Starting phenix.real_space_refine on Mon Sep 14 22:04:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6re4_4841/09_2026/6re4_4841.cif Found real_map, /net/cci-nas-00/data/ceres_data/6re4_4841/09_2026/6re4_4841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6re4_4841/09_2026/6re4_4841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6re4_4841/09_2026/6re4_4841.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6re4_4841/09_2026/6re4_4841.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6re4_4841/09_2026/6re4_4841.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6re4_4841/09_2026/6re4_4841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6re4_4841/09_2026/6re4_4841.map" } resolution = 3.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21526 2.51 5 N 5790 2.21 5 O 6413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 232 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: 33863 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.96, per 1000 atoms: 0.21 Number of scatterers: 33863 At special positions: 0 Unit cell: (164.268, 129.519, 207.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6413 8.00 N 5790 7.00 C 21526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.5 seconds 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8150 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 27 sheets defined 51.9% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 54 through 67 removed outlier: 3.542A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.919A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.628A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.644A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.897A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.679A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 66 removed outlier: 4.001A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.365A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.609A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 4.385A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.783A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.776A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.520A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.157A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 127 removed outlier: 4.328A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 4.341A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.313A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 127 removed outlier: 3.594A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.932A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 90 removed outlier: 4.239A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 94 No H-bonds generated for 'chain 'G' and resid 92 through 94' Processing helix chain 'G' and resid 95 through 126 removed outlier: 4.605A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 4.286A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA H 64 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 92 removed outlier: 3.618A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 127 removed outlier: 3.579A pdb=" N ALA H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE H 126 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 4.278A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.083A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 125 removed outlier: 3.637A pdb=" N GLY I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.667A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.372A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 3.612A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 64 removed outlier: 3.577A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.610A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.779A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 removed outlier: 3.579A pdb=" N THR P 102 " --> pdb=" O THR P 98 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 129 removed outlier: 3.871A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 3.886A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 13 removed outlier: 3.511A pdb=" N GLY Q 13 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 40 removed outlier: 3.686A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 44 removed outlier: 3.633A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 41 through 44' Processing helix chain 'R' and resid 29 through 39 removed outlier: 3.667A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 54 Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 158 through 170 removed outlier: 3.752A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 removed outlier: 3.614A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 79 removed outlier: 3.523A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.458A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 131 removed outlier: 3.562A pdb=" N ILE S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU S 131 " --> pdb=" O LEU S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 151 removed outlier: 3.648A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 183 Processing helix chain 'S' and resid 216 through 221 Processing helix chain 'S' and resid 238 through 274 removed outlier: 3.744A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 276 through 313 removed outlier: 3.642A pdb=" N SER S 280 " --> pdb=" O ASN S 276 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.829A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE T 138 " --> pdb=" O ASP T 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 134 through 138' Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 213 removed outlier: 3.509A pdb=" N ALA T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 249 removed outlier: 3.606A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN T 248 " --> pdb=" O ASN T 244 " (cutoff:3.500A) Processing helix chain 'T' and resid 250 through 253 Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 284 Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 3.630A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.663A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA T 333 " --> pdb=" O LYS T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 354 through 363 removed outlier: 3.834A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 400 Processing helix chain 'T' and resid 409 through 414 removed outlier: 3.729A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) Processing helix chain 'T' and resid 431 through 435 removed outlier: 3.622A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.674A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 457 Processing helix chain 'T' and resid 459 through 463 removed outlier: 4.181A pdb=" N PHE T 462 " --> pdb=" O PHE T 459 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY T 463 " --> pdb=" O ALA T 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 459 through 463' Processing helix chain 'T' and resid 471 through 484 removed outlier: 3.814A pdb=" N GLU T 475 " --> pdb=" O GLN T 471 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 4.012A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 528 removed outlier: 3.619A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 529 through 540 removed outlier: 4.198A pdb=" N PHE T 533 " --> pdb=" O ASN T 529 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 556 removed outlier: 3.860A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 50 removed outlier: 3.523A pdb=" N LEU U 48 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS U 50 " --> pdb=" O GLU U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 63 removed outlier: 3.974A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 72 removed outlier: 3.645A pdb=" N ALA U 69 " --> pdb=" O LYS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 138 removed outlier: 4.039A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.945A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 280 Processing helix chain 'U' and resid 281 through 284 Processing helix chain 'U' and resid 295 through 315 Proline residue: U 303 - end of helix removed outlier: 3.670A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 3.807A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 353 through 363 Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 409 through 414 removed outlier: 3.905A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 457 removed outlier: 4.074A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) Processing helix chain 'U' and resid 469 through 485 removed outlier: 3.535A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 Processing helix chain 'U' and resid 516 through 528 removed outlier: 4.095A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL U 528 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 4.011A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'V' and resid 45 through 49 Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.994A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.935A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE V 138 " --> pdb=" O ASP V 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 