Starting phenix.real_space_refine on Mon Sep 14 21:37:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rea_4847/09_2026/6rea_4847.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rea_4847/09_2026/6rea_4847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rea_4847/09_2026/6rea_4847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rea_4847/09_2026/6rea_4847.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6rea_4847/09_2026/6rea_4847.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rea_4847/09_2026/6rea_4847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rea_4847/09_2026/6rea_4847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rea_4847/09_2026/6rea_4847.map" } resolution = 3.6 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 248 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: 7.10, per 1000 atoms: 0.21 Number of scatterers: 33863 At special positions: 0 Unit cell: (167.427, 135.837, 210.6, 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: 2.89 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: 177 helices and 0 sheets defined 52.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 54 through 68 removed outlier: 3.580A pdb=" N ALA A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.698A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 127 removed outlier: 3.729A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.658A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 Processing helix chain 'B' and resid 111 through 126 removed outlier: 4.032A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 66 removed outlier: 3.966A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.250A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.909A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.998A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 4.332A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.940A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 removed outlier: 3.964A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.012A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 127 removed outlier: 3.790A pdb=" N VAL E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.644A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.239A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 96 Processing helix chain 'F' and resid 97 through 127 removed outlier: 4.147A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 4.944A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 90 removed outlier: 4.323A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.754A 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: 4.410A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 66 removed outlier: 3.898A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS H 66 " --> pdb=" O VAL H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.329A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 127 removed outlier: 4.235A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.693A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.255A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 4.291A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU I 118 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.588A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 92 removed outlier: 4.323A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 96 Processing helix chain 'J' and resid 97 through 126 removed outlier: 3.585A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 64 removed outlier: 3.620A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 84 removed outlier: 3.634A pdb=" N HIS P 84 " --> pdb=" O LEU P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 4.110A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP P 93 " --> pdb=" O ARG P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.736A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 132 removed outlier: 4.437A pdb=" N SER P 132 " --> pdb=" O GLY P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 129 through 132' Processing helix chain 'P' and resid 133 through 149 removed outlier: 4.105A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 13 Processing helix chain 'Q' and resid 15 through 29 removed outlier: 3.624A pdb=" N ASN Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 42 removed outlier: 3.815A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 39 removed outlier: 4.298A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 170 removed outlier: 3.762A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 193 removed outlier: 3.772A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 79 removed outlier: 3.633A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.270A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 131 removed outlier: 3.511A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU S 131 " --> pdb=" O LEU S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 151 removed outlier: 4.139A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 184 removed outlier: 3.536A pdb=" N ALA S 175 " --> pdb=" O THR S 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 221 removed outlier: 5.713A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.520A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.956A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.579A 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 206 through 213 Processing helix chain 'T' and resid 230 through 247 removed outlier: 4.105A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 279 Processing helix chain 'T' and resid 280 through 283 Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.264A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 340 Processing helix chain 'T' and resid 346 through 350 removed outlier: 3.517A pdb=" N ALA T 349 " --> pdb=" O GLY T 346 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.538A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU T 363 " --> pdb=" O SER T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 414 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.587A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 Processing helix chain 'T' and resid 443 through 458 Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.649A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.664A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 513 through 515 No H-bonds generated for 'chain 'T' and resid 513 through 515' Processing helix chain 'T' and resid 516 through 528 removed outlier: 4.170A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 529 through 540 removed outlier: 3.773A pdb=" N PHE T 533 " --> pdb=" O ASN T 529 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 556 removed outlier: 3.787A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 49 removed outlier: 3.728A pdb=" N LEU U 48 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 72 removed outlier: 3.612A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.680A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 212 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.660A 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 317 Proline residue: U 303 - end of helix removed outlier: 4.096A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR U 316 " --> pdb=" O TYR U 312 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY U 317 " --> pdb=" O PHE U 313 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 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 436 through 460 removed outlier: 4.543A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA U 460 " --> pdb=" O VAL U 456 " (cutoff:3.500A) Processing helix chain 'U' and resid 467 through 485 removed outlier: 3.695A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.897A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.708A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.504A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 556 removed outlier: 3.711A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS U 556 " --> pdb=" O ALA U 552 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 Processing helix chain 'V' and resid 57 through 67 removed outlier: 3.564A pdb=" N HIS V 61 " --> pdb=" O TYR V 57 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.976A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.660A 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 removed outlier: 3.683A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 211 removed outlier: 3.829A pdb=" N ALA V 211 " --> pdb=" O LYS V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.894A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 removed outlier: 3.611A pdb=" N VAL V 269 " --> pdb=" O LYS V 265 " (cutoff:3.500A) Processing helix chain 'V' and resid 280 through 283 removed outlier: 4.145A pdb=" N ARG V 283 " --> pdb=" O GLY V 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 280 through 283' Processing helix chain 'V' and resid 