Starting phenix.real_space_refine on Mon Sep 14 22:27:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rdv_4832/09_2026/6rdv_4832.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rdv_4832/09_2026/6rdv_4832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rdv_4832/09_2026/6rdv_4832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rdv_4832/09_2026/6rdv_4832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rdv_4832/09_2026/6rdv_4832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rdv_4832/09_2026/6rdv_4832.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rdv_4832/09_2026/6rdv_4832.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rdv_4832/09_2026/6rdv_4832.cif" } resolution = 3.1 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 21541 2.51 5 N 5795 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 287 residue(s): 0.06s 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: 33891 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: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" 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: "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: "X" 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: "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} Time building chain proxies: 7.14, per 1000 atoms: 0.21 Number of scatterers: 33891 At special positions: 0 Unit cell: (160.056, 134.784, 209.547, 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 6421 8.00 N 5795 7.00 C 21541 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 1.6 seconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 26 sheets defined 51.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 55 through 68 removed outlier: 4.350A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.812A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.755A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 4.024A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 4.092A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 96 Processing helix chain 'B' and resid 98 through 126 removed outlier: 4.418A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.782A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 92 removed outlier: 4.036A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 96 Processing helix chain 'C' and resid 99 through 126 removed outlier: 3.867A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.571A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.958A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 4.127A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.935A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 90 removed outlier: 3.563A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 126 removed outlier: 3.647A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 66 removed outlier: 4.488A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.076A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 124 removed outlier: 4.354A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL F 121 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 Processing helix chain 'G' and resid 71 through 92 Processing helix chain 'G' and resid 95 through 121 removed outlier: 3.737A pdb=" N VAL G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 67 Processing helix chain 'H' and resid 70 through 92 removed outlier: 3.666A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 124 removed outlier: 4.088A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 3.665A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS I 66 " --> pdb=" O VAL I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 3.851A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 126 removed outlier: 4.321A pdb=" N GLY I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE I 126 " --> pdb=" O PHE I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.692A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 89 removed outlier: 3.653A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 125 removed outlier: 3.719A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.622A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.809A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP P 93 " --> pdb=" O ARG P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 105 Processing helix chain 'P' and resid 117 through 128 removed outlier: 3.946A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 146 removed outlier: 3.550A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.613A pdb=" N ALA Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 40 through 44 removed outlier: 3.530A pdb=" N GLN Q 43 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 40 through 44' Processing helix chain 'R' and resid 31 through 38 removed outlier: 3.999A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.597A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR R 55 " --> pdb=" O SER R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 158 through 168 removed outlier: 3.768A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 removed outlier: 3.821A pdb=" N ALA R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.608A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 79 Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.518A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 128 Processing helix chain 'S' and resid 143 through 154 removed outlier: 3.712A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG S 152 " --> pdb=" O SER S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 184 Processing helix chain 'S' and resid 216 through 221 removed outlier: 3.529A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 231 removed outlier: 3.737A pdb=" N ALA S 230 " --> pdb=" O SER S 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 241 removed outlier: 3.526A pdb=" N ASP S 241 " --> pdb=" O GLU S 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 238 through 241' Processing helix chain 'S' and resid 242 through 274 removed outlier: 3.948A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 313 removed outlier: 3.589A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.986A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 213 removed outlier: 3.599A pdb=" N ALA T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.799A pdb=" N ALA T 235 " --> pdb=" O LYS T 231 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 269 through 280 Processing helix chain 'T' and resid 281 through 284 removed outlier: 3.565A pdb=" N TYR T 284 " --> pdb=" O ALA T 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 281 through 284' Processing helix chain 'T' and resid 295 through 300 Processing helix chain 'T' and resid 301 through 316 removed outlier: 4.482A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 removed outlier: 3.545A pdb=" N GLN T 330 " --> pdb=" O ASP T 326 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 351 through 353 No H-bonds generated for 'chain 'T' and resid 351 through 353' Processing helix chain 'T' and resid 354 through 363 removed outlier: 3.837A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG T 360 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 415 removed outlier: 3.501A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.793A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 460 removed outlier: 3.606A pdb=" N GLU T 449 " --> pdb=" O THR T 445 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.689A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 506 removed outlier: 3.709A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 513 through 517 removed outlier: 3.868A pdb=" N ILE T 517 " --> pdb=" O VAL T 514 " (cutoff:3.500A) Processing helix chain 'T' and resid 520 through 527 removed outlier: 3.920A pdb=" N VAL T 524 " --> pdb=" O ALA T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 540 removed outlier: 3.800A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 554 removed outlier: 4.123A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS T 551 " --> pdb=" O ASP T 547 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 46 Processing helix chain 'U' and resid 47 through 49 No H-bonds generated for 'chain 'U' and resid 47 through 49' Processing helix chain 'U' and resid 58 