134 through 138' Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 211 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.904A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.727A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 removed outlier: 3.504A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.718A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 430 through 435 removed outlier: 3.604A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN V 435 " --> pdb=" O SER V 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 430 through 435' Processing helix chain 'V' and resid 438 through 457 removed outlier: 3.713A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 484 removed outlier: 3.681A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.663A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 517 removed outlier: 3.834A pdb=" N ASP V 516 " --> pdb=" O ARG V 513 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 513 through 517' Processing helix chain 'V' and resid 519 through 528 Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.739A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 548 through 554 removed outlier: 3.586A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.563A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 203 Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.137A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.556A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 301 removed outlier: 3.617A pdb=" N PHE X 290 " --> pdb=" O ASN X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 341 through 345 removed outlier: 3.500A pdb=" N ASP X 344 " --> pdb=" O VAL X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 365 through 370 removed outlier: 3.561A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 413 Processing helix chain 'X' and resid 426 through 443 Processing helix chain 'X' and resid 448 through 453 removed outlier: 3.733A pdb=" N GLU X 451 " --> pdb=" O GLN X 448 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL X 452 " --> pdb=" O VAL X 449 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE X 453 " --> pdb=" O ALA X 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 448 through 453' Processing helix chain 'X' and resid 462 through 475 removed outlier: 3.715A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) Processing helix chain 'X' and resid 482 through 486 Processing helix chain 'X' and resid 491 through 501 removed outlier: 3.910A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 531 Processing helix chain 'Y' and resid 114 through 118 removed outlier: 3.768A pdb=" N THR Y 117 " --> pdb=" O GLY Y 114 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU Y 118 " --> pdb=" O ARG Y 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 114 through 118' Processing helix chain 'Y' and resid 149 through 153 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 190 through 201 Processing helix chain 'Y' and resid 202 through 204 No H-bonds generated for 'chain 'Y' and resid 202 through 204' Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 4.226A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.512A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 298 removed outlier: 3.722A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 342 through 345 Processing helix chain 'Y' and resid 348 through 355 Processing helix chain 'Y' and resid 356 through 358 No H-bonds generated for 'chain 'Y' and resid 356 through 358' Processing helix chain 'Y' and resid 365 through 371 Processing helix chain 'Y' and resid 393 through 412 removed outlier: 3.856A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 413 through 420 Processing helix chain 'Y' and resid 421 through 425 removed outlier: 3.687A pdb=" N GLU Y 424 " --> pdb=" O GLY Y 421 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU Y 425 " --> pdb=" O MET Y 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 421 through 425' Processing helix chain 'Y' and resid 426 through 443 removed outlier: 3.584A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Y 441 " --> pdb=" O ARG Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 Processing helix chain 'Y' and resid 491 through 504 removed outlier: 4.100A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 532 Processing helix chain 'Y' and resid 544 through 550 removed outlier: 4.238A pdb=" N ASP Y 548 " --> pdb=" O GLY Y 544 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 removed outlier: 3.692A pdb=" N THR Z 117 " --> pdb=" O GLY Z 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 Processing helix chain 'Z' and resid 188 through 200 Processing helix chain 'Z' and resid 216 through 229 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.531A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.601A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 299 removed outlier: 3.960A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA Z 299 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 342 through 345 removed outlier: 3.681A pdb=" N ASP Z 345 " --> pdb=" O PRO Z 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 342 through 345' Processing helix chain 'Z' and resid 348 through 354 removed outlier: 3.974A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 370 removed outlier: 3.564A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) Processing helix chain 'Z' and resid 393 through 418 removed outlier: 3.993A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 429 through 444 removed outlier: 3.695A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER Z 444 " --> pdb=" O GLN Z 440 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 Processing helix chain 'Z' and resid 491 through 506 removed outlier: 4.043A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 534 removed outlier: 3.778A pdb=" N LEU Z 530 " --> pdb=" O SER Z 526 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 61 through 65 removed outlier: 3.602A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N VAL S 137 " --> pdb=" O TYR S 158 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N LEU S 160 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL S 139 " --> pdb=" O LEU S 160 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE S 162 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER S 141 " --> pdb=" O ILE S 162 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 82 removed outlier: 3.626A pdb=" N SER R 82 " --> pdb=" O PHE R 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 80 through 82 removed outlier: 3.626A pdb=" N SER R 82 " --> pdb=" O PHE R 74 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE R 144 " --> pdb=" O PRO R 71 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASN R 73 " --> pdb=" O ILE R 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.838A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 87 through 89 removed outlier: 6.762A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 37 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AA6, first strand: chain 'T' and resid 87 through 89 removed outlier: 6.762A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 116 through 122 current: chain 'Y' and resid 61 through 65 removed outlier: 4.555A pdb=" N SER Y 61 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 37 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AA7, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AA8, first strand: chain 'T' and resid 163 through 164 removed outlier: 6.573A pdb=" N GLY T 320 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE T 380 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE T 322 " --> pdb=" O PHE T 380 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL T 382 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR T 324 " --> pdb=" O VAL T 382 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLU T 384 " --> pdb=" O TYR T 324 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU T 408 " --> pdb=" O LEU T 222 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE T 224 " --> pdb=" O LEU T 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 117 through 122 removed outlier: 3.758A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AB2, first strand: chain 'U' and resid 163 through 165 removed outlier: 6.473A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 201 through 202 removed outlier: 4.396A pdb=" N ILE U 215 " --> pdb=" O LEU U 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 116 through 122 removed outlier: 3.887A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'V' and resid 163 through 164 removed outlier: 6.210A pdb=" N THR V 164 " --> pdb=" O SER V 289 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'V' and resid 382 through 384 removed outlier: 6.701A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 110 through 113 Processing sheet with id=AB9, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.108A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLN X 250 " --> pdb=" O MET X 122 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL X 213 