295 through 315 Proline residue: V 303 - end of helix removed outlier: 3.907A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 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: 3.591A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.605A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 removed outlier: 3.722A pdb=" N THR V 396 " --> pdb=" O ALA V 392 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 434 removed outlier: 3.885A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 456 removed outlier: 3.829A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 484 removed outlier: 3.507A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.529A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 516 through 528 removed outlier: 4.265A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL V 528 " --> pdb=" O VAL V 524 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.812A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY V 540 " --> pdb=" O LEU V 536 " (cutoff:3.500A) Processing helix chain 'V' and resid 548 through 554 removed outlier: 3.630A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.748A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU X 118 " --> pdb=" O ARG X 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 114 through 118' Processing helix chain 'X' and resid 149 through 153 removed outlier: 3.547A pdb=" N GLN X 153 " --> pdb=" O PHE X 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 188 through 204 Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.076A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.567A 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: 3.914A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 301 removed outlier: 3.686A pdb=" N PHE X 290 " --> pdb=" O ASN X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 323 Processing helix chain 'X' and resid 341 through 345 removed outlier: 3.707A 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 371 Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 413 removed outlier: 3.883A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 413 through 421 removed outlier: 3.939A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 removed outlier: 3.556A pdb=" N LEU X 431 " --> pdb=" O GLU X 427 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 removed outlier: 3.741A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 509 removed outlier: 4.269A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE X 506 " --> pdb=" O MET X 502 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA X 507 " --> pdb=" O ALA X 503 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 534 removed outlier: 3.615A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE X 534 " --> pdb=" O LEU X 530 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 118 removed outlier: 3.683A pdb=" N THR Y 117 " --> pdb=" O GLY Y 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 201 Processing helix chain 'Y' and resid 216 through 231 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 4.113A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 removed outlier: 3.582A pdb=" N ALA Y 259 " --> pdb=" O PRO Y 255 " (cutoff:3.500A) Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.610A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 298 removed outlier: 3.719A 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 348 through 355 removed outlier: 3.759A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) 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 370 Processing helix chain 'Y' and resid 393 through 413 removed outlier: 3.804A pdb=" N LEU Y 413 " --> pdb=" O ASP Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 413 through 420 Processing helix chain 'Y' and resid 421 through 425 removed outlier: 3.996A pdb=" N GLU Y 424 " --> pdb=" O GLY Y 421 " (cutoff:3.500A) removed outlier: 4.016A 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 428 through 444 removed outlier: 3.872A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER Y 444 " --> pdb=" O GLN Y 440 " (cutoff:3.500A) Processing helix chain 'Y' and resid 450 through 455 removed outlier: 3.513A pdb=" N GLY Y 455 " --> pdb=" O GLU Y 451 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 Processing helix chain 'Y' and resid 482 through 486 Processing helix chain 'Y' and resid 491 through 505 removed outlier: 4.020A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 511 through 515 removed outlier: 4.318A pdb=" N ASN Y 514 " --> pdb=" O GLU Y 511 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS Y 515 " --> pdb=" O ALA Y 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 511 through 515' Processing helix chain 'Y' and resid 526 through 533 Processing helix chain 'Z' and resid 114 through 118 removed outlier: 3.560A pdb=" N LEU Z 118 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 Processing helix chain 'Z' and resid 188 through 198 Processing helix chain 'Z' and resid 216 through 230 removed outlier: 3.623A pdb=" N GLY Z 220 " --> pdb=" O ARG Z 216 " (cutoff:3.500A) Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.099A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.546A pdb=" N ARG Z 258 " --> pdb=" O PRO Z 254 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.866A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 314 through 323 Processing helix chain 'Z' and resid 342 through 345 Processing helix chain 'Z' and resid 348 through 354 removed outlier: 3.795A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 371 removed outlier: 3.603A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) Processing helix chain 'Z' and resid 384 through 387 removed outlier: 3.550A pdb=" N LEU Z 387 " --> pdb=" O SER Z 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 384 through 387' Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 418 removed outlier: 4.353A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Z 418 " --> pdb=" O GLN Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 429 through 443 removed outlier: 3.539A pdb=" N VAL Z 433 " --> pdb=" O ASP Z 429 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 452 removed outlier: 3.944A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 475 Processing helix chain 'Z' and resid 483 through 487 Processing helix chain 'Z' and resid 491 through 509 removed outlier: 3.521A pdb=" N VAL Z 495 " --> pdb=" O ASP Z 491 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER Z 508 " --> pdb=" O LYS Z 504 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG Z 509 " --> pdb=" O ASP Z 505 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 534 removed outlier: 3.525A pdb=" N LEU Z 530 " --> pdb=" O SER Z 526 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE Z 534 " --> pdb=" O LEU Z 530 " (cutoff:3.500A) 1433 hydrogen bonds defined for protein. 4188 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: 5.56 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10625 1.34 - 1.46: 4831 1.46 - 1.57: 18707 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34384 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.66e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.43e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 46362 4.21 - 8.41: 212 8.41 - 12.62: 18 12.62 - 16.82: 2 16.82 - 21.03: 4 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 139.87 118.84 21.03 1.00e+00 1.00e+00 4.42e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 119.87 20.00 1.00e+00 1.00e+00 4.00e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 117.79 19.04 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 119.15 17.68 1.00e+00 1.00e+00 3.13e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 124.42 15.45 1.00e+00 1.00e+00 2.39e+02 ... (remaining 46593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 19382 22.61 - 45.22: 1152 45.22 - 67.83: 135 67.83 - 90.44: 39 90.44 - 113.05: 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 -127.03 -52.97 0 5.00e+00 4.00e-02 1.12e+02 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 -131.21 -48.79 0 5.00e+00 4.00e-02 9.52e+01 dihedral pdb=" CA PRO U 250 " pdb=" C PRO U 250 " pdb=" N LYS U 251 " pdb=" CA LYS U 251 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 20707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4115 0.058 - 0.116: 1164 0.116 - 0.174: 212 0.174 - 0.231: 14 0.231 - 0.289: 8 Chirality restraints: 5513 Sorted by residual: chirality pdb=" CB ILE Z 524 " pdb=" CA ILE Z 524 " pdb=" CG1 ILE Z 524 " pdb=" CG2 ILE Z 524 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE B 95 " pdb=" CA ILE B 95 " pdb=" CG1 ILE B 95 " pdb=" CG2 ILE B 95 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB VAL Z 129 " pdb=" CA VAL Z 129 " pdb=" CG1 VAL Z 129 " pdb=" CG2 VAL Z 129 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+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 6.10e-02 3.72e+01 pdb=" C ALA Y 503 " -0.106 