through 72 removed outlier: 5.575A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 3.629A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.786A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE U 138 " --> pdb=" O ASP U 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 134 through 138' Processing helix chain 'U' and resid 206 through 212 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.805A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 283 removed outlier: 3.621A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 280 through 283' Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.892A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 329 through 341 Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.597A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 400 Processing helix chain 'U' and resid 409 through 415 Processing helix chain 'U' and resid 436 through 460 removed outlier: 3.862A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA U 460 " --> pdb=" O VAL U 456 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 485 removed outlier: 3.860A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 506 removed outlier: 3.632A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 4.121A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 529 through 540 removed outlier: 4.249A pdb=" N PHE U 533 " --> pdb=" O ASN U 529 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 3.589A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.734A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 74 removed outlier: 5.847A pdb=" N LYS V 71 " --> pdb=" O PRO V 68 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU V 72 " --> pdb=" O ALA V 69 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU V 74 " --> pdb=" O LYS V 71 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.571A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.905A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 283 removed outlier: 3.608A 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: 3.736A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 341 Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.619A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 414 removed outlier: 3.524A pdb=" N PHE V 413 " --> pdb=" O GLU V 409 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 409 through 414' Processing helix chain 'V' and resid 430 through 435 removed outlier: 4.263A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) Processing helix chain 'V' and resid 439 through 457 removed outlier: 3.674A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 484 removed outlier: 3.629A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU V 484 " --> pdb=" O LEU V 480 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 507 removed outlier: 3.668A pdb=" N GLY V 507 " --> pdb=" O ALA V 503 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 521 Processing helix chain 'V' and resid 521 through 526 removed outlier: 3.541A pdb=" N SER V 526 " --> pdb=" O GLU V 522 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 4.199A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 removed outlier: 4.068A pdb=" N LYS V 551 " --> pdb=" O ASP V 547 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.520A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) removed outlier: 3.535A 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: 3.559A pdb=" N GLN X 153 " --> pdb=" O PHE X 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 removed outlier: 4.763A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 229 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.173A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN X 241 " --> pdb=" O GLU X 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 260 removed outlier: 3.536A pdb=" N ARG X 260 " --> pdb=" O GLY X 256 " (cutoff:3.500A) Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.667A pdb=" N THR X 264 " --> pdb=" O ARG X 260 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 299 removed outlier: 3.720A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 348 through 353 Processing helix chain 'X' and resid 354 through 358 removed outlier: 3.741A pdb=" N LEU X 358 " --> pdb=" O PHE X 355 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 370 Processing helix chain 'X' and resid 393 through 420 removed outlier: 3.529A pdb=" N TYR X 397 " --> pdb=" O GLY X 393 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 421 through 425 removed outlier: 3.865A pdb=" N GLU X 424 " --> pdb=" O GLY X 421 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 491 through 505 Processing helix chain 'X' and resid 526 through 533 removed outlier: 3.622A pdb=" N LEU X 530 " --> pdb=" O SER X 526 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 118 removed outlier: 3.521A 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 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 4.057A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.659A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 298 removed outlier: 3.750A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.623A 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 421 removed outlier: 3.667A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Y 418 " --> pdb=" O GLN Y 414 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 444 removed outlier: 3.868A pdb=" N SER Y 444 " --> pdb=" O GLN Y 440 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 475 Processing helix chain 'Y' and resid 482 through 486 removed outlier: 3.585A pdb=" N PHE Y 486 " --> pdb=" O GLU Y 483 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 508 Processing helix chain 'Y' and resid 526 through 533 Processing helix chain 'Y' and resid 544 through 555 removed outlier: 3.713A pdb=" N ASP Y 548 " --> pdb=" O GLY Y 544 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER Y 555 " --> pdb=" O ALA Y 551 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 188 through 203 Processing helix chain 'Z' and resid 216 through 229 Processing helix chain 'Z' and resid 236 through 242 removed outlier: 4.486A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 260 removed outlier: 3.709A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.548A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.527A pdb=" N PHE Z 290 " --> pdb=" O ASN Z 286 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 removed outlier: 3.930A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 357 removed outlier: 4.158A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS Z 357 " --> pdb=" O THR Z 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 371 Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 411 Processing helix chain 'Z' and resid 421 through 425 removed outlier: 3.859A pdb=" N GLU Z 424 " --> pdb=" O GLY Z 421 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU Z 425 " --> pdb=" O MET Z 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 421 through 425' Processing helix chain 'Z' and resid 426 through 440 removed outlier: 3.711A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 447 through 451 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.746A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 491 through 505 removed outlier: 3.652A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 533 Processing sheet with id=AA1, first strand: chain 'Q' and resid 61 through 65 removed outlier: 7.026A pdb=" N GLN S 159 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL S 139 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA S 161 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER S 141 " --> pdb=" O ALA S 161 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ALA S 163 " --> pdb=" O SER S 141 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS S 99 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLN S 191 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL S 101 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU S 193 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL S 103 " --> pdb=" O LEU S 193 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASN S 195 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N VAL S 105 " --> pdb=" O ASN S 195 