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.510A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC3, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id=AC4, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.312A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER Y 208 " --> pdb=" O THR Y 245 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL Y 247 " --> pdb=" O SER Y 208 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE Y 210 " --> pdb=" O VAL Y 247 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 210 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY Y 212 " --> pdb=" O GLY Y 249 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE Y 207 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N TYR Y 340 " --> pdb=" O VAL Y 284 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS Y 178 " --> pdb=" O ALA Y 360 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR Y 362 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY Y 180 " --> pdb=" O THR Y 362 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.250A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.708A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 121 through 122 removed outlier: 3.563A pdb=" N LEU Z 282 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE Z 179 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL Z 339 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU Z 181 " --> pdb=" O VAL Z 339 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS Z 178 " --> pdb=" O ALA Z 360 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N THR Z 362 " --> pdb=" O LYS Z 178 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY Z 180 " --> pdb=" O THR Z 362 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.159A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 559 through 561 1717 hydrogen bonds defined for protein. 4953 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: 7.59 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5776 1.31 - 1.44: 8165 1.44 - 1.56: 20222 1.56 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34384 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.94e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.83e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.82e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.77e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.42e+01 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 46150 3.89 - 7.77: 406 7.77 - 11.66: 34 11.66 - 15.54: 3 15.54 - 19.43: 5 Bond angle restraints: 46598 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 121.83 18.04 1.00e+00 1.00e+00 3.25e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 120.35 16.48 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 123.56 16.31 1.00e+00 1.00e+00 2.66e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 ... (remaining 46593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.08: 20123 31.08 - 62.17: 537 62.17 - 93.25: 48 93.25 - 124.33: 0 124.33 - 155.42: 2 Dihedral angle restraints: 20710 sinusoidal: 7967 harmonic: 12743 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -128.54 -51.46 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual 180.00 -130.64 -49.36 0 5.00e+00 4.00e-02 9.74e+01 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -132.37 -47.63 0 5.00e+00 4.00e-02 9.07e+01 ... (remaining 20707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3995 0.066 - 0.132: 1296 0.132 - 0.198: 197 0.198 - 0.264: 20 0.264 - 0.330: 5 Chirality restraints: 5513 Sorted by residual: chirality pdb=" CB VAL T 180 " pdb=" CA VAL T 180 " pdb=" CG1 VAL T 180 " pdb=" CG2 VAL T 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB THR Z 334 " pdb=" CA THR Z 334 " pdb=" OG1 THR Z 334 " pdb=" CG2 THR Z 334 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CG LEU Y 266 " pdb=" CB LEU Y 266 " pdb=" CD1 LEU Y 266 " pdb=" CD2 LEU Y 266 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 5510 not shown) Planarity restraints: 5991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" C ALA Y 503 " -0.105 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 5.97e-02 3.57e+01 pdb=" C ALA Z 503 " -0.103 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR T 543 " -0.052 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO T 544 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO T 544 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO T 544 " -0.043 5.00e-02 4.00e+02 ... (remaining 5988 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 325 2.58 - 3.16: 26941 3.16 - 3.74: 54229 3.74 - 4.32: 80406 4.32 - 4.90: 131567 Nonbonded interactions: 293468 Sorted by model distance: nonbonded pdb=" O ALA X 499 " pdb=" N ALA X 503 " model vdw 1.994 3.120 nonbonded pdb=" O ASN Z 514 " pdb=" CG2 VAL Z 517 " model vdw 2.031 3.460 nonbonded pdb=" O1G ATP T1001 " pdb="MG MG T1002 " model vdw 2.084 2.170 nonbonded pdb=" CD1 LEU E 78 " pdb=" OE2 GLU E 111 " model vdw 2.179 3.460 nonbonded pdb=" O ALA X 450 " pdb=" OG1 THR X 454 " model vdw 2.240 3.040 ... (remaining 293463 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and resid 85 through 1002) selection = (chain 'V' and resid 85 through 1002) } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.350 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.920 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:8.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.154 34384 Z= 0.515 Angle : 1.045 19.426 46598 Z= 0.594 Chirality : 0.063 0.330 5513 Planarity : 0.007 0.079 5991 Dihedral : 14.171 155.418 12560 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.69 % Favored : 95.09 % Rotamer: Outliers : 0.34 % Allowed : 6.57 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -3.91 (0.10), residues: 4457 helix: -3.02 (0.08), residues: 2120 sheet: -1.43 (0.21), residues: 543 loop : -2.17 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG X 98 TYR 0.022 0.003 TYR V 324 PHE 0.038 0.003 PHE S 249 TRP 0.021 0.003 TRP Y 141 HIS 0.011 0.002 HIS T 549 Details of bonding type rmsd/Z covalent geometry : bond 0.01199 / 0.51 (34384) covalent geometry : angle 1.04497 / 0.59 (46598) hydrogen bonds : bond 0.18830 / 12.49 ( 1708) hydrogen bonds : angle 7.94110 / 5.64 ( 4953) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 690 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 VAL cc_start: 0.8049 (t) cc_final: 0.7773 (t) REVERT: H 123 LEU cc_start: 0.7847 (mp) cc_final: 0.7539 (mp) REVERT: P 140 ASN cc_start: 0.8511 (m-40) cc_final: 0.8240 (m110) REVERT: P 149 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7946 (pptt) REVERT: R 31 LYS cc_start: 0.7867 (tmtt) cc_final: 0.7661 (tmtt) REVERT: R 40 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7717 (mtpt) REVERT: S 303 GLU cc_start: 0.7591 (mp0) cc_final: 0.7169 (mm-30) REVERT: U 348 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7047 (mt-10) REVERT: V 311 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7386 (mt-10) REVERT: V 471 GLN cc_start: 0.7636 (tt0) cc_final: 0.7351 (mm-40) REVERT: Z 90 MET cc_start: 0.8852 (mmp) cc_final: 0.8385 (mmt) REVERT: Z 437 ARG cc_start: 0.8447 (mtt-85) cc_final: 0.8193 (mtt-85) REVERT: Z 440 GLN cc_start: 0.8109 (mt0) cc_final: 0.7860 (mt0) outliers start: 12 outliers final: 7 residues processed: 701 average time/residue: 0.6869 time to fit residues: 577.8299 Evaluate side-chains 445 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 438 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN C 94 ASN F 98 GLN G 98 GLN P 59 GLN P 66 GLN P 71 GLN P 76 GLN Q 43 GLN Q 46 HIS R 38 ASN R 64 GLN R 73 ASN R 137 HIS R 154 GLN R 178 GLN R 181 ASN S 262 ASN S 267 HIS T 152 ASN ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS T 264 GLN T 358 HIS T 441 GLN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 GLN U 179 ASN U 242 GLN U 246 ASN U 248 GLN U 264 GLN U 271 GLN U 386 GLN U 539 ASN V 78 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN V 179 ASN V 196 GLN V 241 HIS V 244 ASN V 386 GLN V 452 GLN V 486 GLN V 497 GLN V 527 GLN X 144 HIS X 199 ASN X 278 GLN X 294 ASN ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Y 174 GLN Y 199 ASN Y 278 GLN Z 174 GLN Z 278 GLN Z 408 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104155 restraints weight = 50714.190| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.64 r_work: 0.3111 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34384 Z= 0.157 Angle : 0.612 12.141 46598 Z= 0.316 Chirality : 0.044 0.178 5513 Planarity : 0.005 0.061 5991 Dihedral : 6.721 137.623 4829 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 3.12 % Allowed : 14.55 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -2.14 (0.12), residues: 4457 helix: -1.19 (0.10), residues: 2169 sheet: -1.18 (0.21), residues: 577 loop : -1.57 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 169 TYR 0.017 0.001 TYR F 102 PHE 0.021 0.001 PHE B 107 TRP 0.006 0.001 TRP Y 141 HIS 0.004 0.001 HIS T 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (34384) covalent geometry : angle 0.61195 / 0.32 (46598) hydrogen bonds : bond 0.04135 / 2.74 ( 1708) hydrogen bonds : angle 5.12807 / 3.63 ( 4953) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 533 