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 6.02e-02 3.63e+01 pdb=" C ALA Z 503 " -0.104 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 33 " -0.051 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO Q 34 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO Q 34 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO Q 34 " -0.043 5.00e-02 4.00e+02 ... (remaining 5988 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 350 2.57 - 3.15: 26246 3.15 - 3.73: 54545 3.73 - 4.32: 76618 4.32 - 4.90: 126303 Nonbonded interactions: 284062 Sorted by model distance: nonbonded pdb=" O ASN Z 514 " pdb=" CG2 VAL Z 517 " model vdw 1.985 3.460 nonbonded pdb=" O2B ATP V1001 " pdb="MG MG V1002 " model vdw 2.055 2.170 nonbonded pdb=" O1B ATP U1001 " pdb="MG MG U1002 " model vdw 2.059 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.067 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.090 2.170 ... (remaining 284057 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.460 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.380 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.006 0.084 34384 Z= 0.290 Angle : 0.895 21.028 46598 Z= 0.534 Chirality : 0.054 0.289 5513 Planarity : 0.007 0.076 5991 Dihedral : 14.668 113.051 12560 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.17 % Favored : 95.62 % Rotamer: Outliers : 0.20 % Allowed : 8.82 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.12 (0.10), residues: 4457 helix: -2.91 (0.08), residues: 2101 sheet: -2.33 (0.21), residues: 501 loop : -2.42 (0.12), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG T 555 TYR 0.018 0.002 TYR V 356 PHE 0.019 0.002 PHE R 70 TRP 0.013 0.002 TRP X 141 HIS 0.010 0.002 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.29 (34384) covalent geometry : angle 0.89485 / 0.53 (46598) hydrogen bonds : bond 0.15946 / 11.08 ( 1433) hydrogen bonds : angle 6.85599 / 4.91 ( 4188) *********************** 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 801 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 794 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.7097 (tp) cc_final: 0.6819 (mt) REVERT: F 110 THR cc_start: 0.7753 (t) cc_final: 0.7499 (m) REVERT: G 86 ILE cc_start: 0.7333 (mt) cc_final: 0.7042 (mt) REVERT: G 99 LEU cc_start: 0.7267 (mt) cc_final: 0.6712 (mp) REVERT: G 107 PHE cc_start: 0.7284 (t80) cc_final: 0.6948 (t80) REVERT: J 94 ASN cc_start: 0.7659 (t0) cc_final: 0.7419 (t0) REVERT: S 60 MET cc_start: 0.7636 (ttm) cc_final: 0.7087 (mtp) REVERT: S 68 MET cc_start: 0.7229 (ttp) cc_final: 0.6906 (ttt) REVERT: U 58 LEU cc_start: 0.7374 (mt) cc_final: 0.7152 (tp) REVERT: U 151 VAL cc_start: 0.8526 (t) cc_final: 0.8286 (t) REVERT: U 236 ILE cc_start: 0.9170 (mm) cc_final: 0.8894 (mt) REVERT: U 309 MET cc_start: 0.9057 (mtt) cc_final: 0.8856 (mtp) REVERT: U 448 LEU cc_start: 0.8627 (mt) cc_final: 0.8187 (mp) REVERT: U 495 GLU cc_start: 0.7644 (pm20) cc_final: 0.7367 (pm20) REVERT: U 558 LYS cc_start: 0.6019 (tmtt) cc_final: 0.5590 (mmmt) REVERT: V 210 ASP cc_start: 0.7752 (m-30) cc_final: 0.7479 (m-30) REVERT: V 479 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.7678 (tpp-160) REVERT: V 522 GLU cc_start: 0.7287 (tp30) cc_final: 0.7047 (tp30) REVERT: X 198 ASN cc_start: 0.7776 (t0) cc_final: 0.7443 (m-40) REVERT: X 497 GLU cc_start: 0.7490 (pp20) cc_final: 0.7119 (pp20) REVERT: Y 221 ASN cc_start: 0.8710 (t0) cc_final: 0.8456 (t0) REVERT: Y 439 ILE cc_start: 0.8187 (pt) cc_final: 0.7891 (mt) REVERT: Z 225 ARG cc_start: 0.7109 (mmt180) cc_final: 0.6668 (mmm-85) REVERT: Z 401 ARG cc_start: 0.7101 (tpt-90) cc_final: 0.6438 (ptp-170) REVERT: Z 502 MET cc_start: 0.7225 (mtp) cc_final: 0.6744 (mtm) REVERT: Z 535 LYS cc_start: 0.7116 (pttp) cc_final: 0.6859 (mmmt) outliers start: 7 outliers final: 3 residues processed: 799 average time/residue: 0.2272 time to fit residues: 292.4629 Evaluate side-chains 487 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 484 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain Y residue 166 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.0060 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN D 94 ASN E 98 GLN G 94 ASN I 87 ASN P 140 ASN P 148 HIS ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 85 GLN S 70 ASN S 174 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** T 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 GLN U 123 GLN ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 248 GLN U 264 GLN ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 319 HIS ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 527 GLN V 60 GLN V 139 HIS V 149 GLN V 242 GLN V 244 ASN V 264 GLN V 271 GLN V 278 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 386 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 549 HIS X 78 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS X 157 GLN X 199 ASN X 278 GLN X 294 ASN X 337 GLN X 404 GLN X 414 GLN Y 174 GLN Y 199 ASN ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 408 GLN Y 412 ASN Z 174 GLN Z 562 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118588 restraints weight = 61836.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119782 restraints weight = 35635.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120577 restraints weight = 23512.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121072 restraints weight = 20673.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121159 restraints weight = 18571.023| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34384 Z= 0.119 Angle : 0.575 9.609 46598 Z= 0.295 Chirality : 0.043 0.213 5513 Planarity : 0.005 0.056 5991 Dihedral : 5.910 85.354 4823 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.75 % Rotamer: Outliers : 1.91 % Allowed : 14.24 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.34 (0.11), residues: 4457 helix: -1.09 (0.10), residues: 2147 sheet: -2.02 (0.21), residues: 538 loop : -1.80 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 342 TYR 0.033 0.001 TYR C 102 PHE 0.023 0.001 PHE B 107 TRP 0.005 0.001 TRP U 73 HIS 0.006 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (34384) covalent geometry : angle 0.57512 / 0.30 (46598) hydrogen bonds : bond 0.03945 / 2.67 ( 1433) hydrogen bonds : angle 4.59918 / 3.25 ( 4188) *********************** 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 692 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 624 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6997 (ppp) cc_final: 0.6129 (ptt) REVERT: A 123 LEU cc_start: 0.7227 (tp) cc_final: 0.6599 (mt) REVERT: C 95 ILE cc_start: 0.7507 (mp) cc_final: 0.7250 (mp) REVERT: C 99 LEU cc_start: 0.7585 (mt) cc_final: 0.6837 (mt) REVERT: D 91 ARG cc_start: 0.6848 (tpp80) cc_final: 0.6497 (ttm-80) REVERT: E 59 SER cc_start: 0.8192 (t) cc_final: 0.7936 (p) REVERT: F 110 THR cc_start: 0.7687 (t) cc_final: 0.7307 (m) REVERT: G 81 MET cc_start: 0.7709 (tmm) cc_final: 0.7322 (tmm) REVERT: H 95 ILE cc_start: 0.7288 (mm) cc_final: 0.6988 (mm) REVERT: I 61 MET cc_start: 0.5682 (mmp) cc_final: 0.5477 (mmt) REVERT: P 106 SER cc_start: 0.7316 (p) cc_final: 0.7025 (p) REVERT: P 142 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6923 (mt-10) REVERT: R 97 TYR cc_start: 0.7726 (m-80) cc_final: 0.7387 (m-80) REVERT: R 176 PHE cc_start: 0.5276 (t80) cc_final: 0.4905 (t80) REVERT: S 45 GLN cc_start: 0.7342 (mm-40) cc_final: 0.6973 (mm-40) REVERT: S 60 MET cc_start: 0.7900 (ttm) cc_final: 0.7267 (mtp) REVERT: S 68 MET cc_start: 0.7465 (ttp) cc_final: 0.7055 (ttt) REVERT: S 147 ARG cc_start: 0.7336 (pmt-80) cc_final: 0.7037 (pmt-80) REVERT: S 164 ASP cc_start: 0.8251 (m-30) cc_final: 0.7968 (m-30) REVERT: S 303 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: T 213 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8164 (m) REVERT: T 441 GLN cc_start: 0.6887 (pp30) cc_final: 0.6635 (tm-30) REVERT: U 495 GLU cc_start: 0.8237 (pm20) cc_final: 0.7850 (pm20) REVERT: U 558 LYS cc_start: 0.6022 (tmtt) cc_final: 0.5344 (mmmt) REVERT: V 304 TYR cc_start: 0.8822 (m-80) cc_final: 0.8536 (m-80) REVERT: V 439 MET cc_start: 0.8880 (tpp) cc_final: 0.8319 (tpp) REVERT: V 479 ARG cc_start: 0.8168 (mmt-90) cc_final: 0.7830 (tpp-160) REVERT: V 522 GLU cc_start: 0.7950 (tp30) cc_final: 0.7637 (tp30) REVERT: V 537 LYS cc_start: 0.7970 (tptt) cc_final: 0.7686 (ttpp) REVERT: X 187 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7462 (t) REVERT: X 198 ASN cc_start: 0.8001 (t0) cc_final: 0.7630 (m-40) REVERT: Y 221 ASN cc_start: 0.8825 (t0) cc_final: 0.8443 (t0) REVERT: Y 266 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8449 (mm) REVERT: Y 304 ILE cc_start: 0.9111 (mt) cc_final: 0.8904 (mm) REVERT: Z 225 ARG cc_start: 0.7078 (mmt180) cc_final: 0.6784 (mmm-85) REVERT: Z 227 MET cc_start: 0.8597 (mtp) cc_final: 0.8388 (mtp) REVERT: Z 401 ARG cc_start: 0.6657 (tpt-90) cc_final: 0.6063 (ptp-170) REVERT: Z 474 LEU cc_start: 0.8359 (mt) cc_final: 0.8095 (mt) REVERT: Z 502 MET cc_start: 0.6725 (mtp) cc_final: 0.6259 (mtm) REVERT: Z 535 LYS cc_start: 0.7168 (pttp) cc_final: 0.6600 (mmmt) outliers start: 68 outliers final: 36 residues processed: 660 average time/residue: 0.2113 time to fit residues: 230.9520 Evaluate side-chains 517 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 477 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 187 VAL Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 395 GLU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 562 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 328 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 435 optimal weight: 0.0020 chunk 294 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN B 98 GLN I 87 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN S 174 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN U 264 GLN ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN V 196 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN X 414 GLN ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116435 restraints weight = 61902.