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N PHE S 197 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.538A pdb=" N VAL R 89 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.659A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU T 108 " --> pdb=" O THR T 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AA6, first strand: chain 'T' and resid 163 through 164 removed outlier: 6.224A pdb=" N THR T 164 " --> pdb=" O SER T 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 382 through 384 removed outlier: 6.544A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU T 408 " --> pdb=" O LEU T 222 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE T 224 " --> pdb=" O LEU T 408 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'U' and resid 107 through 111 removed outlier: 7.466A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AB1, first strand: chain 'U' and resid 163 through 164 removed outlier: 6.195A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'V' and resid 116 through 122 removed outlier: 3.868A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AB4, first strand: chain 'V' and resid 163 through 164 removed outlier: 6.365A pdb=" N THR V 164 " --> pdb=" O SER V 289 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU V 408 " --> pdb=" O LEU V 222 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE V 224 " --> pdb=" O LEU V 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'V' and resid 201 through 202 removed outlier: 4.553A pdb=" N ILE V 215 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'X' and resid 110 through 113 Processing sheet with id=AB7, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.185A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE X 207 " --> pdb=" O ASP X 279 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.190A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC1, first strand: chain 'Y' and resid 38 through 44 removed outlier: 6.510A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 110 through 111 Processing sheet with id=AC3, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.203A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE Y 207 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS Y 178 " --> pdb=" O ALA Y 360 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR Y 362 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY Y 180 " --> pdb=" O THR Y 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.263A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.540A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.114A pdb=" N MET Z 122 " --> pdb=" O TYR Z 248 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN Z 250 " --> pdb=" O MET Z 122 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS Z 178 " --> pdb=" O ASP Z 359 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N THR Z 361 " --> pdb=" O LYS Z 178 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY Z 180 " --> pdb=" O THR Z 361 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.424A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 559 through 561 1668 hydrogen bonds defined for protein. 4833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.99 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9790 1.33 - 1.45: 5809 1.45 - 1.57: 18592 1.57 - 1.69: 21 1.69 - 1.82: 200 Bond restraints: 34412 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.16e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.96e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.28e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.64e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 46194 3.94 - 7.88: 395 7.88 - 11.82: 40 11.82 - 15.77: 5 15.77 - 19.71: 4 Bond angle restraints: 46638 Sorted by residual: angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 120.16 19.71 1.00e+00 1.00e+00 3.88e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 122.05 17.82 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.74 13.09 1.00e+00 1.00e+00 1.71e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 123.80 13.03 1.00e+00 1.00e+00 1.70e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 20156 33.26 - 66.53: 520 66.53 - 99.79: 52 99.79 - 133.06: 1 133.06 - 166.32: 1 Dihedral angle restraints: 20730 sinusoidal: 7973 harmonic: 12757 Sorted by residual: 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 -120.54 -59.46 0 5.00e+00 4.00e-02 1.41e+02 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 -122.18 -57.82 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual 180.00 -125.88 -54.12 0 5.00e+00 4.00e-02 1.17e+02 ... (remaining 20727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4268 0.072 - 0.144: 1105 0.144 - 0.216: 123 0.216 - 0.288: 16 0.288 - 0.360: 7 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB VAL U 198 " pdb=" CA VAL U 198 " pdb=" CG1 VAL U 198 " pdb=" CG2 VAL U 198 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL Y 124 " pdb=" CA VAL Y 124 " pdb=" CG1 VAL Y 124 " pdb=" CG2 VAL Y 124 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 5516 not shown) Planarity restraints: 5997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" C ALA Z 503 " -0.100 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.037 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 307 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C ALA Z 307 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA Z 307 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL Z 308 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 33 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO Q 34 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO Q 34 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Q 34 " -0.041 5.00e-02 4.00e+02 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 454 2.63 - 3.20: 29157 3.20 - 3.76: 54469 3.76 - 4.33: 78544 4.33 - 4.90: 128713 Nonbonded interactions: 291337 Sorted by model distance: nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.059 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.134 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.151 2.170 nonbonded pdb=" O ALA X 503 " pdb=" CG1 ILE X 506 " model vdw 2.218 3.440 nonbonded pdb=" O GLY X 45 " pdb=" OG1 THR X 93 " model vdw 2.232 3.040 ... (remaining 291332 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 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.850 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.510 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.011 0.124 34412 Z= 0.473 Angle : 1.065 19.707 46638 Z= 0.605 Chirality : 0.063 0.360 5519 Planarity : 0.008 0.074 5997 Dihedral : 15.381 166.320 12570 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.76 % Favored : 93.93 % Rotamer: Outliers : 0.67 % Allowed : 11.39 % Favored : 87.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.10), residues: 4461 helix: -3.14 (0.08), residues: 2150 sheet: -1.46 (0.22), residues: 528 loop : -2.07 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG V 146 TYR 0.025 0.003 TYR P 75 PHE 0.032 0.003 PHE Z 486 TRP 0.038 0.004 TRP Z 141 HIS 0.007 0.002 HIS U 139 Details of bonding type rmsd/Z covalent geometry : bond 0.01095 / 0.47 (34412) covalent geometry : angle 1.06543 / 0.60 (46638) hydrogen bonds : bond 0.18774 / 12.33 ( 1668) hydrogen bonds : angle 7.92449 / 5.58 ( 4833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 582 time to evaluate : 1.249 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: E 61 MET cc_start: 0.5243 (ttm) cc_final: 0.5014 (ttm) REVERT: E 87 ASN cc_start: 0.6826 (m-40) cc_final: 0.6588 (t0) REVERT: J 109 LEU cc_start: 0.7198 (mm) cc_final: 0.6811 (mt) REVERT: P 64 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8375 (mm-30) REVERT: P 119 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7534 (mttt) REVERT: P 128 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7376 (mp0) REVERT: P 135 LEU cc_start: 0.8632 (mt) cc_final: 0.8342 (mt) REVERT: P 136 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7927 (mm-30) REVERT: P 140 ASN cc_start: 0.8798 (m-40) cc_final: 0.8490 (m110) REVERT: P 150 LYS cc_start: 0.6573 (mttp) cc_final: 0.6314 (mmmt) REVERT: S 76 GLU cc_start: 0.5875 (tp30) cc_final: 0.5611 (tp30) REVERT: S 271 MET cc_start: 