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8090 (ttm) REVERT: A 87 ASN cc_start: 0.7186 (t0) cc_final: 0.6906 (t0) REVERT: E 95 ILE cc_start: 0.8108 (pt) cc_final: 0.7505 (mm) REVERT: H 100 VAL cc_start: 0.8055 (t) cc_final: 0.7785 (p) REVERT: I 78 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8438 (tt) REVERT: P 66 GLN cc_start: 0.7341 (mt0) cc_final: 0.6932 (mt0) REVERT: P 140 ASN cc_start: 0.8959 (m-40) cc_final: 0.8706 (m-40) REVERT: P 149 LYS cc_start: 0.8449 (mtmt) cc_final: 0.7873 (pptt) REVERT: Q 43 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8081 (mm110) REVERT: R 53 ASN cc_start: 0.8456 (m110) cc_final: 0.8191 (m110) REVERT: R 127 PHE cc_start: 0.8472 (m-80) cc_final: 0.8225 (m-80) REVERT: R 152 LEU cc_start: 0.7370 (mt) cc_final: 0.7123 (mp) REVERT: S 41 GLN cc_start: 0.7244 (tp40) cc_final: 0.6844 (pm20) REVERT: S 96 ASN cc_start: 0.7676 (m-40) cc_final: 0.7322 (m110) REVERT: S 171 THR cc_start: 0.8776 (p) cc_final: 0.8568 (t) REVERT: S 220 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7874 (mm) REVERT: S 234 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7948 (tm-30) REVERT: T 471 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7789 (tp-100) REVERT: U 199 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7642 (mpt180) REVERT: U 348 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7997 (mt-10) REVERT: U 455 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6452 (mt-10) REVERT: U 522 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7617 (tp30) REVERT: V 67 ILE cc_start: 0.8023 (pp) cc_final: 0.7708 (mp) REVERT: V 311 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7826 (mt-10) REVERT: V 405 GLN cc_start: 0.8337 (pm20) cc_final: 0.8077 (mp10) REVERT: V 407 PHE cc_start: 0.8033 (t80) cc_final: 0.7631 (m-80) REVERT: V 452 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7448 (mp-120) REVERT: V 471 GLN cc_start: 0.7486 (tt0) cc_final: 0.6391 (mm110) REVERT: Y 419 ILE cc_start: 0.8200 (pt) cc_final: 0.7966 (mp) REVERT: Y 428 GLU cc_start: 0.7063 (pp20) cc_final: 0.6844 (pp20) REVERT: Y 550 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8466 (mtpt) REVERT: Z 90 MET cc_start: 0.9110 (mmp) cc_final: 0.8627 (mmt) REVERT: Z 127 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7957 (mt-10) REVERT: Z 278 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: Z 430 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7320 (mtpt) REVERT: Z 437 ARG cc_start: 0.8371 (mtt-85) cc_final: 0.7975 (mtt-85) REVERT: Z 440 GLN cc_start: 0.8115 (mt0) cc_final: 0.7737 (mt0) REVERT: Z 502 MET cc_start: 0.5862 (OUTLIER) cc_final: 0.5615 (mtp) outliers start: 111 outliers final: 38 residues processed: 608 average time/residue: 0.5954 time to fit residues: 442.1939 Evaluate side-chains 494 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 446 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 199 ARG Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 80 MET Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 550 LYS Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 278 GLN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 474 LEU Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 545 LEU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 328 optimal weight: 0.9990 chunk 388 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 253 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN J 87 ASN P 59 GLN P 76 GLN Q 43 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN S 45 GLN S 77 GLN S 267 HIS ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 179 ASN U 196 GLN V 78 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 527 GLN Z 241 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104544 restraints weight = 50402.034| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.71 r_work: 0.3101 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34384 Z= 0.134 Angle : 0.569 10.629 46598 Z= 0.290 Chirality : 0.043 0.200 5513 Planarity : 0.004 0.057 5991 Dihedral : 6.106 132.839 4827 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.57 % Favored : 96.28 % Rotamer: Outliers : 3.51 % Allowed : 16.93 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -1.22 (0.12), residues: 4457 helix: -0.34 (0.11), residues: 2161 sheet: -0.97 (0.22), residues: 577 loop : -1.19 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 385 TYR 0.020 0.001 TYR F 102 PHE 0.022 0.001 PHE Y 453 TRP 0.005 0.001 TRP Z 141 HIS 0.003 0.001 HIS T 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (34384) covalent geometry : angle 0.56919 / 0.29 (46598) hydrogen bonds : bond 0.03671 / 2.44 ( 1708) hydrogen bonds : angle 4.68433 / 3.29 ( 4953) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 509 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 61 MET cc_start: 0.6626 (mpp) cc_final: 0.6333 (mmt) REVERT: G 116 PHE cc_start: 0.5721 (OUTLIER) cc_final: 0.5156 (t80) REVERT: H 100 VAL cc_start: 0.7782 (t) cc_final: 0.7548 (p) REVERT: H 105 LEU cc_start: 0.7306 (tt) cc_final: 0.6197 (mm) REVERT: I 60 LYS cc_start: 0.7041 (mtmm) cc_final: 0.6693 (mtpp) REVERT: I 78 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8413 (tt) REVERT: J 61 MET cc_start: 0.6786 (mmp) cc_final: 0.6573 (mpp) REVERT: P 49 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8267 (m) REVERT: P 136 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8177 (mt-10) REVERT: P 140 ASN cc_start: 0.8962 (m-40) cc_final: 0.8614 (m-40) REVERT: P 149 LYS cc_start: 0.8496 (mtmt) cc_final: 0.7749 (pptt) REVERT: Q 32 LYS cc_start: 0.6043 (mtmm) cc_final: 0.5819 (mtmm) REVERT: Q 43 GLN cc_start: 0.8061 (mt0) cc_final: 0.7804 (mt0) REVERT: R 53 ASN cc_start: 0.8575 (m110) cc_final: 0.8360 (m110) REVERT: R 152 LEU cc_start: 0.7437 (mt) cc_final: 0.7199 (mp) REVERT: S 79 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.8054 (mtt-85) REVERT: S 96 ASN cc_start: 0.7618 (m-40) cc_final: 0.7251 (m110) REVERT: S 144 ASP cc_start: 0.6570 (m-30) cc_final: 0.6367 (m-30) REVERT: S 147 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7140 (ppt90) REVERT: S 220 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7845 (mm) REVERT: S 234 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7608 (tm-30) REVERT: T 407 PHE cc_start: 0.8207 (t80) cc_final: 0.8002 (m-80) REVERT: T 487 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8344 (mtmm) REVERT: T 522 GLU cc_start: 0.8405 (tp30) cc_final: 0.8189 (tm-30) REVERT: U 197 SER cc_start: 0.9066 (p) cc_final: 0.8558 (p) REVERT: U 199 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7571 (mpt180) REVERT: U 348 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8169 (mt-10) REVERT: U 455 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6535 (mt-10) REVERT: U 483 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7461 (tpp) REVERT: U 522 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: V 67 ILE cc_start: 0.8006 (pp) cc_final: 0.7777 (mp) REVERT: V 405 GLN cc_start: 0.8390 (pm20) cc_final: 0.8123 (mp10) REVERT: V 407 PHE cc_start: 0.8050 (t80) cc_final: 0.7751 (m-80) REVERT: V 471 GLN cc_start: 0.7341 (tt0) cc_final: 0.6463 (mm110) REVERT: X 194 MET cc_start: 0.9026 (mtm) cc_final: 0.8816 (mtm) REVERT: X 451 GLU cc_start: 0.8204 (pt0) cc_final: 0.7982 (pt0) REVERT: X 474 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7316 (mm) REVERT: Y 365 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8828 (m) REVERT: Y 428 GLU cc_start: 0.7085 (pp20) cc_final: 0.6874 (pp20) REVERT: Y 480 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7578 (p0) REVERT: Y 550 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8365 (mtpt) REVERT: Z 90 MET cc_start: 0.9117 (mmp) cc_final: 0.8900 (mmt) REVERT: Z 127 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8070 (mt-10) REVERT: Z 440 GLN cc_start: 0.8123 (mt0) cc_final: 0.7725 (mt0) REVERT: Z 502 MET cc_start: 0.5897 (OUTLIER) cc_final: 0.5661 (mtp) outliers start: 125 outliers final: 42 residues processed: 593 average time/residue: 0.6116 time to fit residues: 444.6362 Evaluate side-chains 475 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 419 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 517 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 199 ARG Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 550 LYS Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 474 LEU Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 96 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 414 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 312 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 387 optimal weight: 0.0030 chunk 273 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 98 GLN D 98 GLN J 92 ASN P 76 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 267 HIS ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN T 539 ASN U 152 ASN U 179 ASN V 78 GLN V 126 HIS X 241 ASN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 574 ASN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104148 restraints weight = 50058.775| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.65 r_work: 0.3100 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34384 