LEU cc_start: 0.8820 (mm) cc_final: 0.8553 (mm) REVERT: l 58 ASP cc_start: 0.8257 (t70) cc_final: 0.7796 (t70) REVERT: l 70 THR cc_start: 0.8368 (m) cc_final: 0.7880 (p) REVERT: l 145 GLU cc_start: 0.8240 (mp0) cc_final: 0.7321 (mp0) REVERT: l 310 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8850 (mm) REVERT: l 510 LYS cc_start: 0.8055 (mttm) cc_final: 0.7460 (tptt) REVERT: m 2 MET cc_start: 0.8706 (tpt) cc_final: 0.8446 (tpt) REVERT: m 3 TYR cc_start: 0.8354 (m-80) cc_final: 0.8101 (m-80) REVERT: m 76 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6846 (mp0) REVERT: m 105 TRP cc_start: 0.8149 (t60) cc_final: 0.7763 (t60) REVERT: m 150 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7795 (mtp180) REVERT: m 161 PHE cc_start: 0.8863 (t80) cc_final: 0.8489 (t80) REVERT: n 38 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7535 (t80) REVERT: o 83 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.7893 (p) REVERT: o 102 TYR cc_start: 0.8693 (t80) cc_final: 0.8407 (t80) REVERT: o 106 LYS cc_start: 0.8374 (tttt) cc_final: 0.7610 (ttmm) REVERT: p 14 GLN cc_start: 0.8518 (mt0) cc_final: 0.8197 (mt0) REVERT: p 49 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: r 76 THR cc_start: 0.9549 (p) cc_final: 0.9315 (t) REVERT: r 243 MET cc_start: 0.8713 (mtm) cc_final: 0.8083 (mtt) REVERT: r 264 LEU cc_start: 0.9194 (pp) cc_final: 0.8718 (tp) REVERT: r 355 MET cc_start: 0.8590 (tpp) cc_final: 0.8296 (tpp) REVERT: r 454 ILE cc_start: 0.9438 (mt) cc_final: 0.9083 (mt) REVERT: s 3 MET cc_start: 0.8348 (mmp) cc_final: 0.6862 (ptt) REVERT: s 34 ARG cc_start: 0.8618 (ptm160) cc_final: 0.7582 (mmt90) REVERT: s 185 TRP cc_start: 0.9119 (OUTLIER) cc_final: 0.8668 (t-100) REVERT: s 206 GLU cc_start: 0.7889 (tp30) cc_final: 0.7336 (mp0) REVERT: s 224 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: s 279 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7311 (mpp-170) REVERT: s 281 ARG cc_start: 0.7796 (ttt180) cc_final: 0.7410 (mtm180) REVERT: s 282 TYR cc_start: 0.8092 (t80) cc_final: 0.7807 (t80) REVERT: s 286 MET cc_start: 0.8597 (mmm) cc_final: 0.8204 (mpp) REVERT: u 101 ARG cc_start: 0.8405 (mmm160) cc_final: 0.8071 (tpp-160) REVERT: v 7 ARG cc_start: 0.6534 (ptt90) cc_final: 0.6233 (ptm160) REVERT: v 72 ASP cc_start: 0.8215 (m-30) cc_final: 0.7974 (p0) REVERT: v 82 GLN cc_start: 0.8386 (tp-100) cc_final: 0.8125 (tp-100) REVERT: v 91 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7973 (mm-30) REVERT: v 100 LYS cc_start: 0.8604 (mttt) cc_final: 0.7478 (tttt) REVERT: v 101 GLU cc_start: 0.8137 (mp0) cc_final: 0.7776 (mp0) REVERT: w 115 GLU cc_start: 0.7597 (tm-30) cc_final: 0.6778 (mm-30) REVERT: w 127 ASN cc_start: 0.7409 (m-40) cc_final: 0.6842 (m-40) REVERT: w 306 ASN cc_start: 0.7537 (t0) cc_final: 0.7053 (m-40) outliers start: 147 outliers final: 85 residues processed: 989 average time/residue: 0.2361 time to fit residues: 389.6039 Evaluate side-chains 925 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 827 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain V residue 130 LEU 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 75 THR 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 148 ILE Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 62 SER 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 86 ILE Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 76 ILE Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain d residue 145 SER 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 218 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 240 LEU 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 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 80 SER Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 196 TRP Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 243 VAL 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 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 66 VAL Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 150 ARG Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain p residue 54 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 344 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 84 LEU 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 300 LEU Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain v residue 48 ASP Chi-restraints excluded: chain w residue 98 THR Chi-restraints excluded: chain w residue 157 VAL Chi-restraints excluded: chain w residue 195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 11 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 390 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 46 ASN W 47 HIS Z 21 GLN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** h 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 88 ASN l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 415 GLN s 138 GLN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 99 HIS ** w 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.083101 restraints weight = 91148.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.084853 restraints weight = 48551.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.086374 restraints weight = 30196.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.086653 restraints weight = 24004.