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117277 restraints weight = 37474.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118066 restraints weight = 24907.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118704 restraints weight = 21343.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118747 restraints weight = 18705.702| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2467 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= 0.120 Angle : 0.554 9.523 46598 Z= 0.281 Chirality : 0.043 0.253 5513 Planarity : 0.004 0.049 5991 Dihedral : 5.534 81.774 4819 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.14 % Favored : 96.72 % Rotamer: Outliers : 2.58 % Allowed : 16.09 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.48 (0.12), residues: 4457 helix: -0.28 (0.11), residues: 2145 sheet: -1.77 (0.22), residues: 506 loop : -1.48 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 18 TYR 0.034 0.001 TYR C 102 PHE 0.034 0.001 PHE V 489 TRP 0.004 0.001 TRP U 73 HIS 0.005 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (34384) covalent geometry : angle 0.55383 / 0.28 (46598) hydrogen bonds : bond 0.03737 / 2.51 ( 1433) hydrogen bonds : angle 4.28999 / 3.01 ( 4188) *********************** 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 628 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 536 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6849 (ppp) cc_final: 0.6168 (ptt) REVERT: A 119 LEU cc_start: 0.4030 (OUTLIER) cc_final: 0.3520 (tp) REVERT: A 123 LEU cc_start: 0.6959 (tp) cc_final: 0.6235 (mt) REVERT: C 102 TYR cc_start: 0.6524 (m-80) cc_final: 0.6305 (m-80) REVERT: E 59 SER cc_start: 0.8098 (t) cc_final: 0.7870 (p) REVERT: F 110 THR cc_start: 0.7463 (t) cc_final: 0.6939 (m) REVERT: G 81 MET cc_start: 0.7652 (tmm) cc_final: 0.7354 (tmm) REVERT: H 95 ILE cc_start: 0.7484 (mm) cc_final: 0.7152 (mm) REVERT: P 106 SER cc_start: 0.7400 (p) cc_final: 0.7147 (p) REVERT: P 142 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7005 (mt-10) REVERT: R 101 LYS cc_start: 0.7173 (mmmm) cc_final: 0.6625 (mmmt) REVERT: R 176 PHE cc_start: 0.5238 (t80) cc_final: 0.4876 (t80) REVERT: S 45 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7153 (mm-40) REVERT: S 60 MET cc_start: 0.7872 (ttm) cc_final: 0.7233 (mtp) REVERT: S 68 MET cc_start: 0.7509 (ttp) cc_final: 0.7073 (ttt) REVERT: S 147 ARG cc_start: 0.7196 (pmt-80) cc_final: 0.6910 (pmt-80) REVERT: S 303 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: T 483 MET cc_start: 0.6634 (tmm) cc_final: 0.6379 (tmm) REVERT: U 236 ILE cc_start: 0.9361 (mm) cc_final: 0.8968 (mt) REVERT: U 495 GLU cc_start: 0.8275 (pm20) cc_final: 0.7984 (pm20) REVERT: U 558 LYS cc_start: 0.5846 (tmtt) cc_final: 0.5201 (mmmt) REVERT: U 559 LEU cc_start: 0.7059 (mp) cc_final: 0.6362 (tp) REVERT: V 43 LYS cc_start: 0.6549 (tppt) cc_final: 0.5919 (mttm) REVERT: V 304 TYR cc_start: 0.8857 (m-80) cc_final: 0.8510 (m-80) REVERT: V 452 GLN cc_start: 0.6605 (tp-100) cc_final: 0.6364 (tp-100) REVERT: V 479 ARG cc_start: 0.8171 (mmt-90) cc_final: 0.7838 (tpp-160) REVERT: V 522 GLU cc_start: 0.7951 (tp30) cc_final: 0.7660 (tp30) REVERT: X 187 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7516 (t) REVERT: X 198 ASN cc_start: 0.8023 (t0) cc_final: 0.7669 (m-40) REVERT: X 215 GLU cc_start: 0.6803 (tp30) cc_final: 0.6584 (tp30) REVERT: X 471 GLN cc_start: 0.7769 (tp40) cc_final: 0.7104 (tm-30) REVERT: X 483 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7450 (pt0) REVERT: Y 221 ASN cc_start: 0.8861 (t0) cc_final: 0.8452 (t0) REVERT: Y 266 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8410 (mm) REVERT: Z 225 ARG cc_start: 0.7018 (mmt180) cc_final: 0.6697 (mmm-85) REVERT: Z 316 THR cc_start: 0.9009 (m) cc_final: 0.8688 (m) REVERT: Z 401 ARG cc_start: 0.6631 (tpt-90) cc_final: 0.6035 (ptp-170) REVERT: Z 502 MET cc_start: 0.6866 (mtp) cc_final: 0.6439 (mtm) REVERT: Z 535 LYS cc_start: 0.7062 (pttp) cc_final: 0.6539 (mmmt) outliers start: 92 outliers final: 56 residues processed: 587 average time/residue: 0.2012 time to fit residues: 198.4122 Evaluate side-chains 530 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 470 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 187 VAL Chi-restraints excluded: chain X residue 414 GLN Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 505 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 228 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 96 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 414 optimal weight: 3.9990 chunk 255 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 312 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 387 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 217 optimal weight: 0.0980 chunk 184 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN C 94 ASN D 87 ASN E 98 GLN I 87 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS X 448 GLN Y 278 GLN Y 357 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114152 restraints weight = 61958.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114508 restraints weight = 37227.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115163 restraints weight = 26076.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115756 restraints weight = 23286.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115799 restraints weight = 20199.555| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34384 Z= 0.159 Angle : 0.575 13.304 46598 Z= 0.291 Chirality : 0.044 0.422 5513 Planarity : 0.004 0.049 5991 Dihedral : 5.489 87.380 4819 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.84 % Favored : 96.01 % Rotamer: Outliers : 3.31 % Allowed : 17.13 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.06 (0.12), residues: 4457 helix: 0.13 (0.11), residues: 2148 sheet: -1.75 (0.22), residues: 523 loop : -1.28 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 239 TYR 0.028 0.002 TYR C 102 PHE 0.026 0.001 PHE B 107 TRP 0.006 0.001 TRP U 73 HIS 0.005 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (34384) covalent geometry : angle 0.57468 / 0.29 (46598) hydrogen bonds : bond 0.03826 / 2.58 ( 1433) hydrogen bonds : angle 4.20637 / 2.96 ( 4188) *********************** 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 635 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 517 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6842 (ppp) cc_final: 0.6131 (ptt) REVERT: A 123 LEU cc_start: 0.7043 (tp) cc_final: 0.6169 (mt) REVERT: D 91 ARG cc_start: 0.6654 (tpp80) cc_final: 0.6440 (ttm-80) REVERT: E 59 SER cc_start: 0.7984 (t) cc_final: 0.7749 (p) REVERT: E 71 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7340 (tp) REVERT: F 110 THR cc_start: 0.7444 (t) cc_final: 0.7178 (m) REVERT: G 81 MET cc_start: 0.7593 (tmm) cc_final: 0.7273 (tmm) REVERT: H 78 LEU cc_start: 0.8269 (mt) cc_final: 0.8061 (mp) REVERT: H 95 ILE cc_start: 0.7519 (mm) cc_final: 0.7222 (mm) REVERT: P 79 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7075 (mm-30) REVERT: P 106 SER cc_start: 0.7446 (p) cc_final: 0.7179 (t) REVERT: P 142 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6875 (mt-10) REVERT: Q 35 PHE cc_start: 0.6133 (m-10) cc_final: 0.5681 (m-10) REVERT: R 86 LYS cc_start: 0.6953 (mmtt) cc_final: 0.6678 (mmtt) REVERT: R 126 LYS cc_start: 0.7511 (mtpt) cc_final: 0.6500 (mtmt) REVERT: R 176 PHE cc_start: 0.5246 (t80) cc_final: 0.4881 (t80) REVERT: S 60 MET cc_start: 0.7983 (ttm) cc_final: 0.7398 (mtp) REVERT: S 68 MET cc_start: 0.7543 (ttp) cc_final: 0.7069 (ttt) REVERT: S 147 ARG cc_start: 0.7297 (pmt-80) cc_final: 0.7027 (pmt-80) REVERT: S 303 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: T 284 TYR cc_start: 0.8650 (m-80) cc_final: 0.8364 (m-80) REVERT: T 441 GLN cc_start: 0.7419 (tm-30) cc_final: 0.7213 (tm-30) REVERT: U 53 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7135 (p90) REVERT: U 246 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7622 (t0) REVERT: U 495 GLU cc_start: 0.8262 (pm20) cc_final: 0.8029 (pm20) REVERT: U 558 LYS cc_start: 0.5834 (tmtt) cc_final: 0.5178 (mmmt) REVERT: U 559 LEU cc_start: 0.7164 (mp) cc_final: 0.6507 (tp) REVERT: V 43 LYS cc_start: 0.6654 (tppt) cc_final: 0.5961 (mttm) REVERT: V 304 TYR cc_start: 0.8931 (m-80) cc_final: 0.8596 (m-80) REVERT: V 452 GLN cc_start: 0.6664 (tp-100) cc_final: 0.6453 (tp-100) REVERT: V 522 GLU cc_start: 0.7990 (tp30) cc_final: 0.7728 (tp30) REVERT: X 198 ASN cc_start: 0.8079 (t0) cc_final: 0.7691 (m-40) REVERT: X 471 GLN cc_start: 0.7738 (tp40) cc_final: 0.7125 (tm-30) REVERT: X 483 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7520 (pt0) REVERT: Y 195 GLU cc_start: 0.7388 (tp30) cc_final: 0.7183 (tp30) REVERT: Y 266 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8541 (mm) REVERT: Y 278 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: Z 195 GLU cc_start: 0.6472 (tp30) cc_final: 0.6032 (tp30) REVERT: Z 225 ARG cc_start: 0.7009 (mmt180) cc_final: 0.6658 (mmm-85) REVERT: Z 401 ARG cc_start: 0.6702 (tpt-90) cc_final: 0.6076 (ptp-170) REVERT: Z 429 ASP cc_start: 0.5858 (OUTLIER) cc_final: 0.5636 (p0) REVERT: Z 502 MET cc_start: 0.6883 (mtp) cc_final: 0.6453 (mtm) REVERT: Z 535 LYS cc_start: 0.7174 (pttp) cc_final: 0.6525 (mmmt) outliers start: 118 outliers final: 81 residues processed: 590 average time/residue: 0.2023 time to fit residues: 200.5881 Evaluate side-chains 543 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 455 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 187 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 278 GLN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 3 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 266 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 428 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN I 87 ASN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114306 restraints weight = 62604.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114845 restraints weight = 38570.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115481 restraints weight = 26200.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116129 restraints weight = 22500.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116179 restraints weight = 20079.001| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34384 Z= 0.143 Angle : 0.566 10.496 46598 Z= 0.286 Chirality : 0.043 0.304 5513 Planarity : 0.004 0.055 5991 Dihedral : 5.378 85.675 4819 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 3.65 % Allowed : 18.23 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.75 (0.13), residues: 4457 helix: 0.41 (0.11), residues: 2139 sheet: -1.68 (0.22), residues: 534 loop : -1.12 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 239 TYR 0.038 0.001 TYR C 102 PHE 0.026 0.001 PHE B 107 TRP 0.005 0.001 TRP U 73 HIS 0.005 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (34384) covalent geometry : angle 0.56624 / 0.29 (46598) hydrogen bonds : bond 0.03722 / 2.50 ( 1433) hydrogen bonds : angle 4.16131 / 2.93 ( 4188) *********************** 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 628 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 498 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6788 (ppp) cc_final: 0.6382 (ptt) REVERT: A 119 LEU cc_start: 0.4205 (OUTLIER) cc_final: 0.3796 (tp) REVERT: A 123 LEU cc_start: 0.7004 (tp) cc_final: 0.6103 (mt) REVERT: C 99 LEU cc_start: 0.6501 (tp) cc_final: 0.6272 (tp) REVERT: D 115 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.5725 (mm) REVERT: E 71 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7265 (tp) REVERT: F 110 THR cc_start: 0.7458 (t) cc_final: 0.6995 (m) REVERT: H 78 LEU cc_start: 0.8231 (mt) cc_final: 0.7860 (mp) REVERT: P 106 SER cc_start: 0.7456 (p) cc_final: 0.7168 (t) REVERT: Q 35 PHE cc_start: 0.6002 (m-10) cc_final: 0.5528 (m-10) REVERT: R 176 PHE cc_start: 0.5223 (t80) cc_final: 0.4923 (t80) REVERT: S 60 MET cc_start: 0.7922 (ttm) cc_final: 0.7316 (mtp) REVERT: S 62 MET cc_start: 0.7829 (mmm) cc_final: 0.7545 (mmm) REVERT: S 68 MET cc_start: 0.7494 (ttp) cc_final: 0.7052 (ttt) REVERT: S 133 GLU cc_start: 0.4448 (OUTLIER) cc_final: 0.2870 (pp20) REVERT: S 174 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7499 (mt0) REVERT: S 303 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: T 284 TYR cc_start: 0.8679 (m-80) cc_final: 0.8399 (m-80) REVERT: U 47 GLU cc_start: 0.6950 (pp20) cc_final: 0.6431 (pp20) REVERT: U 53 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.7154 (p90) REVERT: U 236 ILE cc_start: 0.9378 (mm) cc_final: 0.8991 (mt) REVERT: U 558 LYS cc_start: 0.5889 (tmtt) cc_final: 0.5270 (mmmt) REVERT: U 559 LEU cc_start: 0.7112 (mp) cc_final: 0.6588 (tp) REVERT: V 43 LYS cc_start: 0.6604 (tppt) cc_final: 0.5929 (mttm) REVERT: V 304 TYR cc_start: 0.8930 (m-80) cc_final: 0.8611 (m-80) REVERT: V 522 GLU cc_start: 0.7917 (tp30) cc_final: 0.7664 (tp30) REVERT: X 198 ASN cc_start: 0.8090 (t0) cc_final: 0.7708 (m-40) REVERT: X 471 GLN cc_start: 0.7638 (tp40) cc_final: 0.7091 (tm-30) REVERT: Y 266 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8501 (mm) REVERT: Z 195 GLU cc_start: 0.6510 (tp30) cc_final: 0.6063 (tp30) REVERT: Z 225 ARG cc_start: 0.6955 (mmt180) cc_final: 0.6639 (mmm-85) REVERT: Z 401 ARG cc_start: 0.6722 (tpt-90) cc_final: 0.6132 (ptp-170) REVERT: Z 429 ASP cc_start: 0.5799 (OUTLIER) cc_final: 0.5598 (p0) REVERT: Z 502 MET cc_start: 0.6951 (mtp) cc_final: 0.6499 (mtm) REVERT: Z 535 LYS cc_start: 0.7215 (pttp) cc_final: 0.6609 (mmmt) outliers start: 130 outliers final: 88 residues processed: 577 average time/residue: 0.1984 time to fit residues: 194.1765 Evaluate side-chains 557 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 460 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 501 VAL Chi-restraints excluded: chain T residue 539 ASN Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 187 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 380 LEU Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 505 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 429 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 158 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 371 optimal weight: 0.6980 chunk 337 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 429 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN I 87 ASN S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115176 restraints weight = 62021.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115508 restraints weight = 38457.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116182 restraints weight = 26334.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117284 restraints weight = 22616.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117224 restraints weight = 19014.056| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 34384 Z= 0.129 Angle : 0.560 9.483 46598 Z= 0.282 Chirality : 0.043 0.391 5513 Planarity : 0.004 0.052 5991 Dihedral : 5.265 82.187 4819 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.70 % Favored : 96.14 % Rotamer: Outliers : 3.68 % Allowed : 19.01 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.57 (0.13), residues: 4457 helix: 0.57 (0.12), residues: 2141 sheet: -1.57 (0.22), residues: 541 loop : -1.04 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 147 TYR 0.043 0.001 TYR C 102 PHE 0.027 0.001 PHE D 107 TRP 0.003 0.001 TRP X 141 HIS 0.005 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (34384) covalent geometry : angle 0.56035 / 0.28 (46598) hydrogen bonds : bond 0.03653 / 2.46 ( 1433) hydrogen bonds : angle 4.10276 / 2.89 ( 4188) *********************** 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 648 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 517 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6750 (ppp) cc_final: 0.6446 (ptt) REVERT: A 84 SER cc_start: 0.9015 (m) cc_final: 0.8773 (t) REVERT: A 119 LEU cc_start: 0.4194 (OUTLIER) cc_final: 0.3825 (tp) REVERT: A 123 LEU cc_start: 0.6984 (tp) cc_final: 0.6080 (mt) REVERT: D 115 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.5724 (mm) REVERT: E 71 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7273 (tp) REVERT: F 110 THR cc_start: 0.7379 (t) cc_final: 0.6906 (m) REVERT: H 78 LEU cc_start: 0.8182 (mt) cc_final: 0.7934 (mp) REVERT: I 99 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7067 (mp) REVERT: P 75 TYR cc_start: 0.8505 (m-80) cc_final: 0.8212 (m-80) REVERT: P 142 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6730 (mt-10) REVERT: Q 35 PHE cc_start: 0.6008 (m-10) cc_final: 0.5571 (m-10) REVERT: R 135 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: R 176 PHE cc_start: 0.5228 (t80) cc_final: 0.4939 (t80) REVERT: S 60 MET cc_start: 0.7931 (ttm) cc_final: 0.7337 (mtp) REVERT: S 62 MET cc_start: 0.7784 (mmm) cc_final: 0.7501 (mmm) REVERT: S 68 MET