Z= 0.158 Angle : 0.577 9.253 46598 Z= 0.293 Chirality : 0.044 0.172 5513 Planarity : 0.004 0.051 5991 Dihedral : 6.019 124.970 4827 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.75 % Favored : 96.14 % Rotamer: Outliers : 3.96 % Allowed : 17.92 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -0.81 (0.13), residues: 4457 helix: 0.01 (0.11), residues: 2178 sheet: -0.90 (0.22), residues: 572 loop : -0.95 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 385 TYR 0.021 0.001 TYR P 141 PHE 0.024 0.001 PHE B 107 TRP 0.007 0.001 TRP U 73 HIS 0.004 0.001 HIS T 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (34384) covalent geometry : angle 0.57667 / 0.29 (46598) hydrogen bonds : bond 0.03693 / 2.45 ( 1708) hydrogen bonds : angle 4.53537 / 3.18 ( 4953) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 472 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 98 GLN cc_start: 0.7732 (tt0) cc_final: 0.7520 (tt0) REVERT: E 95 ILE cc_start: 0.8024 (pt) cc_final: 0.7684 (mm) REVERT: G 116 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.5316 (t80) REVERT: G 123 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7822 (mp) REVERT: H 80 VAL cc_start: 0.8207 (p) cc_final: 0.7986 (m) REVERT: H 100 VAL cc_start: 0.7622 (t) cc_final: 0.7392 (p) REVERT: H 105 LEU cc_start: 0.7295 (tt) cc_final: 0.6138 (mm) REVERT: J 78 LEU cc_start: 0.8704 (mt) cc_final: 0.8412 (tp) REVERT: P 49 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8263 (m) REVERT: P 66 GLN cc_start: 0.7037 (mt0) cc_final: 0.6664 (mp10) REVERT: P 136 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8191 (mt-10) REVERT: P 140 ASN cc_start: 0.9027 (m-40) cc_final: 0.8652 (m-40) REVERT: P 149 LYS cc_start: 0.8514 (mtmt) cc_final: 0.7806 (pptt) REVERT: Q 25 ASP cc_start: 0.7247 (m-30) cc_final: 0.6811 (m-30) REVERT: Q 32 LYS cc_start: 0.5956 (mtmm) cc_final: 0.5686 (mtmm) REVERT: R 152 LEU cc_start: 0.7400 (mt) cc_final: 0.7149 (mp) REVERT: S 96 ASN cc_start: 0.7728 (m-40) cc_final: 0.7272 (m110) REVERT: S 124 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.7482 (mmp80) REVERT: S 144 ASP cc_start: 0.6631 (m-30) cc_final: 0.6413 (m-30) REVERT: S 147 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7107 (ppt90) REVERT: S 220 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7901 (mm) REVERT: S 234 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7630 (tm-30) REVERT: T 249 VAL cc_start: 0.8800 (t) cc_final: 0.8594 (p) REVERT: T 287 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8269 (tpp) REVERT: T 471 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7744 (tp-100) REVERT: T 487 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8322 (mtmm) REVERT: T 502 TYR cc_start: 0.7988 (t80) cc_final: 0.7094 (t80) REVERT: U 348 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8111 (mt-10) REVERT: U 455 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6624 (mp0) REVERT: U 522 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: V 405 GLN cc_start: 0.8403 (pm20) cc_final: 0.8142 (mp10) REVERT: V 407 PHE cc_start: 0.7964 (t80) cc_final: 0.7692 (m-80) REVERT: V 471 GLN cc_start: 0.7441 (tt0) cc_final: 0.6598 (mm110) REVERT: V 549 HIS cc_start: 0.7100 (OUTLIER) cc_final: 0.6895 (m-70) REVERT: V 550 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7186 (tt) REVERT: X 194 MET cc_start: 0.9055 (mtm) cc_final: 0.8818 (mtm) REVERT: X 429 ASP cc_start: 0.8063 (m-30) cc_final: 0.7795 (m-30) REVERT: X 451 GLU cc_start: 0.8208 (pt0) cc_final: 0.7985 (pt0) REVERT: X 474 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7393 (mm) REVERT: X 497 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: Y 365 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8790 (m) REVERT: Y 550 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8398 (mtpt) REVERT: Z 90 MET cc_start: 0.9143 (mmp) cc_final: 0.8683 (mmt) REVERT: Z 127 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8038 (mt-10) REVERT: Z 278 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6918 (pm20) REVERT: Z 370 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7782 (mm-30) REVERT: Z 440 GLN cc_start: 0.8240 (mt0) cc_final: 0.7841 (mt0) REVERT: Z 502 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5711 (mtp) outliers start: 141 outliers final: 61 residues processed: 570 average time/residue: 0.5845 time to fit residues: 411.4579 Evaluate side-chains 488 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 410 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 419 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 550 LYS Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 278 GLN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 474 LEU Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 3 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 chunk 124 optimal weight: 0.0770 chunk 266 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 428 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 43 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN U 152 ASN U 179 ASN V 78 GLN V 219 GLN Z 278 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105499 restraints weight = 50557.732| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.61 r_work: 0.3109 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34384 Z= 0.131 Angle : 0.560 12.251 46598 Z= 0.283 Chirality : 0.043 0.330 5513 Planarity : 0.004 0.049 5991 Dihedral : 5.829 121.804 4827 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 3.99 % Allowed : 18.81 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -0.53 (0.13), residues: 4457 helix: 0.28 (0.11), residues: 2178 sheet: -0.86 (0.21), residues: 594 loop : -0.83 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 385 TYR 0.018 0.001 TYR T 414 PHE 0.020 0.001 PHE Y 453 TRP 0.024 0.001 TRP U 73 HIS 0.004 0.001 HIS T 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (34384) covalent geometry : angle 0.55957 / 0.28 (46598) hydrogen bonds : bond 0.03467 / 2.31 ( 1708) hydrogen bonds : angle 4.40017 / 3.08 ( 4953) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 467 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8459 (t0) cc_final: 0.7790 (t0) REVERT: D 98 GLN cc_start: 0.7807 (tt0) cc_final: 0.7570 (tt0) REVERT: E 95 ILE cc_start: 0.8050 (pt) cc_final: 0.7668 (mm) REVERT: G 116 PHE cc_start: 0.6100 (OUTLIER) cc_final: 0.5557 (t80) REVERT: G 123 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7831 (mp) REVERT: H 80 VAL cc_start: 0.8289 (p) cc_final: 0.8044 (m) REVERT: H 100 VAL cc_start: 0.7536 (t) cc_final: 0.7322 (p) REVERT: H 105 LEU cc_start: 0.7075 (tt) cc_final: 0.6120 (mm) REVERT: H 115 LEU cc_start: 0.7907 (mm) cc_final: 0.7693 (mt) REVERT: I 60 LYS cc_start: 0.7239 (mtmm) cc_final: 0.6878 (mtmm) REVERT: P 49 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8216 (m) REVERT: P 136 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8184 (mt-10) REVERT: P 140 ASN cc_start: 0.9006 (m-40) cc_final: 0.8658 (m-40) REVERT: P 149 LYS cc_start: 0.8510 (mtmt) cc_final: 0.7829 (pptt) REVERT: R 127 PHE cc_start: 0.8157 (m-80) cc_final: 0.7888 (m-80) REVERT: R 152 LEU cc_start: 0.7368 (mt) cc_final: 0.7120 (mp) REVERT: R 188 TYR cc_start: 0.7470 (m-80) cc_final: 0.7233 (m-80) REVERT: S 96 ASN cc_start: 0.7605 (m-40) cc_final: 0.7146 (m110) REVERT: S 121 LYS cc_start: 0.8471 (mtpp) cc_final: 0.7844 (mmtt) REVERT: S 124 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7450 (mmp80) REVERT: S 147 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7181 (ppt90) REVERT: S 220 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7891 (mm) REVERT: S 234 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7642 (tm-30) REVERT: S 271 MET cc_start: 0.8690 (ttp) cc_final: 0.8475 (ttt) REVERT: T 287 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8317 (tpp) REVERT: T 471 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7751 (tp-100) REVERT: T 487 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8339 (mtmm) REVERT: U 455 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6610 (mp0) REVERT: U 509 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8263 (mp) REVERT: U 521 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6919 (tm-30) REVERT: V 52 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6859 (pttm) REVERT: V 405 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: V 407 PHE cc_start: 0.7943 (t80) cc_final: 0.7727 (m-80) REVERT: V 452 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7097 (mt0) REVERT: V 471 GLN cc_start: 0.7434 (tt0) cc_final: 0.6588 (mm110) REVERT: X 194 MET cc_start: 0.9039 (mtm) cc_final: 0.8817 (mtm) REVERT: X 414 GLN cc_start: 0.7735 (tt0) cc_final: 0.7368 (tm-30) REVERT: X 429 ASP cc_start: 0.8094 (m-30) cc_final: 0.7843 (m-30) REVERT: X 451 GLU cc_start: 0.8256 (pt0) cc_final: 0.8006 (pt0) REVERT: X 474 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7399 (mm) REVERT: Y 365 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8812 (m) REVERT: Y 550 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8336 (mtpt) REVERT: Z 90 MET cc_start: 0.9150 (mmp) cc_final: 0.8700 (mmt) REVERT: Z 127 