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.086685 restraints weight = 22455.066| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 39865 Z= 0.197 Angle : 0.785 15.445 53988 Z= 0.389 Chirality : 0.046 0.239 5940 Planarity : 0.005 0.088 6610 Dihedral : 12.721 179.941 5964 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.97 % Favored : 93.36 % Rotamer: Outliers : 3.74 % Allowed : 17.88 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.12), residues: 4641 helix: 1.13 (0.09), residues: 2922 sheet: -0.54 (1.94), residues: 10 loop : -1.22 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 82 TYR 0.032 0.002 TYR S 61 PHE 0.037 0.002 PHE b 46 TRP 0.029 0.001 TRP u 86 HIS 0.009 0.001 HIS h 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (39853) covalent geometry : angle 0.78448 / 0.39 (53974) SS BOND : bond 0.00520 / 0.23 ( 7) SS BOND : angle 1.95765 / 1.14 ( 14) hydrogen bonds : bond 0.04763 / 3.21 ( 2104) hydrogen bonds : angle 4.61848 / 3.31 ( 6126) Misc. bond : bond 0.00103 / 0.05 ( 5) *********************** 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 1011 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 858 time to evaluate : 1.536 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: S 36 LYS cc_start: 0.8590 (tptm) cc_final: 0.8193 (tppp) REVERT: U 16 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: U 36 SER cc_start: 0.8779 (m) cc_final: 0.8527 (p) REVERT: V 20 ARG cc_start: 0.7524 (mtm-85) cc_final: 0.7240 (mtm-85) REVERT: V 21 LYS cc_start: 0.8197 (mttm) cc_final: 0.7949 (mttm) REVERT: V 99 LEU cc_start: 0.8703 (mm) cc_final: 0.8348 (mm) REVERT: V 118 PHE cc_start: 0.8613 (m-80) cc_final: 0.8230 (m-80) REVERT: V 130 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8980 (mp) REVERT: W 52 LYS cc_start: 0.8767 (mptt) cc_final: 0.8532 (mmtt) REVERT: a 53 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8015 (ptp-170) REVERT: b 25 ASP cc_start: 0.8762 (t70) cc_final: 0.8447 (t0) REVERT: b 40 MET cc_start: 0.4337 (ptm) cc_final: 0.4068 (ptm) REVERT: c 56 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8248 (t0) REVERT: c 132 GLN cc_start: 0.8320 (mp10) cc_final: 0.8059 (mp10) REVERT: d 56 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: e 113 ARG cc_start: 0.8598 (mtp180) cc_final: 0.8350 (mtt180) REVERT: e 121 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7212 (mm-30) REVERT: g 105 LYS cc_start: 0.8718 (mttm) cc_final: 0.8495 (mtpp) REVERT: i 54 GLU cc_start: 0.8724 (pp20) cc_final: 0.8386 (pt0) REVERT: i 90 THR cc_start: 0.8731 (p) cc_final: 0.8504 (p) REVERT: i 120 GLN cc_start: 0.8843 (tt0) cc_final: 0.8041 (tp-100) REVERT: i 218 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9107 (mm) REVERT: i 268 GLU cc_start: 0.8101 (tp30) cc_final: 0.7678 (mm-30) REVERT: j 1 MET cc_start: 0.2931 (ptp) cc_final: 0.1036 (mmp) REVERT: j 8 MET cc_start: 0.8337 (mmm) cc_final: 0.7599 (mtp) REVERT: j 37 TYR cc_start: 0.5000 (p90) cc_final: 0.4238 (m-10) REVERT: j 101 SER cc_start: 0.9177 (t) cc_final: 0.8903 (p) REVERT: k 6 MET cc_start: 0.8247 (mtp) cc_final: 0.7562 (tpt) REVERT: k 7 ASN cc_start: 0.8687 (t0) cc_final: 0.8294 (t0) REVERT: k 25 HIS cc_start: 0.7838 (p-80) cc_final: 0.6849 (t70) REVERT: k 27 MET cc_start: 0.8798 (tpp) cc_final: 0.8315 (mmm) REVERT: k 31 LEU cc_start: 0.8871 (mm) cc_final: 0.8649 (mm) REVERT: l 70 THR cc_start: 0.8444 (m) cc_final: 0.7931 (p) REVERT: l 145 GLU cc_start: 0.8294 (mp0) cc_final: 0.7402 (mp0) REVERT: l 510 LYS cc_start: 0.7934 (mttm) cc_final: 0.7277 (tptt) REVERT: m 2 MET cc_start: 0.8688 (tpt) cc_final: 0.8225 (tpp) REVERT: m 3 TYR cc_start: 0.8352 (m-80) cc_final: 0.8101 (m-80) REVERT: m 51 MET cc_start: 0.8709 (mmm) cc_final: 0.8404 (mmp) REVERT: m 150 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7794 (mtp180) REVERT: m 161 PHE cc_start: 0.8854 (t80) cc_final: 0.8516 (t80) REVERT: n 38 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7547 (t80) REVERT: o 79 ASN cc_start: 0.8914 (m-40) cc_final: 0.8502 (m-40) REVERT: o 83 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.7930 (p) REVERT: o 106 LYS cc_start: 0.8408 (tttt) cc_final: 0.7800 (ttmm) REVERT: p 14 GLN cc_start: 0.8530 (mt0) cc_final: 0.8181 (mt0) REVERT: p 49 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7678 (pm20) REVERT: r 243 MET cc_start: 0.8732 (mtm) cc_final: 0.8252 (mtt) REVERT: r 264 LEU cc_start: 0.9238 (pp) cc_final: 0.8739 (tp) REVERT: r 355 MET cc_start: 0.8629 (tpp) cc_final: 0.8351 (tpp) REVERT: r 454 ILE cc_start: 0.9418 (mt) cc_final: 0.9102 (mt) REVERT: s 3 MET cc_start: 0.8434 (mmp) cc_final: 0.6901 (ptt) REVERT: s 34 ARG cc_start: 0.8609 (ptm160) cc_final: 0.7632 (mmt90) REVERT: s 59 GLU cc_start: 0.8782 (tt0) cc_final: 0.8006 (mp0) REVERT: s 185 TRP cc_start: 0.9121 (OUTLIER) cc_final: 0.8606 (t-100) REVERT: s 206 GLU cc_start: 0.7940 (tp30) cc_final: 0.7360 (mp0) REVERT: s 224 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8456 (m-80) REVERT: s 279 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7326 (mpp-170) REVERT: s 281 ARG cc_start: 0.7786 (ttt180) cc_final: 0.7421 (mtm180) REVERT: s 286 MET cc_start: 0.8600 (mmm) cc_final: 0.8181 (mpp) REVERT: v 7 ARG cc_start: 0.6611 (ptt90) cc_final: 0.6083 (ptm160) REVERT: v 82 GLN cc_start: 0.8341 (tp-100) cc_final: 0.8075 (tp-100) REVERT: v 91 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7985 (mm-30) REVERT: v 99 MET cc_start: 0.8530 (ttm) cc_final: 0.8321 (ttm) REVERT: v 100 LYS cc_start: 0.8696 (mttt) cc_final: 0.7630 (tttt) REVERT: w 60 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7926 (mm) REVERT: w 115 GLU cc_start: 0.7599 (tm-30) cc_final: 0.6912 (mm-30) REVERT: w 306 ASN cc_start: 0.7677 (t0) cc_final: 0.7111 (m-40) outliers start: 153 outliers final: 98 residues processed: 953 average time/residue: 0.2384 time to fit residues: 378.1828 Evaluate side-chains 924 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 