cc_start: 0.7509 (ttp) cc_final: 0.7041 (ttt) REVERT: S 133 GLU cc_start: 0.4378 (OUTLIER) cc_final: 0.2768 (pp20) REVERT: S 303 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: T 284 TYR cc_start: 0.8664 (m-80) cc_final: 0.8407 (m-80) REVERT: T 394 ILE cc_start: 0.8957 (mm) cc_final: 0.8732 (mm) REVERT: U 47 GLU cc_start: 0.6909 (pp20) cc_final: 0.6519 (pp20) REVERT: U 53 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.7091 (p90) REVERT: U 236 ILE cc_start: 0.9375 (mm) cc_final: 0.9015 (mt) REVERT: U 558 LYS cc_start: 0.6007 (tmtt) cc_final: 0.5411 (mmmt) REVERT: U 559 LEU cc_start: 0.7109 (mp) cc_final: 0.6608 (tp) REVERT: V 43 LYS cc_start: 0.6616 (tppt) cc_final: 0.5960 (mttm) REVERT: V 304 TYR cc_start: 0.8925 (m-80) cc_final: 0.8590 (m-80) REVERT: V 439 MET cc_start: 0.8766 (tpp) cc_final: 0.8506 (tpp) REVERT: V 450 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7348 (mm) REVERT: V 522 GLU cc_start: 0.7902 (tp30) cc_final: 0.7639 (tp30) REVERT: V 546 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5975 (tt) REVERT: V 558 LYS cc_start: 0.7215 (tptt) cc_final: 0.6602 (pttt) REVERT: X 127 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: X 198 ASN cc_start: 0.8099 (t0) cc_final: 0.7721 (m-40) REVERT: X 471 GLN cc_start: 0.7589 (tp40) cc_final: 0.7100 (tm-30) REVERT: X 483 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7557 (pt0) REVERT: Y 194 MET cc_start: 0.8259 (mpp) cc_final: 0.7475 (mpp) REVERT: Y 221 ASN cc_start: 0.8876 (t0) cc_final: 0.8456 (t0) REVERT: Y 266 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8496 (mm) REVERT: Z 82 ASP cc_start: 0.7079 (p0) cc_final: 0.6358 (p0) REVERT: Z 195 GLU cc_start: 0.6501 (tp30) cc_final: 0.6070 (tp30) REVERT: Z 225 ARG cc_start: 0.6941 (mmt180) cc_final: 0.6639 (mmm-85) REVERT: Z 386 MET cc_start: 0.7171 (mmm) cc_final: 0.6714 (ttm) REVERT: Z 401 ARG cc_start: 0.6672 (tpt-90) cc_final: 0.6084 (ptp-170) REVERT: Z 502 MET cc_start: 0.6902 (mtp) cc_final: 0.6446 (mtm) REVERT: Z 535 LYS cc_start: 0.7239 (pttp) cc_final: 0.6598 (mmmt) outliers start: 131 outliers final: 92 residues processed: 592 average time/residue: 0.1897 time to fit residues: 190.8553 Evaluate side-chains 565 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 461 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 539 ASN Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 187 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 505 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 170 LEU Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 489 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: 6.9990 chunk 173 optimal weight: 0.9990 chunk 364 optimal weight: 0.9990 chunk 300 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 344 optimal weight: 0.0030 chunk 184 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN F 94 ASN H 98 GLN I 87 ASN R 178 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.115461 restraints weight = 62003.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117168 restraints weight = 39081.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117808 restraints weight = 24380.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118506 restraints weight = 20987.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118493 restraints weight = 18635.366| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34384 Z= 0.120 Angle : 0.575 12.463 46598 Z= 0.287 Chirality : 0.043 0.239 5513 Planarity : 0.004 0.058 5991 Dihedral : 5.081 77.263 4819 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.41 % Favored : 96.43 % Rotamer: Outliers : 3.65 % Allowed : 20.25 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.40 (0.13), residues: 4457 helix: 0.66 (0.12), residues: 2143 sheet: -1.42 (0.22), residues: 543 loop : -0.94 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 195 TYR 0.041 0.001 TYR C 102 PHE 0.035 0.001 PHE D 107 TRP 0.003 0.001 TRP U 73 HIS 0.005 0.001 HIS V 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (34384) covalent geometry : angle 0.57468 / 0.29 (46598) hydrogen bonds : bond 0.03570 / 2.39 ( 1433) hydrogen bonds : angle 4.09356 / 2.89 ( 4188) *********************** 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 656 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 526 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6763 (ppp) cc_final: 0.6306 (ptt) REVERT: A 84 SER cc_start: 0.9013 (m) cc_final: 0.8776 (t) REVERT: A 119 LEU cc_start: 0.3770 (OUTLIER) cc_final: 0.3435 (tp) REVERT: A 123 LEU cc_start: 0.6879 (tp) cc_final: 0.6066 (mt) REVERT: D 115 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6098 (mm) REVERT: E 71 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7296 (tp) REVERT: F 109 LEU cc_start: 0.7121 (tp) cc_final: 0.6828 (tp) REVERT: F 110 THR cc_start: 0.6988 (t) cc_final: 0.6364 (m) REVERT: H 78 LEU cc_start: 0.8270 (mt) cc_final: 0.8059 (mp) REVERT: P 142 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6683 (mt-10) REVERT: Q 35 PHE cc_start: 0.5968 (m-10) cc_final: 0.5649 (m-10) REVERT: R 135 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: S 60 MET cc_start: 0.7902 (ttm) cc_final: 0.7264 (mtp) REVERT: S 62 MET cc_start: 0.7790 (mmm) cc_final: 0.7505 (mmm) REVERT: S 67 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7635 (mttt) REVERT: S 68 MET cc_start: 0.7449 (ttp) cc_final: 0.6995 (ttt) REVERT: S 133 GLU cc_start: 0.4191 (OUTLIER) cc_final: 0.2545 (pp20) REVERT: S 303 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: T 421 LEU cc_start: 0.8566 (tt) cc_final: 0.8038 (mt) REVERT: U 47 GLU cc_start: 0.6894 (pp20) cc_final: 0.6548 (pp20) REVERT: U 53 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7098 (p90) REVERT: U 236 ILE cc_start: 0.9349 (mm) cc_final: 0.8992 (mt) REVERT: U 546 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6543 (mm) REVERT: U 558 LYS cc_start: 0.5965 (tmtt) cc_final: 0.5382 (mmmt) REVERT: U 559 LEU cc_start: 0.7098 (mp) cc_final: 0.6633 (tp) REVERT: V 43 LYS cc_start: 0.6597 (tppt) cc_final: 0.5923 (mttm) REVERT: V 304 TYR cc_start: 0.8892 (m-80) cc_final: 0.8564 (m-80) REVERT: V 450 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7389 (mm) REVERT: V 487 LYS cc_start: 0.8212 (mttm) cc_final: 0.7908 (ptpp) REVERT: V 495 GLU cc_start: 0.8171 (pm20) cc_final: 0.7924 (pm20) REVERT: V 522 GLU cc_start: 0.7973 (tp30) cc_final: 0.7607 (tp30) REVERT: V 546 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.6041 (tt) REVERT: V 558 LYS cc_start: 0.7295 (tptt) cc_final: 0.6695 (pttt) REVERT: X 127 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: X 179 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9070 (mt) REVERT: X 198 ASN cc_start: 0.8105 (t0) cc_final: 0.7738 (m-40) REVERT: X 471 GLN cc_start: 0.7545 (tp40) cc_final: 0.7075 (tm-30) REVERT: X 483 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7528 (pt0) REVERT: Y 221 ASN cc_start: 0.8763 (t0) cc_final: 0.8282 (t0) REVERT: Y 266 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8456 (mm) REVERT: Z 82 ASP cc_start: 0.7048 (p0) cc_final: 0.6287 (p0) REVERT: Z 195 GLU cc_start: 0.6505 (tp30) cc_final: 0.6087 (tp30) REVERT: Z 225 ARG cc_start: 0.6963 (mmt180) cc_final: 0.6641 (mmm-85) REVERT: Z 386 MET cc_start: 0.7161 (mmm) cc_final: 0.6630 (ttm) REVERT: Z 401 ARG cc_start: 0.6599 (tpt-90) cc_final: 0.6042 (ptp-170) REVERT: Z 502 MET cc_start: 0.6783 (mtp) cc_final: 0.6342 (mtm) REVERT: Z 535 LYS cc_start: 0.7123 (pttp) cc_final: 0.6611 (mmmt) outliers start: 130 outliers final: 95 residues processed: 604 average time/residue: 0.1859 time to fit residues: 190.4330 Evaluate side-chains 583 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 475 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 539 ASN Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 179 ILE Chi-restraints excluded: chain X residue 187 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 489 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: 1.9990 chunk 61 optimal weight: 9.9990 chunk 415 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 376 optimal weight: 0.8980 chunk 386 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 346 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 87 ASN R 178 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115295 restraints weight = 62150.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115428 restraints weight = 41312.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116234 restraints weight = 28665.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117102 restraints weight = 23805.