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8113 (mt-10) REVERT: Z 370 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: Z 440 GLN cc_start: 0.8229 (mt0) cc_final: 0.7829 (mt0) REVERT: Z 502 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.5731 (mtp) outliers start: 142 outliers final: 64 residues processed: 565 average time/residue: 0.6151 time to fit residues: 426.2850 Evaluate side-chains 504 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 424 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 419 ILE Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 550 LYS Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 474 LEU Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 158 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 371 optimal weight: 5.9990 chunk 337 optimal weight: 0.0970 chunk 239 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 429 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 252 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 43 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 267 HIS T 179 ASN ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN U 152 ASN V 78 GLN V 219 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 388 ASN ** 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 = 0.3665 r_free = 0.3665 target = 0.136286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106793 restraints weight = 50236.554| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.62 r_work: 0.3141 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34384 Z= 0.114 Angle : 0.550 14.725 46598 Z= 0.277 Chirality : 0.043 0.405 5513 Planarity : 0.004 0.048 5991 Dihedral : 5.639 118.354 4827 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.50 % Rotamer: Outliers : 3.85 % Allowed : 19.49 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -0.27 (0.13), residues: 4457 helix: 0.51 (0.12), residues: 2182 sheet: -0.82 (0.22), residues: 590 loop : -0.69 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 385 TYR 0.016 0.001 TYR P 141 PHE 0.027 0.001 PHE B 107 TRP 0.014 0.001 TRP U 73 HIS 0.003 0.001 HIS Z 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (34384) covalent geometry : angle 0.55044 / 0.28 (46598) hydrogen bonds : bond 0.03287 / 2.20 ( 1708) hydrogen bonds : angle 4.29466 / 3.00 ( 4953) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 485 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8476 (t0) cc_final: 0.7795 (t0) REVERT: D 61 MET cc_start: 0.6608 (mpp) cc_final: 0.6249 (mmt) REVERT: D 98 GLN cc_start: 0.7817 (tt0) cc_final: 0.7613 (tt0) REVERT: E 95 ILE cc_start: 0.7986 (pt) cc_final: 0.7603 (mm) REVERT: F 104 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7054 (mp) REVERT: G 116 PHE cc_start: 0.6070 (m-80) cc_final: 0.5538 (t80) REVERT: G 123 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7679 (mp) REVERT: G 124 ILE cc_start: 0.8298 (mm) cc_final: 0.7851 (mp) REVERT: H 80 VAL cc_start: 0.8208 (p) cc_final: 0.7977 (m) REVERT: H 105 LEU cc_start: 0.7001 (tt) cc_final: 0.6112 (mm) REVERT: I 60 LYS cc_start: 0.7231 (mtmm) cc_final: 0.6764 (mtmm) REVERT: J 78 LEU cc_start: 0.8684 (mt) cc_final: 0.8394 (tp) REVERT: J 125 LEU cc_start: 0.7291 (mt) cc_final: 0.7067 (mm) REVERT: P 49 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8236 (m) REVERT: P 136 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8197 (mt-10) REVERT: P 140 ASN cc_start: 0.8971 (m-40) cc_final: 0.8622 (m-40) REVERT: P 149 LYS cc_start: 0.8486 (mtmt) cc_final: 0.7750 (pptt) REVERT: R 127 PHE cc_start: 0.8122 (m-80) cc_final: 0.7840 (m-80) REVERT: R 152 LEU cc_start: 0.7339 (mt) cc_final: 0.7101 (mp) REVERT: S 96 ASN cc_start: 0.7382 (m-40) cc_final: 0.6898 (m110) REVERT: S 121 LYS cc_start: 0.8437 (mtpp) cc_final: 0.7835 (mmtt) REVERT: S 124 ARG cc_start: 0.7738 (ttp-170) cc_final: 0.7479 (mmp80) REVERT: S 147 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7191 (ppt90) REVERT: S 220 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7851 (mm) REVERT: S 234 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7594 (tm-30) REVERT: S 271 MET cc_start: 0.8643 (ttp) cc_final: 0.8417 (ttt) REVERT: T 471 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7727 (tp-100) REVERT: T 487 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8325 (mtmm) REVERT: T 516 ASP cc_start: 0.7481 (m-30) cc_final: 0.7085 (t0) REVERT: U 509 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8194 (mp) REVERT: V 52 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6872 (pttm) REVERT: V 405 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: V 452 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7089 (mt0) REVERT: V 516 ASP cc_start: 0.7916 (t0) cc_final: 0.7616 (t0) REVERT: X 55 GLU cc_start: 0.7535 (tp30) cc_final: 0.7289 (tm-30) REVERT: X 101 LYS cc_start: 0.9147 (tttt) cc_final: 0.8267 (mptt) REVERT: X 414 GLN cc_start: 0.7822 (tt0) cc_final: 0.7438 (tm-30) REVERT: X 429 ASP cc_start: 0.8055 (m-30) cc_final: 0.7840 (m-30) REVERT: X 451 GLU cc_start: 0.8239 (pt0) cc_final: 0.7916 (pt0) REVERT: X 474 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7442 (mm) REVERT: X 528 ASP cc_start: 0.8312 (m-30) cc_final: 0.7628 (t70) REVERT: X 550 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7051 (mmmt) REVERT: Y 155 THR cc_start: 0.9118 (p) cc_final: 0.8856 (p) REVERT: Y 365 SER cc_start: 0.9014 (OUTLIER) cc_final: 0.8772 (m) REVERT: Z 430 LYS cc_start: 0.7407 (ttmt) cc_final: 0.7015 (mtpt) REVERT: Z 437 ARG cc_start: 0.8461 (mtt-85) cc_final: 0.8250 (mtp-110) REVERT: Z 502 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5709 (mtp) outliers start: 137 outliers final: 61 residues processed: 573 average time/residue: 0.5806 time to fit residues: 409.7662 Evaluate side-chains 507 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 432 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain U residue 442 VAL Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 282 MET Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 391 SER Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 550 LYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 480 ASP Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 440 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 364 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 344 optimal weight: 0.4980 chunk 184 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 92 ASN P 76 GLN Q 43 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 179 ASN ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN V 179 ASN X 250 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.135637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106316 restraints weight = 50322.482| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.66 r_work: 0.3135 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34384 Z= 0.124 Angle : 0.555 9.572 46598 Z= 0.281 Chirality : 0.043 0.295 5513 Planarity : 0.004 0.086 5991 Dihedral : 5.577 114.861 4827 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 3.48 % Allowed : 20.44 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -0.14 (0.13), residues: 4457 helix: 0.62 (0.12), residues: 2187 sheet: -0.80 (0.21), residues: 595 loop : -0.63 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Y 385 TYR 0.021 0.001 TYR T 502 PHE 0.027 0.001 PHE D 107 TRP 0.011 0.001 TRP U 73 HIS 0.005 0.001 HIS T 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (34384) covalent geometry : angle 0.55516 / 0.28 (46598) hydrogen bonds : bond 0.03329 / 2.22 ( 1708) hydrogen bonds : angle 4.26611 / 2.98 ( 4953) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 464 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8434 (t0) cc_final: 0.7738 (t0) REVERT: D 61 MET cc_start: 0.6666 (mpp) cc_final: 0.6270 (mmt) REVERT: E 95 ILE cc_start: 0.7987 (pt) cc_final: 0.7616 (mm) REVERT: G 123 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7751 (mp) REVERT: G 124 ILE cc_start: 0.8273 (mm) cc_final: 0.7823 (mp) REVERT: H 100 VAL cc_start: 0.8428 (p) cc_final: 0.8139 (t) REVERT: H 105 LEU cc_start: 0.6965 (tt) cc_final: 0.6093 (mm) REVERT: H 115 LEU cc_start: 0.7923 (mm) cc_final: 0.7708 (mt) REVERT: J 78 LEU cc_start: 0.8680 (mt) cc_final: 0.8415 (tp) REVERT: P 49 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8173 (m) REVERT: P 149 LYS cc_start: 0.8505 (mtmt) cc_final: 0.7787 (pptt) REVERT: Q 32 LYS cc_start: 0.5855 (mtmm) cc_final: 0.5564 (mttp) REVERT: R 127 PHE cc_start: 0.8162 (m-80) cc_final: 0.7863 (m-80) REVERT: R 152 LEU cc_start: 0.7305 (mt) cc_final: 0.7062 (mp) REVERT: S 96 ASN cc_start: 0.7390 (m-40) cc_final: 0.6894 (m110) REVERT: S 121 LYS cc_start: 0.8440 (mtpp) cc_final: 0.7834 (mmtt) REVERT: S 124 ARG cc_start: 0.7753 (ttp-170) cc_final: 0.7467 (mmp80) REVERT: S 147 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7211 (ppt90) REVERT: S 220 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7878 (mm) REVERT: S 234 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7614 (tm-30) REVERT: S 271 MET cc_start: 0.8645 (ttp) cc_final: 0.8408 (ttt) REVERT: T 247 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: T 249 VAL cc_start: 0.8810 (t) cc_final: 0.8604 (p) REVERT: T 471 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7760 (tp-100) REVERT: T 487 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8313 (mtmm) REVERT: T 516 ASP cc_start: 0.7540 (m-30) cc_final: 0.6935 (t0) REVERT: U 465 ASP cc_start: 0.5083 (OUTLIER) cc_final: 0.4733 (m-30) REVERT: U 509 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8185 (mp) REVERT: U 521 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6650 (tm-30) REVERT: V 52 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6882 (pttm) REVERT: V 471 GLN cc_start: 0.7496 (tt0) cc_final: 0.6622 (mm110) REVERT: V 516 ASP cc_start: 0.8033 (t0) cc_final: 0.7722 (t0) REVERT: X 55 GLU cc_start: 0.7544 (tp30) cc_final: 0.7292 (tm-30) REVERT: X 101 LYS cc_start: 0.9142 (tttt) cc_final: 0.8256 (mptt) REVERT: X 414 GLN cc_start: 0.7800 (tt0) cc_final: 0.7463 (tm-30) REVERT: X 429 ASP cc_start: 0.8067 (m-30) cc_final: 0.7823 (m-30) REVERT: X 451 GLU cc_start: 0.8244 (pt0) cc_final: 0.7938 (pt0) REVERT: X 474 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7417 (mm) REVERT: X 550 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6925 (mmmt) REVERT: Y 155 THR cc_start: 0.9113 (p) cc_final: 0.8854 (p) REVERT: Y 181 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9064 (mt) REVERT: Y 365 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8829 (m) REVERT: Z 430 LYS cc_start: 0.7345 (ttmt) cc_final: 0.6845 (mtpt) REVERT: Z 440 GLN cc_start: 0.8320 (mt0) cc_final: 0.7935 (mt0) REVERT: Z 488 MET cc_start: 0.8512 (tpp) cc_final: 0.7707 (mpp) REVERT: Z 502 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5702 (mtp) outliers start: 124 outliers final: 64 residues processed: 547 average time/residue: 0.5672 time to fit residues: 383.9773 Evaluate side-chains 506 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 428 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 247 GLU Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 487 LYS Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 442 VAL Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 282 MET Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 391 SER Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 550 LYS Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 241 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 415 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 376 optimal weight: 0.9990 chunk 386 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 346 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 GLN P 71 GLN P 140 ASN Q 43 GLN R 154 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN U 152 ASN V 78 GLN X 250 GLN Y 278 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.133856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104075 restraints weight = 50329.348| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.61 r_work: 0.3118 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34384 Z= 0.157 Angle : 0.586 11.491 46598 Z= 0.296 Chirality : 0.044 0.272 5513 Planarity : 0.004 0.069 5991 Dihedral : 5.663 112.862 4826 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.61 % Favored : 96.32 % Rotamer: Outliers : 3.48 % Allowed : 20.86 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -0.16 (0.13), residues: 4457 helix: 0.61 (0.11), residues: 2190 sheet: -0.83 (0.21), residues: 592 loop : -0.64 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Y 385 TYR 0.022 0.001 TYR T 502 PHE 0.028 0.001 PHE B 107 TRP 0.009 0.001 TRP U 73 HIS 0.005 0.001 HIS T 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (34384) covalent geometry : angle 0.58578 / 0.30 (46598) hydrogen bonds : bond 0.03528 / 2.35 ( 1708) hydrogen bonds : angle 4.33453 / 3.03 ( 4953) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 451 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8475 (t0) cc_final: 0.7712 (t0) REVERT: E 95 ILE cc_start: 0.7860 (pt) cc_final: 0.7544 (mm) REVERT: F 104 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7010 (mp) REVERT: G 123 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7837 (mp) REVERT: G 124 ILE cc_start: 0.8159 (mm) cc_final: 0.7739 (mp) REVERT: H 80 VAL cc_start: 0.8368 (p) cc_final: 0.8119 (m) REVERT: H 105 LEU cc_start: 0.7002 (tt) cc_final: 0.6105 (mm) REVERT: P 49 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8175 (m) REVERT: R 127 PHE cc_start: 0.8136 (m-80) cc_final: 0.7867 (m-80) REVERT: R 152 LEU cc_start: 0.7304 (mt) cc_final: 0.7041 (mp) REVERT: S 96 ASN cc_start: 0.7528 (m-40) cc_final: 0.7032 (m110) REVERT: S 121 LYS cc_start: 0.8472 (mtpp) cc_final: 0.7837 (mmtt) REVERT: S 124 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7481 (mmp80) REVERT: S 147 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7188 (ppt90) REVERT: S 220 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7902 (mm) REVERT: S 234 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7595 (tm-30) REVERT: T 287 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8314 (tpp) REVERT: T 471 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7662 (tp-100) REVERT: T 516 ASP cc_start: 0.7536 (m-30) cc_final: 0.6901 (t0) REVERT: U 509 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8276 (mp) REVERT: V 52 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6850 (pttm) REVERT: V 471 GLN cc_start: 0.7537 (tt0) cc_final: 0.6660 (mm110) REVERT: V 516 ASP cc_start: 0.8054 (t0) cc_final: 0.7742 (t0) REVERT: X 55 GLU cc_start: 0.7547 (tp30) cc_final: 0.7304 (tm-30) REVERT: X 414 GLN cc_start: 0.7801 (tt0) cc_final: 0.7471 (tm-30) REVERT: X 429 ASP cc_start: 0.8026 (m-30) cc_final: 0.7759 (m-30) REVERT: X 441 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7587 (mpt180) REVERT: X 451 GLU cc_start: 0.8235 (pt0) cc_final: 0.8024 (pt0) REVERT: X 474 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7433 (mm) REVERT: X 550 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6837 (mmmt) REVERT: Y 70 VAL cc_start: 0.8900 (m) cc_final: 0.8642 (p) REVERT: Y 155 THR cc_start: 0.9134 (p) cc_final: 0.8877 (p) REVERT: Y 365 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8827 (m) REVERT: Z 430 LYS cc_start: 0.7307 (ttmt) cc_final: 0.6818 (mtpt) REVERT: Z 502 MET cc_start: 0.5935 (OUTLIER) cc_final: 0.5711 (mtp) outliers start: 124 outliers final: 73 residues processed: 535 average time/residue: 0.6077 time to fit residues: 399.5719 Evaluate side-chains 514 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 428 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 442 VAL Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 391 SER Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 441 ARG Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 550 LYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 332 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 384 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 418 optimal weight: 0.6980 chunk 258 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN D 98 GLN E 98 GLN P 71 GLN P 140 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN U 152 ASN V 78 GLN X 250 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.133829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103991 restraints weight = 50115.640| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.62 r_work: 0.3116 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34384 Z= 0.154 Angle : 0.589 13.963 46598 Z= 0.296 Chirality : 0.044 0.252 5513 Planarity : 0.004 0.063 5991 Dihedral : 5.645 114.154 4826 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.61 % Favored : 96.32 % Rotamer: Outliers : 3.20 % Allowed : 21.51 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -0.14 (0.13), residues: 4457 helix: 0.62 (0.11), residues: 2193 sheet: -0.80 (0.22), residues: 580 loop : -0.64 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 385 TYR 0.022 0.001 TYR T 414 PHE 0.032 0.001 PHE D 107 TRP 0.024 0.001 TRP U 73 HIS 0.005 0.001 HIS T 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (34384) covalent geometry : angle 0.58935 / 0.30 (46598) hydrogen bonds : bond 0.03527 / 2.35 ( 1708) hydrogen bonds : angle 4.35984 / 3.05 ( 4953) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 446 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8481 (t0) cc_final: 0.7692 (t0) REVERT: D 61 MET cc_start: 0.6527 (mpp) cc_final: 0.6214 (mmt) REVERT: E 95 ILE cc_start: 0.8000 (pt) cc_final: 0.7626 (mm) REVERT: F 104 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6980 (mp) REVERT: G 116 PHE cc_start: 0.6100 (OUTLIER) cc_final: 0.5540 (t80) REVERT: G 123 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7808 (mp) REVERT: G 124 ILE cc_start: 0.8121 (mm) cc_final: 0.7228 (mp) REVERT: H 80 VAL cc_start: 0.8414 (p) cc_final: 0.8165 (m) REVERT: H 105 LEU cc_start: 0.6970 (tt) cc_final: 0.6085 (mm) REVERT: J 61 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6231 (mmp) REVERT: J 78 LEU cc_start: 0.8693 (mt) cc_final: 0.8468 (tp) REVERT: P 49 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8136 (m) REVERT: Q 32 LYS cc_start: 0.5670 (mtmm) cc_final: 0.5257 (pttm) REVERT: R 127 PHE cc_start: 0.8145 (m-80) cc_final: 0.7854 (m-80) REVERT: R 152 LEU