813 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 40 HIS Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain V residue 130 LEU 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 148 ILE Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 62 SER 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 98 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 82 SER Chi-restraints excluded: chain c residue 144 CYS 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 76 ILE Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 98 ASN Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain d residue 145 SER 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 13 ILE Chi-restraints excluded: chain i residue 218 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 240 LEU 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 k residue 30 LEU Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 80 SER 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 196 TRP Chi-restraints excluded: chain l residue 218 LEU Chi-restraints excluded: chain l residue 243 VAL 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 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 66 VAL Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 150 ARG Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain p residue 54 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 442 SER Chi-restraints excluded: chain s residue 1 MET 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 61 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 84 LEU 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 s residue 306 SER Chi-restraints excluded: chain u residue 154 ILE Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 48 ASP Chi-restraints excluded: chain w residue 60 ILE 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 173 MET Chi-restraints excluded: chain w residue 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 394 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 342 optimal weight: 0.5980 chunk 296 optimal weight: 2.9990 chunk 350 optimal weight: 0.6980 chunk 379 optimal weight: 0.6980 chunk 304 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 135 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 67 ASN W 47 HIS ** a 90 ASN ** 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 i 63 GLN l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 103 GLN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 138 GLN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 61 HIS ** w 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084699 restraints weight = 90640.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.086721 restraints weight = 46709.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.087525 restraints weight = 28654.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.087585 restraints weight = 26664.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.087661 restraints weight = 25308.247| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 39865 Z= 0.159 Angle : 0.775 15.351 53988 Z= 0.382 Chirality : 0.045 0.360 5940 Planarity : 0.005 0.082 6610 Dihedral : 12.323 177.654 5962 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.84 % Favored : 93.54 % Rotamer: Outliers : 3.35 % Allowed : 18.40 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.12), residues: 4641 helix: 1.20 (0.09), residues: 2927 sheet: -0.56 (1.72), residues: 10 loop : -1.24 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG W 82 TYR 0.032 0.002 TYR S 61 PHE 0.034 0.002 PHE b 46 TRP 0.025 0.001 TRP u 86 HIS 0.010 0.001 HIS h 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (39853) covalent geometry : angle 0.77419 / 0.38 (53974) SS BOND : bond 0.00342 / 0.14 ( 7) SS BOND : angle 1.68730 / 0.97 ( 14) hydrogen bonds : bond 0.04549 / 3.06 ( 2104) hydrogen bonds : angle 4.52726 / 3.25 ( 6126) Misc. bond : bond 0.00045 / 0.02 ( 5) *********************** 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 1018 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 881 time to evaluate : 1.581 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: S 36 LYS cc_start: 0.8555 (tptm) cc_final: 0.8269 (tppp) REVERT: S 43 TYR cc_start: 0.8967 (t80) cc_final: 0.8696 (t80) REVERT: U 16 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: U 36 SER cc_start: 0.8779 (m) cc_final: 0.8500 (p) REVERT: V 20 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.7295 (mtm-85) REVERT: V 21 LYS cc_start: 0.8200 (mttm) cc_final: 0.7963 (mttm) REVERT: V 40 ARG cc_start: 0.8735 (mmm160) cc_final: 0.8347 (mmm160) REVERT: V 99 LEU cc_start: 0.8676 (mm) cc_final: 0.8341 (mm) REVERT: V 118 PHE cc_start: 0.8597 (m-80) cc_final: 0.8231 (m-80) REVERT: V 130 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8952 (mp) REVERT: Z 41 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7677 (mp) REVERT: a 53 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7976 (ptp-170) REVERT: b 25 ASP cc_start: 0.8705 (t70) cc_final: 0.8379 (t0) REVERT: b 40 MET cc_start: 0.4327 (ptm) cc_final: 0.4053 (ptm) REVERT: c 56 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8286 (t0) REVERT: c 132 GLN cc_start: 0.8213 (mp10) cc_final: 0.7914 (mp10) REVERT: d 56 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.8069 (m-10) REVERT: d 95 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7983 (mm-30) REVERT: e 121 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7682 (mm-30) REVERT: e 141 CYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7550 (m) REVERT: g 105 LYS cc_start: 0.8765 (mttm) cc_final: 