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117151 restraints weight = 20295.378| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34384 Z= 0.140 Angle : 0.596 11.725 46598 Z= 0.297 Chirality : 0.044 0.348 5513 Planarity : 0.004 0.066 5991 Dihedral : 5.038 71.237 4819 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.12 % Rotamer: Outliers : 3.59 % Allowed : 20.98 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.36 (0.13), residues: 4457 helix: 0.72 (0.12), residues: 2121 sheet: -1.40 (0.22), residues: 544 loop : -0.92 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 195 TYR 0.042 0.002 TYR C 102 PHE 0.031 0.001 PHE D 107 TRP 0.004 0.001 TRP U 73 HIS 0.005 0.001 HIS V 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (34384) covalent geometry : angle 0.59619 / 0.30 (46598) hydrogen bonds : bond 0.03710 / 2.48 ( 1433) hydrogen bonds : angle 4.15835 / 2.94 ( 4188) *********************** 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 631 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 503 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6699 (ppp) cc_final: 0.6369 (ptt) REVERT: A 84 SER cc_start: 0.9040 (m) cc_final: 0.8818 (t) REVERT: A 119 LEU cc_start: 0.3983 (OUTLIER) cc_final: 0.3611 (tp) REVERT: A 123 LEU cc_start: 0.7089 (tp) cc_final: 0.6238 (mt) REVERT: B 85 LEU cc_start: 0.8452 (tp) cc_final: 0.8090 (mp) REVERT: B 124 ILE cc_start: 0.6082 (mm) cc_final: 0.5867 (mm) REVERT: D 68 THR cc_start: 0.7670 (p) cc_final: 0.7410 (t) REVERT: D 115 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.5944 (mm) REVERT: E 71 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7327 (tp) REVERT: F 109 LEU cc_start: 0.7208 (tp) cc_final: 0.7006 (tp) REVERT: F 110 THR cc_start: 0.7027 (t) cc_final: 0.6375 (m) REVERT: H 78 LEU cc_start: 0.8391 (mt) cc_final: 0.8094 (mp) REVERT: Q 35 PHE cc_start: 0.6072 (m-10) cc_final: 0.5781 (m-10) REVERT: R 86 LYS cc_start: 0.6207 (ttmt) cc_final: 0.5937 (tttt) REVERT: R 135 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: R 176 PHE cc_start: 0.4774 (t80) cc_final: 0.4561 (t80) REVERT: S 60 MET cc_start: 0.7941 (ttm) cc_final: 0.7323 (mtp) REVERT: S 62 MET cc_start: 0.7765 (mmm) cc_final: 0.7492 (mmm) REVERT: S 67 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7759 (mttt) REVERT: S 68 MET cc_start: 0.7463 (ttp) cc_final: 0.6990 (ttt) REVERT: S 133 GLU cc_start: 0.4205 (OUTLIER) cc_final: 0.2508 (pp20) REVERT: S 272 SER cc_start: 0.8641 (m) cc_final: 0.8112 (t) REVERT: S 303 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: U 47 GLU cc_start: 0.6949 (pp20) cc_final: 0.6642 (pp20) REVERT: U 53 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.7077 (p90) REVERT: U 558 LYS cc_start: 0.5975 (tmtt) cc_final: 0.5421 (mmmt) REVERT: U 559 LEU cc_start: 0.7091 (mp) cc_final: 0.6639 (tp) REVERT: V 43 LYS cc_start: 0.6620 (tppt) cc_final: 0.5924 (mttm) REVERT: V 213 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8576 (m) REVERT: V 287 MET cc_start: 0.8562 (tpp) cc_final: 0.8050 (tpt) REVERT: V 304 TYR cc_start: 0.8939 (m-80) cc_final: 0.8518 (m-80) REVERT: V 439 MET cc_start: 0.8775 (tpp) cc_final: 0.8373 (mtt) REVERT: V 450 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7357 (mm) REVERT: V 487 LYS cc_start: 0.8203 (mttm) cc_final: 0.7953 (ptpp) REVERT: V 522 GLU cc_start: 0.7942 (tp30) cc_final: 0.7620 (tp30) REVERT: V 546 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6073 (tt) REVERT: V 558 LYS cc_start: 0.7235 (tptt) cc_final: 0.6628 (pttt) REVERT: X 127 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: X 179 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9110 (mt) REVERT: X 198 ASN cc_start: 0.8114 (t0) cc_final: 0.7733 (m-40) REVERT: X 471 GLN cc_start: 0.7527 (tp40) cc_final: 0.7069 (tm-30) REVERT: X 483 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7547 (pt0) REVERT: Y 221 ASN cc_start: 0.8832 (t0) cc_final: 0.8431 (t0) REVERT: Y 266 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8514 (mm) REVERT: Z 82 ASP cc_start: 0.6974 (p0) cc_final: 0.6113 (p0) REVERT: Z 195 GLU cc_start: 0.6525 (tp30) cc_final: 0.6069 (tp30) REVERT: Z 225 ARG cc_start: 0.6970 (mmt180) cc_final: 0.6642 (mmm-85) REVERT: Z 386 MET cc_start: 0.7115 (mmm) cc_final: 0.6628 (ttm) REVERT: Z 401 ARG cc_start: 0.6659 (tpt-90) cc_final: 0.6072 (ptp-170) REVERT: Z 441 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7770 (mmm160) REVERT: Z 471 GLN cc_start: 0.6237 (tt0) cc_final: 0.5977 (tp40) REVERT: Z 502 MET cc_start: 0.6859 (mtp) cc_final: 0.6435 (mtm) REVERT: Z 535 LYS cc_start: 0.7143 (pttp) cc_final: 0.6666 (mmmt) outliers start: 128 outliers final: 100 residues processed: 582 average time/residue: 0.1941 time to fit residues: 192.3006 Evaluate side-chains 584 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 471 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 116 PHE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 539 ASN Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 212 LEU Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 179 ILE Chi-restraints excluded: chain X residue 187 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 489 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 332 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 chunk 249 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 384 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 418 optimal weight: 8.9990 chunk 258 optimal weight: 0.3980 chunk 162 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 87 ASN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN S 191 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 HIS Z 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116446 restraints weight = 61692.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116614 restraints weight = 39687.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117561 restraints weight = 27792.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118101 restraints weight = 22943.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118241 restraints weight = 20367.847| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34384 Z= 0.121 Angle : 0.602 11.712 46598 Z= 0.297 Chirality : 0.044 0.305 5513 Planarity : 0.004 0.072 5991 Dihedral : 4.942 67.729 4819 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 3.23 % Allowed : 21.71 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.28 (0.13), residues: 4457 helix: 0.73 (0.12), residues: 2140 sheet: -1.34 (0.23), residues: 520 loop : -0.83 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 195 TYR 0.040 0.001 TYR C 102 PHE 0.036 0.001 PHE I 82 TRP 0.002 0.001 TRP U 73 HIS 0.006 0.001 HIS V 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (34384) covalent geometry : angle 0.60169 / 0.30 (46598) hydrogen bonds : bond 0.03646 / 2.44 ( 1433) hydrogen bonds : angle 4.17302 / 2.95 ( 4188) *********************** 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 624 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 509 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.9020 (m) cc_final: 0.8737 (t) REVERT: A 119 LEU cc_start: 0.3722 (OUTLIER) cc_final: 0.3394 (tp) REVERT: A 123 LEU cc_start: 0.6959 (tp) cc_final: 0.6100 (mt) REVERT: B 85 LEU cc_start: 0.8117 (tp) cc_final: 0.7801 (mp) REVERT: D 115 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6014 (mm) REVERT: E 71 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7331 (tp) REVERT: E 98 GLN cc_start: 0.6858 (tm-30) cc_final: 0.6285 (tt0) REVERT: F 110 THR cc_start: 0.6912 (t) cc_final: 0.6217 (m) REVERT: H 109 LEU cc_start: 0.8705 (mp) cc_final: 0.8487 (mt) REVERT: Q 35 PHE cc_start: 0.5996 (m-10) cc_final: 0.5697 (m-10) REVERT: R 135 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: R 176 PHE cc_start: 0.4882 (t80) cc_final: 0.4567 (t80) REVERT: S 60 MET cc_start: 0.7945 (ttm) cc_final: 0.7314 (mtp) REVERT: S 62 MET cc_start: 0.7751 (mmm) cc_final: 0.7452 (mmm) REVERT: S 67 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7705 (mttt) REVERT: S 68 MET cc_start: 0.7479 (ttp) cc_final: 0.6998 (ttt) REVERT: S 133 GLU cc_start: 0.4193 (OUTLIER) cc_final: 0.2477 (pp20) REVERT: S 232 ASP cc_start: 0.7729 (t0) cc_final: 0.7318 (t0) REVERT: S 272 SER cc_start: 0.8548 (m) cc_final: 0.8096 (t) REVERT: S 303 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: T 309 MET cc_start: 0.8031 (mtt) cc_final: 0.7680 (mtt) REVERT: T 452 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7428 (mm-40) REVERT: U 53 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.7016 (p90) REVERT: U 212 LEU cc_start: 0.8319 (mp) cc_final: 0.8086 (mp) REVERT: U 558 LYS cc_start: 0.5898 (tmtt) cc_final: 0.5351 (mmmt) REVERT: U 559 LEU cc_start: 0.7065 (mp) cc_final: 0.6590 (tp) REVERT: V 43 LYS cc_start: 0.6630 (tppt) cc_final: 0.5897 (mttm) REVERT: V 287 MET cc_start: 0.8545 (tpp) cc_final: 0.8081 (tpt) REVERT: V 304 TYR cc_start: 0.8891 (m-80) cc_final: 0.8536 (m-80) REVERT: V 439 MET cc_start: 0.8752 (tpp) cc_final: 0.8420 (mtt) REVERT: V 487 LYS cc_start: 0.8228 (mttm) cc_final: 0.8013 (ptpp) REVERT: V 522 GLU cc_start: 0.7981 (tp30) cc_final: 0.7634 (tp30) REVERT: V 546 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5581 (tt) REVERT: V 558 LYS cc_start: 0.7311 (tptt) cc_final: 0.6730 (pttt) REVERT: X 82 ASP