cc_start: 0.7330 (mt) cc_final: 0.7121 (mp) REVERT: S 96 ASN cc_start: 0.7536 (m-40) cc_final: 0.7016 (m110) REVERT: S 121 LYS cc_start: 0.8488 (mtpp) cc_final: 0.7854 (mmtt) REVERT: S 124 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7527 (mmp80) REVERT: S 147 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7165 (ppt90) REVERT: S 220 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7847 (mm) REVERT: S 234 GLU cc_start: 0.8519 (tm-30) cc_final: 0.7698 (tm-30) REVERT: T 287 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8340 (tpp) REVERT: T 471 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7666 (tp-100) REVERT: T 516 ASP cc_start: 0.7545 (m-30) cc_final: 0.6970 (t0) REVERT: V 52 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6862 (pttm) REVERT: V 287 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7816 (mtp) REVERT: V 471 GLN cc_start: 0.7569 (tt0) cc_final: 0.6703 (mm110) REVERT: V 516 ASP cc_start: 0.8016 (t0) cc_final: 0.7737 (t0) REVERT: X 55 GLU cc_start: 0.7566 (tp30) cc_final: 0.7331 (tm-30) REVERT: X 414 GLN cc_start: 0.7751 (tt0) cc_final: 0.7425 (tm-30) REVERT: X 429 ASP cc_start: 0.8055 (m-30) cc_final: 0.7762 (m-30) REVERT: X 441 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7592 (mpt180) REVERT: X 451 GLU cc_start: 0.8212 (pt0) cc_final: 0.8009 (pt0) REVERT: X 474 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7434 (mm) REVERT: X 550 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6830 (mmmt) REVERT: Y 70 VAL cc_start: 0.8898 (m) cc_final: 0.8635 (p) REVERT: Y 155 THR cc_start: 0.9134 (p) cc_final: 0.8874 (p) REVERT: Y 365 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8810 (m) REVERT: Y 497 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: Z 395 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: Z 430 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6863 (mtpt) REVERT: Z 488 MET cc_start: 0.8576 (tpp) cc_final: 0.7640 (mpp) REVERT: Z 502 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.5706 (mtp) outliers start: 114 outliers final: 71 residues processed: 518 average time/residue: 0.6181 time to fit residues: 394.8347 Evaluate side-chains 508 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 420 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 391 SER Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 441 ARG Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 550 LYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 497 GLU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 146 optimal weight: 4.9990 chunk 399 optimal weight: 0.3980 chunk 93 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 413 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 434 optimal weight: 0.9990 chunk 364 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN D 98 GLN P 59 GLN P 71 GLN P 140 ASN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN T 529 ASN U 152 ASN U 241 HIS V 78 GLN X 250 GLN Y 278 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 412 ASN Y 471 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.136850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107287 restraints weight = 50354.019| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.67 r_work: 0.3154 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34384 Z= 0.115 Angle : 0.565 13.527 46598 Z= 0.282 Chirality : 0.043 0.230 5513 Planarity : 0.004 0.052 5991 Dihedral : 5.361 111.539 4826 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 2.61 % Allowed : 21.96 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.02 (0.13), residues: 4457 helix: 0.77 (0.12), residues: 2201 sheet: -0.68 (0.22), residues: 564 loop : -0.60 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 385 TYR 0.021 0.001 TYR T 502 PHE 0.029 0.001 PHE B 107 TRP 0.032 0.001 TRP U 73 HIS 0.005 0.001 HIS T 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (34384) covalent geometry : angle 0.56478 / 0.28 (46598) hydrogen bonds : bond 0.03240 / 2.17 ( 1708) hydrogen bonds : angle 4.26177 / 2.98 ( 4953) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 477 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8447 (t0) cc_final: 0.7768 (t0) REVERT: D 61 MET cc_start: 0.6512 (mpp) cc_final: 0.6107 (mmt) REVERT: E 95 ILE cc_start: 0.7730 (pt) cc_final: 0.7413 (mm) REVERT: F 104 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6808 (mp) REVERT: G 123 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7837 (mp) REVERT: G 124 ILE cc_start: 0.7986 (mm) cc_final: 0.7679 (mp) REVERT: H 80 VAL cc_start: 0.8347 (p) cc_final: 0.8106 (m) REVERT: H 105 LEU cc_start: 0.6810 (tt) cc_final: 0.6055 (mm) REVERT: H 111 GLU cc_start: 0.7493 (tt0) cc_final: 0.7205 (tp30) REVERT: J 60 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7247 (tppp) REVERT: Q 32 LYS cc_start: 0.5676 (mtmm) cc_final: 0.5152 (pttt) REVERT: R 127 PHE cc_start: 0.8071 (m-80) cc_final: 0.7819 (m-80) REVERT: R 152 LEU cc_start: 0.7309 (mt) cc_final: 0.7065 (mp) REVERT: S 73 ILE cc_start: 0.8207 (pp) cc_final: 0.7852 (tp) REVERT: S 96 ASN cc_start: 0.7359 (m-40) cc_final: 0.6870 (m110) REVERT: S 121 LYS cc_start: 0.8452 (mtpp) cc_final: 0.7858 (mmtt) REVERT: S 147 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7145 (ppt170) REVERT: S 234 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7772 (tm-30) REVERT: T 471 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7689 (tp-100) REVERT: T 511 LYS cc_start: 0.8356 (pptt) cc_final: 0.7584 (ptpp) REVERT: T 516 ASP cc_start: 0.7427 (m-30) cc_final: 0.7021 (t0) REVERT: U 465 ASP cc_start: 0.4969 (OUTLIER) cc_final: 0.4740 (m-30) REVERT: V 471 GLN cc_start: 0.7511 (tt0) cc_final: 0.6651 (mm110) REVERT: V 516 ASP cc_start: 0.8037 (t0) cc_final: 0.7740 (t0) REVERT: X 55 GLU cc_start: 0.7623 (tp30) cc_final: 0.7375 (tm-30) REVERT: X 414 GLN cc_start: 0.7776 (tt0) cc_final: 0.7410 (tm-30) REVERT: X 429 ASP cc_start: 0.8027 (m-30) cc_final: 0.7735 (m-30) REVERT: X 441 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7879 (mpt180) REVERT: X 451 GLU cc_start: 0.8208 (pt0) cc_final: 0.7975 (pt0) REVERT: X 474 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7404 (mm) REVERT: X 502 MET cc_start: 0.7518 (ttm) cc_final: 0.6709 (mtp) REVERT: X 550 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6693 (mmmt) REVERT: Y 70 VAL cc_start: 0.8864 (m) cc_final: 0.8625 (p) REVERT: Y 155 THR cc_start: 0.9110 (p) cc_final: 0.8847 (p) REVERT: Y 365 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8805 (m) REVERT: Y 497 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: Z 430 LYS cc_start: 0.7266 (ttmt) cc_final: 0.6877 (mtpt) REVERT: Z 488 MET cc_start: 0.8476 (tpp) cc_final: 0.7667 (mpp) REVERT: Z 502 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5682 (mtp) outliers start: 93 outliers final: 56 residues processed: 541 average time/residue: 0.6226 time to fit residues: 412.6025 Evaluate side-chains 508 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 441 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 147 ARG Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 445 THR Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 442 VAL Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 391 SER Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 452 GLN Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 441 ARG Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 550 LYS Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 497 GLU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 0.8980 chunk 323 optimal weight: 0.6980 chunk 384 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 410 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 330 optimal weight: 0.0020 chunk 348 optimal weight: 0.0040 chunk 396 optimal weight: 3.9990 chunk 407 optimal weight: 5.9990 chunk 387 optimal weight: 0.0870 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN D 98 GLN J 87 ASN J 92 ASN P 71 GLN P 140 ASN T 179 ASN ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN U 241 HIS U 319 HIS V 78 GLN V 121 ASN X 132 GLN X 250 GLN Y 471 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107723 restraints weight = 50384.475| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.64 r_work: 0.3175 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 34384 Z= 0.109 Angle : 0.569 13.488 46598 Z= 0.286 Chirality : 0.043 0.215 5513 Planarity : 0.004 0.073 5991 Dihedral : 5.261 108.954 4826 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 2.11 % Allowed : 22.97 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: 0.16 (0.13), residues: 4457 helix: 0.91 (0.12), residues: 2180 sheet: -0.64 (0.22), residues: 574 loop : -0.56 (0.16), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 79 TYR 0.025 0.001 TYR T 414 PHE 0.024 0.001 PHE D 107 TRP 0.044 0.002 TRP U 73 HIS 0.004 0.001 HIS Z 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (34384) covalent geometry : angle 0.56948 / 0.29 (46598) hydrogen bonds : bond 0.03155 / 2.11 ( 1708) hydrogen bonds : angle 4.22065 / 2.96 ( 4953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13077.52 seconds wall clock time: 223 minutes 19.15 seconds (13399.15 seconds total)