0.8513 (mtpp) REVERT: h 60 TYR cc_start: 0.8829 (t80) cc_final: 0.8622 (t80) REVERT: i 54 GLU cc_start: 0.8657 (pp20) cc_final: 0.8362 (pt0) REVERT: i 120 GLN cc_start: 0.8780 (tt0) cc_final: 0.7973 (tp-100) REVERT: i 240 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8523 (pp) REVERT: i 268 GLU cc_start: 0.8131 (tp30) cc_final: 0.7689 (mm-30) REVERT: j 1 MET cc_start: 0.2866 (ptp) cc_final: 0.1075 (mmp) REVERT: j 8 MET cc_start: 0.8347 (mmm) cc_final: 0.7581 (mtm) REVERT: j 37 TYR cc_start: 0.5262 (p90) cc_final: 0.4296 (m-10) REVERT: j 89 MET cc_start: 0.7725 (tmm) cc_final: 0.7362 (tmm) REVERT: j 101 SER cc_start: 0.9150 (t) cc_final: 0.8886 (p) REVERT: k 6 MET cc_start: 0.8253 (mtp) cc_final: 0.7542 (tpt) REVERT: k 7 ASN cc_start: 0.8694 (t0) cc_final: 0.8243 (t0) REVERT: k 25 HIS cc_start: 0.7546 (p-80) cc_final: 0.6793 (t70) REVERT: k 27 MET cc_start: 0.8788 (tpp) cc_final: 0.8499 (tpp) REVERT: k 31 LEU cc_start: 0.8799 (mm) cc_final: 0.8530 (mm) REVERT: l 58 ASP cc_start: 0.8394 (t70) cc_final: 0.7939 (t70) REVERT: l 70 THR cc_start: 0.8358 (m) cc_final: 0.7840 (p) REVERT: l 145 GLU cc_start: 0.8292 (mp0) cc_final: 0.7657 (mp0) REVERT: l 310 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8826 (mm) REVERT: l 338 MET cc_start: 0.8710 (mmm) cc_final: 0.7849 (tmm) REVERT: l 510 LYS cc_start: 0.7974 (mttm) cc_final: 0.7305 (tptt) REVERT: m 2 MET cc_start: 0.8671 (tpt) cc_final: 0.8263 (tpp) REVERT: m 51 MET cc_start: 0.8704 (mmm) cc_final: 0.8401 (mmp) REVERT: m 73 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5595 (mmt) REVERT: m 150 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7704 (mtp180) REVERT: m 161 PHE cc_start: 0.8778 (t80) cc_final: 0.8444 (t80) REVERT: n 38 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7548 (t80) REVERT: o 75 ASN cc_start: 0.8049 (t0) cc_final: 0.7743 (t0) REVERT: o 79 ASN cc_start: 0.8855 (m-40) cc_final: 0.8587 (m-40) REVERT: o 83 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.7905 (p) REVERT: o 106 LYS cc_start: 0.8361 (tttt) cc_final: 0.7890 (ttpp) REVERT: p 14 GLN cc_start: 0.8468 (mt0) cc_final: 0.8159 (mt0) REVERT: p 49 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: r 76 THR cc_start: 0.9531 (p) cc_final: 0.9330 (t) REVERT: r 195 MET cc_start: 0.8966 (ttm) cc_final: 0.8766 (ttm) REVERT: r 243 MET cc_start: 0.8708 (mtm) cc_final: 0.8136 (mtt) REVERT: r 264 LEU cc_start: 0.9159 (pp) cc_final: 0.8809 (tp) REVERT: r 355 MET cc_start: 0.8521 (tpp) cc_final: 0.8279 (tpp) REVERT: r 454 ILE cc_start: 0.9424 (mt) cc_final: 0.9089 (mt) REVERT: s 3 MET cc_start: 0.8539 (mmp) cc_final: 0.6973 (ptt) REVERT: s 34 ARG cc_start: 0.8553 (ptm160) cc_final: 0.7615 (mmt90) REVERT: s 59 GLU cc_start: 0.8783 (tt0) cc_final: 0.8008 (mp0) REVERT: s 185 TRP cc_start: 0.9112 (OUTLIER) cc_final: 0.8645 (t-100) REVERT: s 206 GLU cc_start: 0.7798 (tp30) cc_final: 0.7272 (mp0) REVERT: s 224 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: s 277 TYR cc_start: 0.8137 (m-10) cc_final: 0.7903 (m-10) REVERT: s 279 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7272 (mpp-170) REVERT: s 281 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7458 (mtm180) REVERT: s 282 TYR cc_start: 0.8113 (t80) cc_final: 0.7848 (t80) REVERT: s 286 MET cc_start: 0.8589 (mmm) cc_final: 0.8134 (mpp) REVERT: s 294 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8736 (tt) REVERT: v 7 ARG cc_start: 0.6566 (ptt90) cc_final: 0.6066 (ptm160) REVERT: v 82 GLN cc_start: 0.8378 (tp-100) cc_final: 0.8062 (tp-100) REVERT: v 99 MET cc_start: 0.8518 (ttm) cc_final: 0.8298 (ttm) REVERT: v 101 GLU cc_start: 0.8159 (mp0) cc_final: 0.7880 (mp0) REVERT: w 60 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7972 (mm) REVERT: w 115 GLU cc_start: 0.7626 (tm-30) cc_final: 0.6916 (mm-30) outliers start: 137 outliers final: 87 residues processed: 969 average time/residue: 0.2345 time to fit residues: 379.9374 Evaluate side-chains 937 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 832 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 40 HIS Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain V residue 130 LEU Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 54 MET 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 98 LEU Chi-restraints excluded: chain b residue 89 HIS Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 76 ILE Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 141 CYS 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 13 ILE Chi-restraints excluded: chain i residue 99 MET Chi-restraints excluded: chain i residue 201 THR Chi-restraints excluded: chain i residue 218 LEU Chi-restraints excluded: chain i residue 240 LEU 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 71 LEU Chi-restraints excluded: chain k residue 30 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 80 SER Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 243 VAL 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 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 73 MET 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 126 ILE Chi-restraints excluded: chain m residue 150 ARG Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 59 LEU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain p residue 54 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 167 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 344 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 83 LEU Chi-restraints excluded: chain s residue 84 LEU 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 294 LEU Chi-restraints excluded: chain s