0.7530 (ttp) cc_final: 0.7092 (tmm) REVERT: T 389 ASP cc_start: 0.8002 (t0) cc_final: 0.7552 (p0) REVERT: T 447 LYS cc_start: 0.8266 (ptpt) cc_final: 0.7485 (tttt) REVERT: T 483 MET cc_start: 0.7064 (ttp) cc_final: 0.6745 (ptp) REVERT: T 488 GLN cc_start: 0.7823 (tp40) cc_final: 0.7498 (tp40) REVERT: T 516 ASP cc_start: 0.7793 (t70) cc_final: 0.7078 (t0) REVERT: T 518 VAL cc_start: 0.8421 (m) cc_final: 0.7789 (t) REVERT: T 534 LYS cc_start: 0.7745 (mttp) cc_final: 0.7323 (mmtt) REVERT: U 118 MET cc_start: 0.8549 (ttt) cc_final: 0.8147 (tmm) REVERT: U 439 MET cc_start: 0.8798 (tpp) cc_final: 0.8369 (tpt) REVERT: U 449 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6815 (mt-10) REVERT: U 502 TYR cc_start: 0.8178 (t80) cc_final: 0.7771 (t80) REVERT: U 535 ILE cc_start: 0.8712 (mt) cc_final: 0.8462 (mm) REVERT: V 61 HIS cc_start: 0.7921 (t70) cc_final: 0.7335 (m90) REVERT: V 409 GLU cc_start: 0.6842 (tp30) cc_final: 0.6596 (tp30) REVERT: V 508 PHE cc_start: 0.8364 (m-80) cc_final: 0.7957 (m-80) REVERT: V 527 GLN cc_start: 0.8267 (mm110) cc_final: 0.7860 (mt0) REVERT: V 555 ARG cc_start: 0.6135 (mtt-85) cc_final: 0.5788 (mmt180) REVERT: X 195 GLU cc_start: 0.7803 (tp30) cc_final: 0.7417 (tp30) REVERT: X 557 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6439 (mm-30) REVERT: Y 385 ARG cc_start: 0.7749 (mmt90) cc_final: 0.7503 (mmt-90) REVERT: Y 405 LYS cc_start: 0.7814 (tptt) cc_final: 0.7261 (tttt) REVERT: Y 409 ASP cc_start: 0.7246 (m-30) cc_final: 0.6497 (m-30) REVERT: Y 413 LEU cc_start: 0.7874 (mt) cc_final: 0.7532 (mt) REVERT: Y 414 GLN cc_start: 0.7473 (mt0) cc_final: 0.7069 (mt0) REVERT: Y 430 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7827 (mttm) REVERT: Y 437 ARG cc_start: 0.7411 (mtt-85) cc_final: 0.7001 (mtt90) outliers start: 24 outliers final: 17 residues processed: 602 average time/residue: 0.2261 time to fit residues: 214.7979 Evaluate side-chains 428 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 411 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 332 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 326 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.9980 chunk 424 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 94 ASN P 65 ASN P 71 GLN Q 46 HIS Q 74 ASN R 181 ASN ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN S 185 HIS S 262 ASN S 297 GLN T 196 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 386 GLN T 441 GLN T 497 GLN ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN U 248 GLN U 386 GLN U 441 GLN U 471 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN V 242 GLN V 264 GLN V 271 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 278 GLN X 414 GLN X 471 GLN Y 83 ASN Y 174 GLN Y 414 GLN Z 42 GLN Z 78 GLN Z 199 ASN Z 241 ASN Z 250 GLN Z 278 GLN Z 388 ASN Z 404 GLN Z 440 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.164042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127438 restraints weight = 48867.359| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.75 r_work: 0.3339 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34412 Z= 0.128 Angle : 0.591 10.229 46638 Z= 0.308 Chirality : 0.043 0.176 5519 Planarity : 0.005 0.050 5997 Dihedral : 6.898 129.334 4847 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.34 % Favored : 96.44 % Rotamer: Outliers : 1.63 % Allowed : 14.45 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.32 (0.12), residues: 4461 helix: -1.45 (0.10), residues: 2183 sheet: -1.01 (0.22), residues: 513 loop : -1.61 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 496 TYR 0.022 0.001 TYR S 256 PHE 0.023 0.001 PHE A 116 TRP 0.014 0.002 TRP R 37 HIS 0.006 0.001 HIS T 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (34412) covalent geometry : angle 0.59080 / 0.31 (46638) hydrogen bonds : bond 0.03942 / 2.57 ( 1668) hydrogen bonds : angle 5.11586 / 3.57 ( 4833) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 515 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7154 (mtp) REVERT: E 87 ASN cc_start: 0.6602 (m-40) cc_final: 0.6182 (t0) REVERT: G 61 MET cc_start: 0.5974 (ttp) cc_final: 0.5288 (tpp) REVERT: J 109 LEU cc_start: 0.7614 (mm) cc_final: 0.6967 (mt) REVERT: P 79 GLU cc_start: 0.8039 (tp30) cc_final: 0.7696 (tp30) REVERT: P 128 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7357 (mp0) REVERT: P 140 ASN cc_start: 0.8783 (m-40) cc_final: 0.8577 (m110) REVERT: P 145 MET cc_start: 0.8292 (mmm) cc_final: 0.8018 (mmm) REVERT: Q 18 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.6973 (mtt90) REVERT: Q 40 GLN cc_start: 0.5602 (tp-100) cc_final: 0.5193 (mp10) REVERT: R 32 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6582 (tp30) REVERT: R 35 GLU cc_start: 0.6251 (mp0) cc_final: 0.5844 (mp0) REVERT: R 177 GLU cc_start: 0.6669 (mp0) cc_final: 0.5744 (tp30) REVERT: S 271 MET cc_start: 0.8073 (ttp) cc_final: 0.7601 (tmm) REVERT: T 389 ASP cc_start: 0.8028 (t0) cc_final: 0.7613 (p0) REVERT: T 447 LYS cc_start: 0.8011 (ptpt) cc_final: 0.7269 (tttt) REVERT: T 515 GLN cc_start: 0.7388 (mt0) cc_final: 0.7173 (pt0) REVERT: U 118 MET cc_start: 0.9052 (ttt) cc_final: 0.8606 (tmm) REVERT: U 497 GLN cc_start: 0.7954 (tt0) cc_final: 0.7714 (tt0) REVERT: V 409 GLU cc_start: 0.7251 (tp30) cc_final: 0.6895 (tp30) REVERT: V 489 PHE cc_start: 0.6545 (m-80) cc_final: 0.6273 (m-10) REVERT: V 508 PHE cc_start: 0.8474 (m-80) cc_final: 0.8116 (m-80) REVERT: V 527 GLN cc_start: 0.8243 (mm110) cc_final: 0.7855 (mt0) REVERT: V 551 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7041 (ttpp) REVERT: X 49 ASP cc_start: 0.7903 (m-30) cc_final: 0.7589 (m-30) REVERT: X 195 GLU cc_start: 0.8585 (tp30) cc_final: 0.8160 (tp30) REVERT: X 390 ASN cc_start: 0.8710 (m110) cc_final: 0.8417 (m110) REVERT: X 557 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6517 (mm-30) REVERT: Y 405 LYS cc_start: 0.7744 (tptt) cc_final: 0.7122 (tttt) REVERT: Y 409 ASP cc_start: 0.7552 (m-30) cc_final: 0.6954 (m-30) REVERT: Y 411 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8169 (mtmt) REVERT: Y 414 GLN cc_start: 0.7440 (mt0) cc_final: 0.7086 (mt0) REVERT: Y 437 ARG cc_start: 0.7993 (mtt-85) cc_final: 0.7509 (mtt90) REVERT: Y 502 MET cc_start: 0.6274 (mtp) cc_final: 0.6000 (mtm) REVERT: Z 365 SER cc_start: 0.8658 (t) cc_final: 0.8123 (m) REVERT: Z 441 ARG cc_start: 0.8188 (mmt-90) cc_final: 0.7968 (mmt-90) outliers start: 58 outliers final: 32 residues processed: 555 average time/residue: 0.2324 time to fit residues: 207.5086 Evaluate side-chains 446 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 412 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain P residue 63 LYS Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 472 TYR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 416 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 107 optimal weight: 7.9990 chunk 304 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 264 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 422 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 396 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 52 GLN P 71 GLN P 76 GLN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 196 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 358 HIS ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 198 ASN X 390 ASN X 414 GLN Z 42 GLN Z 278 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.160736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124256 restraints weight = 48910.960| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.78 r_work: 0.3254 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34412 Z= 0.174 Angle : 0.599 10.252 46638 Z= 0.309 Chirality : 0.045 0.215 5519 Planarity : 0.004 0.048 5997 Dihedral : 6.535 113.301 4835 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.30 % Favored : 95.43 % Rotamer: Outliers : 2.72 % Allowed : 15.94 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.52 (0.12), residues: 4461 helix: -0.67 (0.11), residues: 2175 sheet: -0.96 (0.22), residues: 531 loop : -1.26 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 42 TYR 0.028 0.002 TYR P 75 PHE 0.021 0.001 PHE A 116 TRP 0.029 0.003 TRP V 73 HIS 0.004 0.001 HIS S 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (34412) covalent geometry : angle 0.59867 / 0.31 (46638) hydrogen bonds : bond 0.03866 / 2.52 ( 1668) hydrogen bonds : angle 4.76120 / 3.31 ( 4833) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 454 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ILE cc_start: 0.3864 (OUTLIER) cc_final: 0.3157 (mm) REVERT: C 81 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7491 (ttp) REVERT: F 61 MET cc_start: 0.5868 (mtm) cc_final: 0.5666 (mtm) REVERT: G 61 MET cc_start: 0.5511 (OUTLIER) cc_final: 0.4570 (mmm) REVERT: I 95 ILE cc_start: 0.5187 (OUTLIER) cc_final: 0.4592 (mm) REVERT: J 109 LEU cc_start: 0.7779 (mm) cc_final: 0.7196 (mt) REVERT: P 128 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7398 (mp0) REVERT: P 136 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8462 (mm-30) REVERT: Q 14 MET cc_start: 0.6163 (tmm) cc_final: 0.5623 (tmm) REVERT: Q 48 ARG cc_start: 0.7079 (ptt-90) cc_final: 0.6796 (ptt-90) REVERT: R 32 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6431 (tp30) REVERT: R 35 GLU cc_start: 0.6213 (mp0) cc_final: 0.5967 (mp0) REVERT: R 177 GLU cc_start: 0.6866 (mp0) cc_final: 0.5872 (tp30) REVERT: S 271 MET cc_start: 0.8247 (ttp) cc_final: 0.7753 (tmm) REVERT: T 121 ASN cc_start: 0.8887 (p0) cc_final: 0.8663 (p0) REVERT: T 389 ASP cc_start: 0.8194 (t0) cc_final: 0.7821 (p0) REVERT: T 447 LYS cc_start: 0.8180 (ptpt) cc_final: 0.7323 (tttt) REVERT: T 513 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.7166 (ttm-80) REVERT: T 516 ASP cc_start: 0.8243 (t70) cc_final: 0.7370 (t0) REVERT: U 45 LEU cc_start: 0.8330 (mm) cc_final: 0.7714 (mm) REVERT: U 118 MET cc_start: 0.9102 (ttt) cc_final: 0.8632 (tmm) REVERT: U 385 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8030 (p) REVERT: U 449 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6972 (mt-10) REVERT: V 409 GLU cc_start: 0.7292 (tp30) cc_final: 0.6968 (tp30) REVERT: V 489 PHE cc_start: 0.6755 (m-80) cc_final: 0.6312 (m-10) REVERT: V 508 PHE cc_start: 0.8549 (m-80) cc_final: 0.8016 (m-80) REVERT: V 527 GLN cc_start: 0.8164 (mm110) cc_final: 0.7830 (mt0) REVERT: V 546 LEU cc_start: 0.7738 (tp) cc_final: 0.7492 (tp) REVERT: V 555 ARG cc_start: 0.6642 (mtt180) cc_final: 0.5960 (mmt180) REVERT: X 49 ASP cc_start: 0.7945 (m-30) cc_final: 0.7645 (m-30) REVERT: X 178 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8592 (mttm) REVERT: X 195 GLU cc_start: 0.8654 (tp30) cc_final: 0.8261 (tp30) REVERT: X 325 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8659 (mt) REVERT: X 390 ASN cc_start: 0.8693 (m-40) cc_final: 0.8415 (m110) REVERT: X 429 ASP cc_start: 0.7538 (m-30) cc_final: 0.7307 (m-30) REVERT: X 557 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6556 (mm-30) REVERT: Y 405 LYS cc_start: 0.7820 (tptt) cc_final: 0.7220 (tttt) REVERT: Y 409 ASP cc_start: 0.7609 (m-30) cc_final: 0.6970 (m-30) REVERT: Y 411 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8046 (mtmt) REVERT: Y 414 GLN cc_start: 0.7412 (mt0) cc_final: 0.7038 (mt0) REVERT: Y 437 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7461 (mtt90) REVERT: Z 365 SER cc_start: 0.8659 (t) cc_final: 0.8267 (m) REVERT: Z 441 ARG cc_start: 0.8268 (mmt-90) cc_final: 0.8061 (mmt-90) outliers start: 97 outliers final: 52 residues processed: 524 average time/residue: 0.2272 time to fit residues: 195.6700 Evaluate side-chains 464 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 405 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 515 GLN Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 385 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 535 ILE Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 171 optimal weight: 1.9990 chunk 295 optimal weight: 0.7980 chunk 221 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 374 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN P 76 GLN R 85 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 278 GLN Z 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.161978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126460 restraints weight = 48448.978| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.84 r_work: 0.3302 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34412 Z= 0.134 Angle : 0.565 10.365 46638 Z= 0.288 Chirality : 0.043 0.170 5519 Planarity : 0.004 0.046 5997 Dihedral : 6.144 102.226 4835 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.41 % Favored : 96.39 % Rotamer: Outliers : 2.81 % Allowed : 17.48 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.98 (0.13), residues: 4461 helix: -0.19 (0.11), residues: 2173 sheet: -0.73 (0.22), residues: 514 loop : -1.04 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 42 TYR 0.019 0.001 TYR X 487 PHE 0.018 0.001 PHE G 107 TRP 0.026 0.002 TRP V 73 HIS 0.003 0.001 HIS T 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (34412) covalent geometry : angle 0.56498 / 0.29 (46638) hydrogen bonds : bond 0.03436 / 2.24 ( 1668) hydrogen bonds : angle 4.53317 / 3.15 ( 4833) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 467 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.4965 (tp-100) cc_final: 0.4712 (tp40) REVERT: B 61 MET cc_start: 0.5512 (mmm) cc_final: 0.4757 (ptp) REVERT: B 95 ILE cc_start: 0.3633 (OUTLIER) cc_final: 0.2968 (mm) REVERT: B 118 LEU cc_start: 0.5887 (mt) cc_final: 0.5545 (tt) REVERT: C 81 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7596 (ttp) REVERT: D 61 MET cc_start: 0.5365 (mmt) cc_final: 0.5161 (tpp) REVERT: E 61 MET cc_start: 0.5638 (mtp) cc_final: 0.5293 (ptm) REVERT: E 105 LEU cc_start: 0.4201 (tt) cc_final: 0.3144 (mm) REVERT: F 61 MET cc_start: 0.6380 (mtm) cc_final: 0.6096 (mtm) REVERT: G 61 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.4682 (tpp) REVERT: G 105 LEU cc_start: 0.5575 (OUTLIER) cc_final: 0.5346 (tp) REVERT: G 122 PHE cc_start: 0.3738 (OUTLIER) cc_final: 0.3270 (m-80) REVERT: I 95 ILE cc_start: 0.5086 (OUTLIER) cc_final: 0.4488 (mm) REVERT: J 56 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.3399 (pp) REVERT: P 49 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7354 (m) REVERT: P 128 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7306 (mp0) REVERT: Q 14 MET cc_start: 0.6183 (tmm) cc_final: 0.5302 (tmm) REVERT: Q 48 ARG cc_start: 0.7078 (ptt-90) cc_final: 0.6810 (ptt-90) REVERT: R 32 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6690 (tp30) REVERT: R 177 GLU cc_start: 0.6939 (mp0) cc_final: 0.6117 (tp30) REVERT: S 147 ARG cc_start: 0.7392 (ptm160) cc_final: 0.7009 (ptm160) REVERT: S 271 MET cc_start: 0.8247 (ttp) cc_final: 0.7904 (tmm) REVERT: T 389 ASP cc_start: 0.8130 (t0) cc_final: 0.7880 (p0) REVERT: T 447 LYS cc_start: 0.8211 (ptpt) cc_final: 0.7451 (tttt) REVERT: T 516 ASP cc_start: 0.8325 (t70) cc_final: 0.7448 (t0) REVERT: U 45 LEU cc_start: 0.8332 (mm) cc_final: 0.7739 (mm) REVERT: U 118 MET cc_start: 0.9079 (ttt) cc_final: 0.8605 (tmm) REVERT: U 322 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8846 (tp) REVERT: U 439 MET cc_start: 0.8757 (tpp) cc_final: 0.8373 (tpt) REVERT: U 449 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6834 (mt-10) REVERT: U 502 TYR cc_start: 0.8761 (t80) cc_final: 0.8419 (t80) REVERT: U 509 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7763 (mp) REVERT: V 409 GLU cc_start: 0.7261 (tp30) cc_final: 0.6974 (tp30) REVERT: V 489 PHE cc_start: 0.6720 (m-80) cc_final: 0.6350 (m-10) REVERT: V 508 PHE cc_start: 0.8549 (m-80) cc_final: 0.8273 (m-80) REVERT: V 527 GLN cc_start: 0.8038 (mm110) cc_final: 0.7834 (mt0) REVERT: V 546 LEU cc_start: 0.7742 (tp) cc_final: 0.7462 (tp) REVERT: V 551 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7229 (ttpp) REVERT: X 49 ASP cc_start: 0.7930 (m-30) cc_final: 0.7626 (m-30) REVERT: X 178 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8562 (mttm) REVERT: X 195 GLU cc_start: 0.8692 (tp30) cc_final: 0.8307 (tp30) REVERT: X 325 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8646 (mt) REVERT: X 390 ASN cc_start: 0.8592 (m-40) cc_final: 0.8383 (m110) REVERT: X 557 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6415 (mm-30) REVERT: Y 405 LYS cc_start: 0.7761 (tptt) cc_final: 0.7007 (ttmt) REVERT: Y 409 ASP cc_start: 0.7689 (m-30) cc_final: 0.7075 (m-30) REVERT: Y 414 GLN cc_start: 0.7355 (mt0) cc_final: 0.6985 (mt0) REVERT: Y 437 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7480 (mtt90) REVERT: Z 365 SER cc_start: 0.8667 (t) cc_final: 0.8304 (m) REVERT: Z 441 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.8018 (mmt-90) outliers start: 100 outliers final: 66 residues processed: 537 average time/residue: 0.2196 time to fit residues: 193.3886 Evaluate side-chains 502 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 424 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 247 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 515 GLN Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 322 ILE Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 332 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 419 ILE Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 42 GLN Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 241 optimal weight: 3.9990 chunk 290 optimal weight: 0.0870 chunk 106 optimal weight: 0.8980 chunk 424 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 406 optimal weight: 5.9990 chunk 273 optimal weight: 0.5980 chunk 300 optimal weight: 4.9990 chunk 278 optimal weight: 0.2980 chunk 255 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 76 GLN T 549 HIS ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN V 121 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 486 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 132 GLN Z 278 GLN Z 294 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.163854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128654 restraints weight = 48803.981| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.85 r_work: 0.3300 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34412 Z= 0.106 Angle : 0.539 9.667 46638 Z= 0.273 Chirality : 0.042 0.166 5519 Planarity : 0.004 0.045 5997 Dihedral : 5.768 94.408 4834 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 3.03 % Allowed : 18.32 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.61 (0.13), residues: 4461 helix: 0.15 (0.12), residues: 2191 sheet: -0.63 (0.22), residues: 515 loop : -0.90 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 42 TYR 0.025 0.001 TYR S 256 PHE 0.023 0.001 PHE A 116 TRP 0.024 0.001 TRP V 73 HIS 0.003 0.001 HIS T 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (34412) covalent geometry : angle 0.53939 / 0.27 (46638) hydrogen bonds : bond 0.03165 / 2.06 ( 1668) hydrogen bonds : angle 4.32024 / 3.01 ( 4833) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 467 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5391 (mmm) cc_final: 0.4698 (ptp) REVERT: B 95 ILE cc_start: 0.3462 (OUTLIER) cc_final: 0.2819 (mm) REVERT: B 118 LEU cc_start: 0.5720 (mt) cc_final: 0.5405 (tt) REVERT: C 81 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7448 (ttp) REVERT: E 61 MET cc_start: 0.5561 (mtp) cc_final: 0.5272 (ptm) REVERT: E 85 LEU cc_start: 0.6139 (tp) cc_final: 0.5897 (tp) REVERT: E 105 LEU cc_start: 0.4538 (tt) cc_final: 0.3408 (mm) REVERT: G 61 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.4894 (tpp) REVERT: G 122 PHE cc_start: 0.3851 (OUTLIER) cc_final: 0.3411 (m-80) REVERT: I 95 ILE cc_start: 0.4995 (OUTLIER) cc_final: 0.4587 (mp) REVERT: J 56 LEU cc_start: 0.4396 (OUTLIER) cc_final: 0.3407 (pp) REVERT: J 109 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7031 (mt) REVERT: P 49 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.6830 (m) REVERT: Q 14 MET cc_start: 0.6307 (tmm) cc_final: 0.5351 (tmm) REVERT: R 32 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6705 (tp30) REVERT: R 177 GLU cc_start: 0.6958 (mp0) cc_final: 0.6118 (tp30) REVERT: S 101 VAL cc_start: 0.5538 (t) cc_final: 0.5315 (t) REVERT: S 147 ARG cc_start: 0.7269 (ptm160) cc_final: 0.6938 (ptm160) REVERT: S 256 TYR cc_start: 0.8925 (t80) cc_final: 0.8663 (t80) REVERT: S 271 MET cc_start: 0.8251 (ttp) cc_final: 0.7911 (tmm) REVERT: T 300 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8928 (t80) REVERT: T 335 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8530 (ttt180) REVERT: T 439 MET cc_start: 0.8795 (tpp) cc_final: 0.8506 (tpp) REVERT: T 447 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7427 (tttm) REVERT: T 516 ASP cc_start: 0.8348 (t70) cc_final: 0.7481 (t0) REVERT: U 45 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7673 (mm) REVERT: U 118 MET cc_start: 0.9051 (ttt) cc_final: 0.8574 (tmm) REVERT: U 322 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8849 (tp) REVERT: U 439 MET cc_start: 0.8765 (tpp) cc_final: 0.8412 (tpt) REVERT: U 449 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6739 (mt-10) REVERT: U 502 TYR cc_start: 0.8739 (t80) cc_final: 0.8322 (t80) REVERT: V 489 PHE cc_start: 0.6680 (m-80) cc_final: 0.6413 (m-80) REVERT: V 508 PHE cc_start: 0.8426 (m-80) cc_final: 0.7969 (m-80) REVERT: V 546 LEU cc_start: 0.7539 (tp) cc_final: 0.7296 (tp) REVERT: V 549 HIS cc_start: 0.7700 (OUTLIER) cc_final: 0.7082 (m-70) REVERT: V 555 ARG cc_start: 0.6512 (mtt90) cc_final: 0.6024 (mmt180) REVERT: X 49 ASP cc_start: 0.7869 (m-30) cc_final: 0.7610 (m-30) REVERT: X 178 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8560 (mttm) REVERT: X 195 GLU cc_start: 0.8654 (tp30) cc_final: 0.8292 (tp30) REVERT: X 325 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8634 (mt) REVERT: X 557 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6386 (mm-30) REVERT: Y 405 LYS cc_start: 0.7744 (tptt) cc_final: 0.6966 (ttmt) REVERT: Y 409 ASP cc_start: 0.7627 (m-30) cc_final: 0.7032 (m-30) REVERT: Y 411 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8029 (mtmt) REVERT: Y 414 GLN cc_start: 0.7293 (mt0) cc_final: 0.6923 (mt0) REVERT: Z 365 SER cc_start: 0.8647 (t) cc_final: 0.8301 (m) outliers start: 108 outliers final: 63 residues processed: 544 average time/residue: 0.2137 time to fit residues: 192.2179 Evaluate side-chains 497 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 419 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 515 GLN Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 322 ILE Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 332 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 391 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 127 optimal weight: 0.8980 chunk 269 optimal weight: 0.0020 chunk 407 optimal weight: 5.9990 chunk 426 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 237 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 382 optimal weight: 3.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 76 GLN S 186 ASN ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 486 GLN V 527 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 390 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.163151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128025 restraints weight = 48567.613| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.83 r_work: 0.3326 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34412 Z= 0.121 Angle : 0.550 9.608 46638 Z= 0.279 Chirality : 0.043 0.180 5519 Planarity : 0.004 0.049 5997 Dihedral : 5.684 84.585 4834 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.94 % Rotamer: Outliers : 3.11 % Allowed : 18.86 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.42 (0.13), residues: 4461 helix: 0.34 (0.12), residues: 2183 sheet: -0.60 (0.22), residues: 527 loop : -0.83 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 42 TYR 0.024 0.001 TYR S 256 PHE 0.023 0.001 PHE G 107 TRP 0.021 0.002 TRP R 37 HIS 0.002 0.001 HIS U 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (34412) covalent geometry : angle 0.54978 / 0.28 (46638) hydrogen bonds : bond 0.03225 / 2.10 ( 1668) hydrogen bonds : angle 4.29574 / 2.99 ( 4833) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 438 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5270 (mmm) cc_final: 0.4776 (ptp) REVERT: B 95 ILE cc_start: 0.3470 (OUTLIER) cc_final: 0.2831 (mm) REVERT: B 104 LEU cc_start: 0.4955 (OUTLIER) cc_final: 0.4746 (tp) REVERT: B 118 LEU cc_start: 0.5649 (mt) cc_final: 0.5314 (tt) REVERT: C 81 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7586 (ttp) REVERT: E 85 LEU cc_start: 0.6114 (tp) cc_final: 0.5893 (tp) REVERT: E 105 LEU cc_start: 0.4505 (tt) cc_final: 0.3408 (mm) REVERT: G 122 PHE cc_start: 0.3802 (OUTLIER) cc_final: 0.3337 (m-80) REVERT: I 95 ILE cc_start: 0.5118 (OUTLIER) cc_final: 0.4695 (mp) REVERT: J 56 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.3474 (pp) REVERT: J 109 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7039 (mt) REVERT: P 49 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7304 (m) REVERT: Q 14 MET cc_start: 0.6062 (tmm) cc_final: 0.5214 (tmm) REVERT: Q 48 ARG cc_start: 0.7097 (ptt-90) cc_final: 0.6804 (ptt-90) REVERT: R 32 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6672 (tp30) REVERT: R 127 PHE cc_start: 0.6065 (m-80) cc_final: 0.5815 (m-80) REVERT: R 177 GLU cc_start: 0.6918 (mp0) cc_final: 0.6054 (tp30) REVERT: S 101 VAL cc_start: 0.5650 (t) cc_final: 0.5435 (t) REVERT: S 256 TYR cc_start: 0.8990 (t80) cc_final: 0.8780 (t80) REVERT: S 271 MET cc_start: 0.8246 (ttp) cc_final: 0.7947 (tmm) REVERT: T 300 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8845 (t80) REVERT: T 439 MET cc_start: 0.8836 (tpp) cc_final: 0.8602 (tpp) REVERT: T 447 LYS cc_start: 0.8184 (ptpt) cc_final: 0.7533 (tttm) REVERT: T 449 GLU cc_start: 0.7403 (tt0) cc_final: 0.7011 (tp30) REVERT: T 516 ASP cc_start: 0.8301 (t70) cc_final: 0.7440 (t0) REVERT: U 45 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7797 (mm) REVERT: U 60 GLN cc_start: 0.7840 (mt0) cc_final: 0.7540 (tt0) REVERT: U 118 MET cc_start: 0.9041 (ttt) cc_final: 0.8581 (tmm) REVERT: U 322 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8813 (tp) REVERT: U 439 MET cc_start: 0.8730 (tpp) cc_final: 0.8328 (tpt) REVERT: U 455 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7486 (tm-30) REVERT: U 502 TYR cc_start: 0.8789 (t80) cc_final: 0.8405 (t80) REVERT: V 253 GLN cc_start: 0.8971 (tt0) cc_final: 0.8732 (tt0) REVERT: V 489 PHE cc_start: 0.6525 (m-80) cc_final: 0.6262 (m-80) REVERT: V 508 PHE cc_start: 0.8475 (m-80) cc_final: 0.7898 (m-80) REVERT: V 549 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7194 (m-70) REVERT: V 555 ARG cc_start: 0.6735 (mtt90) cc_final: 0.6172 (mmt180) REVERT: X 49 ASP cc_start: 0.7841 (m-30) cc_final: 0.7578 (m-30) REVERT: X 178 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8582 (mttm) REVERT: X 195 GLU cc_start: 0.8678 (tp30) cc_final: 0.8347 (tp30) REVERT: X 325 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8657 (mt) REVERT: X 557 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6437 (mm-30) REVERT: Y 159 ILE cc_start: 0.8354 (mp) cc_final: 0.8128 (mp) REVERT: Y 405 LYS cc_start: 0.7817 (tptt) cc_final: 0.7060 (ttmt) REVERT: Y 409 ASP cc_start: 0.7634 (m-30) cc_final: 0.7039 (m-30) REVERT: Y 411 LYS cc_start: 0.8337 (mtmt) cc_final: 0.8117 (mtmt) REVERT: Y 414 GLN cc_start: 0.7326 (mt0) cc_final: 0.6976 (mt0) REVERT: Y 437 ARG cc_start: 0.7954 (mtt-85) cc_final: 0.7675 (mtt90) REVERT: Z 365 SER cc_start: 0.8689 (t) cc_final: 0.8354 (m) outliers start: 111 outliers final: 78 residues processed: 516 average time/residue: 0.2201 time to fit residues: 186.3287 Evaluate side-chains 508 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 416 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 322 ILE Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 332 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 419 ILE Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 59 optimal weight: 3.9990 chunk 433 optimal weight: 3.9990 chunk 424 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 chunk 436 optimal weight: 20.0000 chunk 246 optimal weight: 5.9990 chunk 137 optimal weight: 0.0770 chunk 145 optimal weight: 2.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN F 94 ASN P 76 GLN Q 43 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 293 ASN T 104 GLN T 228 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 486 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 390 ASN Y 132 GLN Z 78 GLN Z 198 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122402 restraints weight = 48924.732| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.68 r_work: 0.3218 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 34412 Z= 0.229 Angle : 0.640 9.647 46638 Z= 0.327 Chirality : 0.047 0.219 5519 Planarity : 0.004 0.063 5997 Dihedral : 6.053 85.862 4833 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.80 % Favored : 94.96 % Rotamer: Outliers : 3.42 % Allowed : 19.19 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.64 (0.13), residues: 4461 helix: 0.15 (0.11), residues: 2175 sheet: -0.71 (0.22), residues: 520 loop : -0.91 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 42 TYR 0.024 0.002 TYR S 256 PHE 0.020 0.002 PHE A 116 TRP 0.037 0.003 TRP R 37 HIS 0.005 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 (34412) covalent geometry : angle 0.63969 / 0.33 (46638) hydrogen bonds : bond 0.03935 / 2.56 ( 1668) hydrogen bonds : angle 4.63500 / 3.21 ( 4833) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 414 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5700 (mmm) cc_final: 0.5062 (ptp) REVERT: B 95 ILE cc_start: 0.3930 (OUTLIER) cc_final: 0.3231 (mm) REVERT: C 124 ILE cc_start: 0.5367 (OUTLIER) cc_final: 0.4958 (tp) REVERT: G 122 PHE cc_start: 0.3598 (OUTLIER) cc_final: 0.3215 (m-80) REVERT: I 95 ILE cc_start: 0.4926 (OUTLIER) cc_final: 0.4244 (mm) REVERT: Q 14 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5224 (tmm) REVERT: Q 48 ARG cc_start: 0.7122 (ptt-90) cc_final: 0.6778 (ptt-90) REVERT: R 32 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: R 177 GLU cc_start: 0.7011 (mp0) cc_final: 0.6135 (tp30) REVERT: S 234 GLU cc_start: 0.7941 (tp30) cc_final: 0.7703 (tp30) REVERT: S 245 ASP cc_start: 0.7860 (m-30) cc_final: 0.7408 (m-30) REVERT: S 256 TYR cc_start: 0.8986 (t80) cc_final: 0.8749 (t80) REVERT: S 271 MET cc_start: 0.8314 (ttp) cc_final: 0.7937 (tmm) REVERT: T 300 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8744 (t80) REVERT: T 335 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8901 (ttp-170) REVERT: T 439 MET cc_start: 0.8886 (tpp) cc_final: 0.8660 (tpp) REVERT: T 447 LYS cc_start: 0.8240 (ptpt) cc_final: 0.7509 (tttt) REVERT: T 449 GLU cc_start: 0.7426 (tt0) cc_final: 0.7011 (tp30) REVERT: T 516 ASP cc_start: 0.8412 (t70) cc_final: 0.7567 (t0) REVERT: U 45 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7921 (mm) REVERT: U 60 GLN cc_start: 0.7944 (mt0) cc_final: 0.7594 (tt0) REVERT: U 118 MET cc_start: 0.9122 (ttt) cc_final: 0.8624 (tmm) REVERT: U 322 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8875 (tp) REVERT: U 449 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6645 (mt-10) REVERT: U 502 TYR cc_start: 0.8805 (t80) cc_final: 0.8443 (t80) REVERT: V 476 ARG cc_start: 0.7443 (tpp80) cc_final: 0.6779 (tpp80) REVERT: V 508 PHE cc_start: 0.8601 (m-80) cc_final: 0.7900 (m-80) REVERT: V 549 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7176 (m-70) REVERT: V 555 ARG cc_start: 0.6746 (mtt90) cc_final: 0.6053 (mmt180) REVERT: X 49 ASP cc_start: 0.7917 (m-30) cc_final: 0.7701 (m-30) REVERT: X 178 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8604 (mttm) REVERT: X 195 GLU cc_start: 0.8679 (tp30) cc_final: 0.8334 (tp30) REVERT: X 337 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9131 (pt0) REVERT: X 557 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6496 (mm-30) REVERT: Y 405 LYS cc_start: 0.7771 (tptt) cc_final: 0.7009 (ttmt) REVERT: Y 409 ASP cc_start: 0.7714 (m-30) cc_final: 0.7022 (m-30) REVERT: Y 411 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7939 (mtmt) REVERT: Z 323 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8411 (mm-30) REVERT: Z 365 SER cc_start: 0.8666 (t) cc_final: 0.8283 (m) outliers start: 122 outliers final: 83 residues processed: 507 average time/residue: 0.2159 time to fit residues: 177.9317 Evaluate side-chains 492 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 397 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 14 MET Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 37 TRP Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 210 ASP Chi-restraints excluded: chain U residue 322 ILE Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 332 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 486 GLN Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 337 GLN Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 