cc_start: 0.6791 (t70) cc_final: 0.6544 (t70) REVERT: X 179 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9112 (mt) REVERT: X 198 ASN cc_start: 0.8104 (t0) cc_final: 0.7757 (m-40) REVERT: X 471 GLN cc_start: 0.7581 (tp40) cc_final: 0.7045 (tm-30) REVERT: Y 221 ASN cc_start: 0.8830 (t0) cc_final: 0.8363 (t0) REVERT: Y 239 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8334 (ttp80) REVERT: Y 266 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8449 (mm) REVERT: Z 82 ASP cc_start: 0.6955 (p0) cc_final: 0.6176 (p0) REVERT: Z 195 GLU cc_start: 0.6512 (tp30) cc_final: 0.6070 (tp30) REVERT: Z 225 ARG cc_start: 0.6958 (mmt180) cc_final: 0.6617 (mmm-85) REVERT: Z 401 ARG cc_start: 0.6548 (tpt-90) cc_final: 0.6008 (ptp-170) REVERT: Z 471 GLN cc_start: 0.6153 (tt0) cc_final: 0.5904 (tp40) REVERT: Z 502 MET cc_start: 0.6718 (mtp) cc_final: 0.6287 (mtm) REVERT: Z 535 LYS cc_start: 0.7158 (pttp) cc_final: 0.6616 (mmmt) outliers start: 115 outliers final: 90 residues processed: 579 average time/residue: 0.1985 time to fit residues: 195.0980 Evaluate side-chains 581 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 481 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 539 ASN Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 179 ILE Chi-restraints excluded: chain X residue 187 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 489 VAL Chi-restraints excluded: chain Z residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 146 optimal weight: 5.9990 chunk 399 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 413 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 434 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 87 ASN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.137287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114373 restraints weight = 62433.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114938 restraints weight = 40267.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115523 restraints weight = 27040.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115768 restraints weight = 24281.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115982 restraints weight = 22812.440| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34384 Z= 0.157 Angle : 0.626 13.833 46598 Z= 0.312 Chirality : 0.045 0.285 5513 Planarity : 0.004 0.072 5991 Dihedral : 5.029 68.612 4819 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.06 % Favored : 95.78 % Rotamer: Outliers : 3.06 % Allowed : 21.79 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.36 (0.13), residues: 4457 helix: 0.65 (0.12), residues: 2146 sheet: -1.39 (0.23), residues: 537 loop : -0.84 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 195 TYR 0.042 0.002 TYR C 102 PHE 0.034 0.002 PHE G 107 TRP 0.005 0.001 TRP U 73 HIS 0.005 0.001 HIS V 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (34384) covalent geometry : angle 0.62563 / 0.31 (46598) hydrogen bonds : bond 0.03850 / 2.57 ( 1433) hydrogen bonds : angle 4.25955 / 3.01 ( 4188) ********************** 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 600 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 491 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.9098 (m) cc_final: 0.8722 (t) REVERT: A 119 LEU cc_start: 0.3724 (OUTLIER) cc_final: 0.3497 (tp) REVERT: A 123 LEU cc_start: 0.7137 (tp) cc_final: 0.6282 (mt) REVERT: B 98 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7165 (mp10) REVERT: B 102 TYR cc_start: 0.6168 (m-80) cc_final: 0.5927 (m-80) REVERT: D 115 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.5705 (mm) REVERT: E 71 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7325 (tp) REVERT: E 98 GLN cc_start: 0.6856 (tm-30) cc_final: 0.6357 (tt0) REVERT: H 109 LEU cc_start: 0.8703 (mp) cc_final: 0.8456 (mt) REVERT: I 61 MET cc_start: 0.6318 (tpp) cc_final: 0.5804 (ptp) REVERT: Q 35 PHE cc_start: 0.6153 (m-10) cc_final: 0.5867 (m-10) REVERT: R 135 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: R 176 PHE cc_start: 0.4856 (t80) cc_final: 0.4563 (t80) REVERT: S 60 MET cc_start: 0.7945 (ttm) cc_final: 0.7309 (mtp) REVERT: S 62 MET cc_start: 0.7773 (mmm) cc_final: 0.7494 (mmm) REVERT: S 67 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7735 (mttt) REVERT: S 68 MET cc_start: 0.7500 (ttp) cc_final: 0.7034 (ttt) REVERT: S 133 GLU cc_start: 0.4234 (OUTLIER) cc_final: 0.2518 (pp20) REVERT: S 174 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7731 (mt0) REVERT: S 272 SER cc_start: 0.8532 (m) cc_final: 0.8086 (t) REVERT: S 303 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: U 53 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.7054 (p90) REVERT: U 502 TYR cc_start: 0.6778 (t80) cc_final: 0.6547 (t80) REVERT: U 558 LYS cc_start: 0.5934 (tmtt) cc_final: 0.5440 (mmmt) REVERT: V 43 LYS cc_start: 0.6586 (tppt) cc_final: 0.5898 (mttm) REVERT: V 287 MET cc_start: 0.8555 (tpp) cc_final: 0.8115 (tpt) REVERT: V 304 TYR cc_start: 0.8945 (m-80) cc_final: 0.8546 (m-80) REVERT: V 439 MET cc_start: 0.8793 (tpp) cc_final: 0.8461 (mtt) REVERT: V 452 GLN cc_start: 0.6691 (tp-100) cc_final: 0.6411 (tp40) REVERT: V 487 LYS cc_start: 0.8214 (mttm) cc_final: 0.7975 (ptpp) REVERT: V 522 GLU cc_start: 0.7976 (tp30) cc_final: 0.7653 (tp30) REVERT: V 546 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5997 (tt) REVERT: V 558 LYS cc_start: 0.7374 (tptt) cc_final: 0.6791 (pttt) REVERT: X 82 ASP cc_start: 0.6757 (t70) cc_final: 0.6543 (t70) REVERT: X 198 ASN cc_start: 0.8125 (t0) cc_final: 0.7814 (m-40) REVERT: X 471 GLN cc_start: 0.7559 (tp40) cc_final: 0.7086 (tm-30) REVERT: X 488 MET cc_start: 0.7819 (mmt) cc_final: 0.7369 (tmm) REVERT: Y 221 ASN cc_start: 0.8918 (t0) cc_final: 0.8524 (t0) REVERT: Y 239 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8353 (ttp80) REVERT: Y 266 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8525 (mm) REVERT: Z 82 ASP cc_start: 0.6983 (p0) cc_final: 0.6084 (p0) REVERT: Z 195 GLU cc_start: 0.6543 (tp30) cc_final: 0.6060 (tp30) REVERT: Z 225 ARG cc_start: 0.6953 (mmt180) cc_final: 0.6636 (mmm-85) REVERT: Z 401 ARG cc_start: 0.6638 (tpt-90) cc_final: 0.6031 (ptp-170) REVERT: Z 441 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7555 (mmm160) REVERT: Z 502 MET cc_start: 0.6851 (mtp) cc_final: 0.6394 (mtm) REVERT: Z 535 LYS cc_start: 0.7158 (pttp) cc_final: 0.6618 (mmmt) outliers start: 109 outliers final: 91 residues processed: 556 average time/residue: 0.1945 time to fit residues: 182.9267 Evaluate side-chains 566 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 465 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 228 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 539 ASN Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 187 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 489 VAL Chi-restraints excluded: chain Z residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 7.9990 chunk 323 optimal weight: 8.9990 chunk 384 optimal weight: 0.0770 chunk 108 optimal weight: 2.9990 chunk 410 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 330 optimal weight: 7.9990 chunk 348 optimal weight: 0.0060 chunk 396 optimal weight: 0.0870 chunk 407 optimal weight: 0.9990 chunk 387 optimal weight: 0.0770 overall best weight: 0.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 87 ASN S 174 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 HIS ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 422 ASN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS X 337 GLN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 HIS Z 144 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118815 restraints weight = 61770.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119568 restraints weight = 36671.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120026 restraints weight = 24941.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120613 restraints weight = 23075.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120712 restraints weight = 20198.488| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 34384 Z= 0.110 Angle : 0.612 18.201 46598 Z= 0.300 Chirality : 0.043 0.264 5513 Planarity : 0.004 0.076 5991 Dihedral : 4.792 64.844 4819 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.01 % Favored : 96.84 % Rotamer: Outliers : 2.42 % Allowed : 22.69 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.20 (0.13), residues: 4457 helix: 0.73 (0.12), residues: 2161 sheet: -1.29 (0.23), residues: 529 loop : -0.72 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 91 TYR 0.043 0.001 TYR C 102 PHE 0.036 0.001 PHE G 107 TRP 0.002 0.001 TRP R 37 HIS 0.006 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (34384) covalent geometry : angle 0.61180 / 0.30 (46598) hydrogen bonds : bond 0.03560 / 2.37 ( 1433) hydrogen bonds : angle 4.19736 / 2.96 ( 4188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6034.50 seconds wall clock time: 105 minutes 14.99 seconds (6314.99 seconds total)