residue 300 LEU Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 154 ILE Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 118 LYS Chi-restraints excluded: chain w residue 60 ILE 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 195 ILE Chi-restraints excluded: chain w residue 227 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 154 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 370 optimal weight: 4.9990 chunk 352 optimal weight: 0.6980 chunk 272 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 294 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 217 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 67 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 i 63 GLN i 88 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 205 ASN ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 505 ASN ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 103 GLN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 138 GLN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN ** w 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.084922 restraints weight = 90616.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087067 restraints weight = 47028.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088248 restraints weight = 29348.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.088413 restraints weight = 25476.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.088510 restraints weight = 23303.900| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 39865 Z= 0.158 Angle : 0.783 15.644 53988 Z= 0.385 Chirality : 0.045 0.244 5940 Planarity : 0.005 0.077 6610 Dihedral : 11.963 175.412 5958 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.05 % Favored : 93.36 % Rotamer: Outliers : 2.98 % Allowed : 19.55 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.12), residues: 4641 helix: 1.24 (0.10), residues: 2922 sheet: -0.38 (1.73), residues: 10 loop : -1.24 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG W 82 TYR 0.029 0.002 TYR S 61 PHE 0.033 0.002 PHE b 46 TRP 0.068 0.001 TRP l 196 HIS 0.010 0.001 HIS h 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (39853) covalent geometry : angle 0.78294 / 0.38 (53974) SS BOND : bond 0.00514 / 0.18 ( 7) SS BOND : angle 1.71480 / 0.99 ( 14) hydrogen bonds : bond 0.04482 / 3.02 ( 2104) hydrogen bonds : angle 4.48637 / 3.22 ( 6126) Misc. bond : bond 0.00046 / 0.02 ( 5) *********************** 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 999 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 877 time to evaluate : 1.523 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: S 36 LYS cc_start: 0.8516 (tptm) cc_final: 0.8226 (tppp) REVERT: S 43 TYR cc_start: 0.8969 (t80) cc_final: 0.8728 (t80) REVERT: U 36 SER cc_start: 0.8743 (m) cc_final: 0.8495 (p) REVERT: V 20 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7291 (mtm-85) REVERT: V 21 LYS cc_start: 0.8200 (mttm) cc_final: 0.7976 (mttm) REVERT: V 40 ARG cc_start: 0.8728 (mmm160) cc_final: 0.7769 (tpt90) REVERT: V 99 LEU cc_start: 0.8628 (mm) cc_final: 0.8301 (mm) REVERT: V 118 PHE cc_start: 0.8608 (m-80) cc_final: 0.8249 (m-80) REVERT: V 130 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8982 (mp) REVERT: Z 41 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7631 (mp) REVERT: a 53 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7947 (ptp-170) REVERT: a 172 GLU cc_start: 0.7423 (tp30) cc_final: 0.7165 (tp30) REVERT: b 25 ASP cc_start: 0.8670 (t70) cc_final: 0.8346 (t0) REVERT: b 40 MET cc_start: 0.4318 (ptm) cc_final: 0.4048 (ptm) REVERT: c 56 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8284 (t0) REVERT: d 56 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.8013 (m-10) REVERT: d 95 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7915 (mm-30) REVERT: e 121 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7675 (mm-30) REVERT: g 105 LYS cc_start: 0.8723 (mttm) cc_final: 0.8506 (mtpp) REVERT: i 54 GLU cc_start: 0.8645 (pp20) cc_final: 0.8338 (pt0) REVERT: i 108 MET cc_start: 0.8086 (mtm) cc_final: 0.7872 (mtp) REVERT: i 120 GLN cc_start: 0.8783 (tt0) cc_final: 0.7914 (tp-100) REVERT: i 268 GLU cc_start: 0.8121 (tp30) cc_final: 0.7641 (mm-30) REVERT: i 344 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8447 (mm) REVERT: j 1 MET cc_start: 0.2711 (ptp) cc_final: 0.1009 (mmm) REVERT: j 8 MET cc_start: 0.8283 (mmm) cc_final: 0.7543 (mtm) REVERT: j 37 TYR cc_start: 0.5332 (p90) cc_final: 0.4342 (m-10) REVERT: j 56 PHE cc_start: 0.7911 (t80) cc_final: 0.7559 (t80) REVERT: j 89 MET cc_start: 0.7723 (tmm) cc_final: 0.7398 (tmm) REVERT: j 101 SER cc_start: 0.9147 (t) cc_final: 0.8883 (p) REVERT: k 6 MET cc_start: 0.8320 (mtp) cc_final: 0.7495 (tpt) REVERT: k 7 ASN cc_start: 0.8683 (t0) cc_final: 0.8278 (t0) REVERT: k 25 HIS cc_start: 0.7470 (p-80) cc_final: 0.6828 (t70) REVERT: k 27 MET cc_start: 0.8772 (tpp) cc_final: 0.8515 (mmm) REVERT: k 31 LEU cc_start: 0.8814 (mm) cc_final: 0.8508 (mm) REVERT: k 33 LEU cc_start: 0.8904 (mt) cc_final: 0.8567 (mp) REVERT: l 58 ASP cc_start: 0.8257 (t70) cc_final: 0.8039 (t70) REVERT: l 70 THR cc_start: 0.8268 (m) cc_final: 0.7639 (p) REVERT: l 145 GLU cc_start: 0.8220 (mp0) cc_final: 0.7665 (mp0) REVERT: l 310 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8766 (mm) REVERT: l 338 MET cc_start: 0.8669 (mmm) cc_final: 0.7944 (tmm) REVERT: l 510 LYS cc_start: 0.7931 (mttm) cc_final: 0.7312 (tptt) REVERT: m 2 MET cc_start: 0.8625 (tpt) cc_final: 0.8262 (tpp) REVERT: m 51 MET cc_start: 0.8706 (mmm) cc_final: 0.8452 (mmp) REVERT: m 69 TYR cc_start: 0.8625 (t80) cc_final: 0.8249 (m-80) REVERT: m 150 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7687 (mtp180) REVERT: m 161 PHE cc_start: 0.8756 (t80) cc_final: 0.7915 (t80) REVERT: m 165 TYR cc_start: 0.8088 (m-10) cc_final: 0.7872 (m-80) REVERT: n 38 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7493 (t80) REVERT: o 75 ASN cc_start: 0.8035 (t0) cc_final: 0.7693 (t0) REVERT: o 79 ASN cc_start: 0.8845 (m-40) cc_final: 0.8526 (m-40) REVERT: o 83 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.7625 (p) REVERT: p 14 GLN cc_start: 0.8500 (mt0) cc_final: 0.8196 (mt0) REVERT: p 49 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: r 76 THR cc_start: 0.9536 (p) cc_final: 0.9333 (t) REVERT: r 114 GLU cc_start: 0.7569 (tp30) cc_final: 0.6977 (tp30) REVERT: r 195 MET cc_start: 0.8966 (ttm) cc_final: 0.8736 (ttm) REVERT: r 264 LEU cc_start: 0.9119 (pp) cc_final: 0.8833 (tp) REVERT: r 355 MET cc_start: 0.8589 (tpp) cc_final: 0.8378 (tpp) REVERT: r 454 ILE cc_start: 0.9340 (mt) cc_final: 0.9099 (mt) REVERT: s 3 MET cc_start: 0.8529 (mmp) cc_final: 0.6988 (ptt) REVERT: s 34 ARG cc_start: 0.8534 (ptm160) cc_final: 0.7538 (mmt90) REVERT: s 185 TRP cc_start: 0.9098 (OUTLIER) cc_final: 0.8614 (t-100) REVERT: s 206 GLU cc_start: 0.7826 (tp30) cc_final: 0.7270 (mp0) REVERT: s 224 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: s 279 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7297 (mpp-170) REVERT: s 281 ARG cc_start: 0.7756 (ttt180) cc_final: 0.7466 (mtm180) REVERT: s 282 TYR cc_start: 0.8101 (t80) cc_final: 0.7832 (t80) REVERT: s 286 MET cc_start: 0.8592 (mmm) cc_final: 0.8034 (mpp) REVERT: s 294 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8680 (tt) REVERT: v 7 ARG cc_start: 0.6547 (ptt90) cc_final: 0.6042 (ptm160) REVERT: v 82 GLN cc_start: 0.8369 (tp-100) cc_final: 0.8063 (tp-100) REVERT: v 91 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7921 (mm-30) REVERT: w 60 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7986 (mm) REVERT: w 115 GLU cc_start: 0.7654 (tm-30) cc_final: 0.6978 (mm-30) outliers start: 122 outliers final: 84 residues processed: 952 average time/residue: 0.2255 time to fit residues: 358.3255 Evaluate side-chains 920 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 821 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 40 HIS Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 69 HIS Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain V residue 130 LEU 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 148 ILE Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 41 LEU 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 186 THR 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 44 THR Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 61 GLN Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 98 ASN Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 147 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 13 ILE Chi-restraints excluded: chain i residue 99 MET Chi-restraints excluded: chain i residue 201 THR Chi-restraints excluded: chain i residue 218 LEU Chi-restraints excluded: chain i residue 240 LEU Chi-restraints excluded: chain i residue 326 LEU Chi-restraints excluded: chain i residue 344 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 30 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 80 SER Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 279 CYS Chi-restraints excluded: chain l residue 310 LEU Chi-restraints excluded: chain l residue 555 LEU 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 126 ILE Chi-restraints excluded: chain m residue 150 ARG Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain p residue 54 GLU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 167 THR 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 83 LEU Chi-restraints excluded: chain s residue 140 ILE 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 294 LEU Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 154 ILE Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 60 ILE 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 195 ILE Chi-restraints excluded: chain w residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 62 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 178 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 331 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 67 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 117 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** r 304 GLN s 138 GLN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 142 GLN ** w 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.106014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.085236 restraints weight = 90415.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087044 restraints weight = 46895.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.088417 restraints weight = 29415.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088662 restraints weight = 23878.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.088753 restraints weight = 22353.558| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 39865 Z= 0.163 Angle : 0.806 15.362 53988 Z= 0.395 Chirality : 0.045 0.312 5940 Planarity : 0.005 0.075 6610 Dihedral : 11.775 173.860 5958 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.97 % Favored : 93.47 % Rotamer: Outliers : 2.67 % Allowed : 20.55 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4641 helix: 1.23 (0.10), residues: 2936 sheet: None (None), residues: 0 loop : -1.23 (0.16), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG W 82 TYR 0.035 0.002 TYR i 59 PHE 0.039 0.002 PHE l 326 TRP 0.077 0.001 TRP l 196 HIS 0.009 0.001 HIS h 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (39853) covalent geometry : angle 0.80534 / 0.39 (53974) SS BOND : bond 0.00472 / 0.18 ( 7) SS BOND : angle 1.90329 / 1.08 ( 14) hydrogen bonds : bond 0.04456 / 2.99 ( 2104) hydrogen bonds : angle 4.51362 / 3.24 ( 6126) Misc. bond : bond 0.00043 / 0.02 ( 5) ********************** 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 986 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 877 time to evaluate : 1.066 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: S 31 ASN cc_start: 0.7591 (m-40) cc_final: 0.7068 (m-40) REVERT: S 36 LYS cc_start: 0.8594 (tptm) cc_final: 0.8235 (tppp) REVERT: S 43 TYR cc_start: 0.8975 (t80) cc_final: 0.8749 (t80) REVERT: U 36 SER cc_start: 0.8745 (m) cc_final: 0.8502 (p) REVERT: U 83 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8655 (ptpp) REVERT: V 14 ASP cc_start: 0.7641 (p0) cc_final: 0.6909 (t0) REVERT: V 20 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7273 (mtm-85) REVERT: V 21 LYS cc_start: 0.8217 (mttm) cc_final: 0.7958 (mttm) REVERT: V 40 ARG cc_start: 0.8734 (mmm160) cc_final: 0.7758 (tpt90) REVERT: V 85 ASP cc_start: 0.8403 (m-30) cc_final: 0.7414 (p0) REVERT: V 99 LEU cc_start: 0.8710 (mm) cc_final: 0.8367 (mm) REVERT: V 118 PHE cc_start: 0.8525 (m-80) cc_final: 0.8175 (m-80) REVERT: V 130 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8995 (mp) REVERT: W 82 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8424 (ttt90) REVERT: W 100 ASP cc_start: 0.7031 (p0) cc_final: 0.6780 (p0) REVERT: Z 27 THR cc_start: 0.8022 (p) cc_final: 0.7788 (p) REVERT: Z 41 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7617 (mp) REVERT: a 53 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7948 (ptp-170) REVERT: a 172 GLU cc_start: 0.7406 (tp30) cc_final: 0.7081 (tp30) REVERT: b 25 ASP cc_start: 0.8672 (t70) cc_final: 0.8342 (t0) REVERT: b 40 MET cc_start: 0.4360 (ptm) cc_final: 0.4137 (ptm) REVERT: c 56 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8293 (t0) REVERT: c 132 GLN cc_start: 0.8349 (mp10) cc_final: 0.8113 (mp10) REVERT: d 28 MET cc_start: 0.7169 (mmt) cc_final: 0.6627 (mmt) REVERT: d 56 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.8035 (m-10) REVERT: d 95 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7911 (mm-30) REVERT: g 79 ASP cc_start: 0.8602 (m-30) cc_final: 0.8236 (m-30) REVERT: g 89 MET cc_start: 0.8655 (ttp) cc_final: 0.8347 (ttm) REVERT: g 105 LYS cc_start: 0.8724 (mttm) cc_final: 0.8503 (mtpp) REVERT: i 54 GLU cc_start: 0.8647 (pp20) cc_final: 0.8309 (pt0) REVERT: i 72 MET cc_start: 0.8687 (tpt) cc_final: 0.8387 (tpt) REVERT: i 120 GLN cc_start: 0.8751 (tt0) cc_final: 0.7892 (tp-100) REVERT: i 268 GLU cc_start: 0.8176 (tp30) cc_final: 0.7710 (mm-30) REVERT: i 344 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8457 (mm) REVERT: j 1 MET cc_start: 0.2804 (ptp) cc_final: 0.1176 (mmm) REVERT: j 8 MET cc_start: 0.8232 (mmm) cc_final: 0.7541 (mtm) REVERT: j 37 TYR cc_start: 0.5415 (p90) cc_final: 0.4412 (m-10) REVERT: j 56 PHE cc_start: 0.7940 (t80) cc_final: 0.7607 (t80) REVERT: j 89 MET cc_start: 0.7711 (tmm) cc_final: 0.7311 (tmm) REVERT: j 101 SER cc_start: 0.9122 (t) cc_final: 0.8858 (p) REVERT: k 6 MET cc_start: 0.8312 (mtp) cc_final: 0.7464 (tpt) REVERT: k 7 ASN cc_start: 0.8735 (t0) cc_final: 0.8322 (t0) REVERT: k 25 HIS cc_start: 0.7449 (p-80) cc_final: 0.6810 (t70) REVERT: k 27 MET cc_start: 0.8760 (tpp) cc_final: 0.8522 (mmm) REVERT: k 31 LEU cc_start: 0.8789 (mm) cc_final: 0.8476 (mm) REVERT: l 58 ASP cc_start: 0.8161 (t70) cc_final: 0.7960 (t70) REVERT: l 70 THR cc_start: 0.8318 (m) cc_final: 0.7679 (p) REVERT: l 145 GLU cc_start: 0.8225 (mp0) cc_final: 0.7678 (mp0) REVERT: l 310 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8811 (mm) REVERT: l 313 MET cc_start: 0.8479 (mtp) cc_final: 0.8235 (mtm) REVERT: l 338 MET cc_start: 0.8689 (mmm) cc_final: 0.8199 (tmm) REVERT: l 510 LYS cc_start: 0.7943 (mttm) cc_final: 0.7352 (tptt) REVERT: m 2 MET cc_start: 0.8632 (tpt) cc_final: 0.8266 (tpp) REVERT: m 51 MET cc_start: 0.8752 (mmm) cc_final: 0.8447 (mmp) REVERT: m 69 TYR cc_start: 0.8580 (t80) cc_final: 0.8174 (m-80) REVERT: m 73 MET cc_start: 0.6032 (OUTLIER) cc_final: 0.5532 (mmt) REVERT: m 150 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7708 (mtp180) REVERT: m 161 PHE cc_start: 0.8772 (t80) cc_final: 0.7943 (t80) REVERT: m 165 TYR cc_start: 0.8095 (m-10) cc_final: 0.7881 (m-80) REVERT: n 38 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7493 (t80) REVERT: o 75 ASN cc_start: 0.7959 (t0) cc_final: 0.7629 (t0) REVERT: o 79 ASN cc_start: 0.8860 (m-40) cc_final: 0.8529 (m-40) REVERT: o 83 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8100 (p) REVERT: o 102 TYR cc_start: 0.8702 (t80) cc_final: 0.8467 (t80) REVERT: p 14 GLN cc_start: 0.8501 (mt0) cc_final: 0.8183 (mt0) REVERT: p 49 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: r 1 MET cc_start: 0.7956 (tpp) cc_final: 0.7258 (tpp) REVERT: r 23 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8602 (mt) REVERT: r 114 GLU cc_start: 0.7602 (tp30) cc_final: 0.7051 (tp30) REVERT: r 195 MET cc_start: 0.8962 (ttm) cc_final: 0.8749 (ttm) REVERT: r 199 TYR cc_start: 0.8856 (m-10) cc_final: 0.8650 (m-10) REVERT: r 222 GLU cc_start: 0.7356 (tt0) cc_final: 0.7129 (tt0) REVERT: r 243 MET cc_start: 0.8674 (mtm) cc_final: 0.8159 (mtp) REVERT: r 264 LEU cc_start: 0.9124 (pp) cc_final: 0.8829 (tp) REVERT: r 355 MET cc_start: 0.8575 (tpp) cc_final: 0.8347 (tpp) REVERT: r 454 ILE cc_start: 0.9244 (mt) cc_final: 0.8995 (mt) REVERT: s 3 MET cc_start: 0.8501 (mmp) cc_final: 0.6996 (ptt) REVERT: s 34 ARG cc_start: 0.8509 (ptm160) cc_final: 0.7537 (mmt90) REVERT: s 59 GLU cc_start: 0.8790 (tt0) cc_final: 0.8023 (mp0) REVERT: s 185 TRP cc_start: 0.9082 (OUTLIER) cc_final: 0.8690 (t-100) REVERT: s 206 GLU cc_start: 0.7850 (tp30) cc_final: 0.7285 (mp0) REVERT: s 224 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: s 279 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7315 (mpp-170) REVERT: s 281 ARG cc_start: 0.7779 (ttt180) cc_final: 0.7484 (mtm180) REVERT: s 282 TYR cc_start: 0.8081 (t80) cc_final: 0.7853 (t80) REVERT: s 294 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8661 (tt) REVERT: v 7 ARG cc_start: 0.6556 (ptt90) cc_final: 0.6052 (ptm160) REVERT: v 82 GLN cc_start: 0.8307 (tp-100) cc_final: 0.8001 (tp-100) REVERT: w 115 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7089 (mm-30) outliers start: 109 outliers final: 77 residues processed: 944 average time/residue: 0.2296 time to fit residues: 362.7662 Evaluate side-chains 923 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 830 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 40 HIS Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain U residue 69 HIS Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 104 ARG Chi-restraints excluded: chain V residue 130 LEU Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 75 THR 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 148 ILE Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Z residue 41 LEU 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 186 THR 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 44 THR Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 122 THR Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 97 ILE Chi-restraints excluded: chain d residue 118 ASN Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain e residue 147 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 13 ILE Chi-restraints excluded: chain i residue 201 THR Chi-restraints excluded: chain i residue 218 LEU Chi-restraints excluded: chain i residue 240 LEU Chi-restraints excluded: chain i residue 326 LEU Chi-restraints excluded: chain i residue 344 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 30 LEU Chi-restraints excluded: chain k residue 80 SER Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 279 CYS Chi-restraints excluded: chain l residue 310 LEU Chi-restraints excluded: chain l residue 555 LEU 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 73 MET Chi-restraints excluded: chain m residue 78 TYR Chi-restraints excluded: chain m residue 117 ASN Chi-restraints excluded: chain m residue 150 ARG Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain p residue 54 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 442 SER Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 83 LEU Chi-restraints excluded: chain s residue 140 ILE 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 294 LEU Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 154 ILE Chi-restraints excluded: chain v residue 40 VAL 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 195 ILE Chi-restraints excluded: chain w residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 151 optimal weight: 0.7980 chunk 399 optimal weight: 0.7980 chunk 309 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 367 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 229 optimal weight: 0.4980 chunk 217 optimal weight: 2.9990 chunk 181 optimal weight: 0.3980 chunk 448 optimal weight: 8.9990 chunk 379 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 67 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 181 HIS ** 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** i 319 HIS ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 117 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** r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 138 GLN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.106323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085527 restraints weight = 90826.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.087325 restraints weight = 47361.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.088803 restraints weight = 29524.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.089023 restraints weight = 23617.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089101 restraints weight = 22301.598| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 39865 Z= 0.162 Angle : 0.810 15.358 53988 Z= 0.396 Chirality : 0.046 0.276 5940 Planarity : 0.005 0.073 6610 Dihedral : 11.587 172.112 5958 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.18 % Favored : 93.30 % Rotamer: Outliers : 2.59 % Allowed : 20.96 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.13), residues: 4641 helix: 1.25 (0.10), residues: 2919 sheet: None (None), residues: 0 loop : -1.27 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 53 TYR 0.035 0.002 TYR i 59 PHE 0.039 0.002 PHE l 326 TRP 0.064 0.001 TRP l 196 HIS 0.009 0.001 HIS h 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (39853) covalent geometry : angle 0.80970 / 0.40 (53974) SS BOND : bond 0.00391 / 0.15 ( 7) SS BOND : angle 1.82304 / 1.05 ( 14) hydrogen bonds : bond 0.04463 / 3.01 ( 2104) hydrogen bonds : angle 4.51721 / 3.25 ( 6126) Misc. bond : bond 0.00043 / 0.02 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8516.04 seconds wall clock time: 147 minutes 33.55 seconds (8853.55 seconds total)