292 GLN Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 41 optimal weight: 4.9990 chunk 371 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 379 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 263 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 233 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN P 76 GLN P 148 HIS ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 486 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Z 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.161610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125977 restraints weight = 48607.958| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.68 r_work: 0.3311 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34412 Z= 0.126 Angle : 0.563 9.394 46638 Z= 0.287 Chirality : 0.043 0.187 5519 Planarity : 0.004 0.048 5997 Dihedral : 5.656 88.463 4833 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 3.09 % Allowed : 19.58 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.38 (0.13), residues: 4461 helix: 0.38 (0.12), residues: 2183 sheet: -0.61 (0.22), residues: 540 loop : -0.80 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 42 TYR 0.035 0.001 TYR Q 19 PHE 0.022 0.001 PHE U 300 TRP 0.034 0.002 TRP R 37 HIS 0.015 0.001 HIS V 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (34412) covalent geometry : angle 0.56295 / 0.29 (46638) hydrogen bonds : bond 0.03336 / 2.18 ( 1668) hydrogen bonds : angle 4.39741 / 3.06 ( 4833) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 433 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5604 (mmm) cc_final: 0.5065 (ptp) REVERT: B 95 ILE cc_start: 0.3871 (OUTLIER) cc_final: 0.3198 (mm) REVERT: B 98 GLN cc_start: 0.6073 (OUTLIER) cc_final: 0.5871 (tt0) REVERT: G 61 MET cc_start: 0.4957 (mtm) cc_final: 0.3972 (tpp) REVERT: G 122 PHE cc_start: 0.3758 (OUTLIER) cc_final: 0.3271 (m-80) REVERT: I 95 ILE cc_start: 0.4974 (OUTLIER) cc_final: 0.4595 (mp) REVERT: J 56 LEU cc_start: 0.4363 (mm) cc_final: 0.3402 (pp) REVERT: J 109 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6808 (mt) REVERT: P 49 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7212 (m) REVERT: Q 14 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5198 (tmm) REVERT: Q 42 ARG cc_start: 0.6911 (mtm-85) cc_final: 0.6523 (mtm-85) REVERT: R 32 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6739 (tp30) REVERT: R 177 GLU cc_start: 0.6953 (mp0) cc_final: 0.6108 (tp30) REVERT: S 101 VAL cc_start: 0.5787 (t) cc_final: 0.5559 (t) REVERT: S 196 LYS cc_start: 0.8018 (tptt) cc_final: 0.7489 (tptm) REVERT: S 256 TYR cc_start: 0.8990 (t80) cc_final: 0.8763 (t80) REVERT: S 271 MET cc_start: 0.8243 (ttp) cc_final: 0.7926 (tmm) REVERT: T 300 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8846 (t80) REVERT: T 335 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8474 (ttt180) REVERT: T 447 LYS cc_start: 0.8134 (ptpt) cc_final: 0.7512 (tttm) REVERT: T 449 GLU cc_start: 0.7306 (tt0) cc_final: 0.6918 (tp30) REVERT: T 516 ASP cc_start: 0.8350 (t70) cc_final: 0.7510 (t0) REVERT: T 541 LYS cc_start: 0.7526 (ttpp) cc_final: 0.7010 (tttp) REVERT: U 45 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7818 (mm) REVERT: U 60 GLN cc_start: 0.7915 (mt0) cc_final: 0.7629 (tt0) REVERT: U 118 MET cc_start: 0.9046 (ttt) cc_final: 0.8525 (tmm) REVERT: U 322 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8827 (tp) REVERT: U 439 MET cc_start: 0.8742 (tpp) cc_final: 0.8361 (tpt) REVERT: U 449 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6615 (mt-10) REVERT: U 502 TYR cc_start: 0.8743 (t80) cc_final: 0.8534 (t80) REVERT: U 529 ASN cc_start: 0.7783 (t0) cc_final: 0.7334 (t0) REVERT: V 253 GLN cc_start: 0.8967 (tt0) cc_final: 0.8718 (tt0) REVERT: V 476 ARG cc_start: 0.7334 (tpp80) cc_final: 0.6967 (tpp80) REVERT: V 489 PHE cc_start: 0.6678 (m-80) cc_final: 0.6365 (m-80) REVERT: V 508 PHE cc_start: 0.8457 (m-80) cc_final: 0.7870 (m-80) REVERT: V 549 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.7103 (m-70) REVERT: V 551 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7521 (ttpp) REVERT: V 555 ARG cc_start: 0.6688 (mtt90) cc_final: 0.6137 (mmt180) REVERT: X 49 ASP cc_start: 0.7816 (m-30) cc_final: 0.7569 (m-30) REVERT: X 178 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8598 (mttm) REVERT: X 195 GLU cc_start: 0.8679 (tp30) cc_final: 0.8360 (tp30) REVERT: X 557 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6472 (mm-30) REVERT: Y 405 LYS cc_start: 0.7805 (tptt) cc_final: 0.7089 (ttmt) REVERT: Y 409 ASP cc_start: 0.7619 (m-30) cc_final: 0.7053 (m-30) REVERT: Y 411 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7978 (mtmt) REVERT: Y 437 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7667 (mtt90) REVERT: Z 365 SER cc_start: 0.8717 (t) cc_final: 0.8384 (m) outliers start: 110 outliers final: 76 residues processed: 513 average time/residue: 0.2098 time to fit residues: 177.0740 Evaluate side-chains 499 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 410 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 14 MET Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 37 TRP Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 202 SER Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 322 ILE Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 332 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 391 VAL Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 307 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 438 optimal weight: 0.8980 chunk 397 optimal weight: 0.5980 chunk 254 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 433 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 76 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS V 486 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 390 ASN Y 198 ASN Y 414 GLN Z 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.162241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126775 restraints weight = 48489.588| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.63 r_work: 0.3312 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34412 Z= 0.124 Angle : 0.568 14.772 46638 Z= 0.287 Chirality : 0.043 0.185 5519 Planarity : 0.004 0.050 5997 Dihedral : 5.539 87.466 4833 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 2.97 % Allowed : 19.75 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.21 (0.13), residues: 4461 helix: 0.52 (0.12), residues: 2177 sheet: -0.51 (0.22), residues: 536 loop : -0.72 (0.16), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 42 TYR 0.044 0.001 TYR Q 19 PHE 0.021 0.001 PHE U 300 TRP 0.033 0.003 TRP V 73 HIS 0.004 0.001 HIS V 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (34412) covalent geometry : angle 0.56764 / 0.29 (46638) hydrogen bonds : bond 0.03304 / 2.16 ( 1668) hydrogen bonds : angle 4.33362 / 3.01 ( 4833) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 431 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5439 (mmm) cc_final: 0.4912 (ptp) REVERT: B 95 ILE cc_start: 0.3929 (OUTLIER) cc_final: 0.3303 (mm) REVERT: G 61 MET cc_start: 0.4912 (mtm) cc_final: 0.3870 (tpp) REVERT: G 122 PHE cc_start: 0.3790 (OUTLIER) cc_final: 0.3349 (m-80) REVERT: I 85 LEU cc_start: 0.7629 (mt) cc_final: 0.7176 (tp) REVERT: I 95 ILE cc_start: 0.4918 (OUTLIER) cc_final: 0.4551 (mp) REVERT: J 56 LEU cc_start: 0.4092 (OUTLIER) cc_final: 0.3190 (pp) REVERT: J 109 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6869 (mt) REVERT: P 49 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7281 (m) REVERT: Q 10 ARG cc_start: 0.6172 (tpp-160) cc_final: 0.5629 (tpt-90) REVERT: Q 14 MET cc_start: 0.5831 (OUTLIER) cc_final: 0.5091 (tmm) REVERT: R 177 GLU cc_start: 0.7007 (mp0) cc_final: 0.6165 (tp30) REVERT: S 101 VAL cc_start: 0.5634 (t) cc_final: 0.5405 (t) REVERT: S 196 LYS cc_start: 0.8064 (tptt) cc_final: 0.7517 (tptm) REVERT: S 256 TYR cc_start: 0.8944 (t80) cc_final: 0.8689 (t80) REVERT: S 271 MET cc_start: 0.8258 (ttp) cc_final: 0.7915 (tmm) REVERT: T 300 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8777 (t80) REVERT: T 335 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8417 (ttt180) REVERT: T 447 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7529 (tttm) REVERT: T 449 GLU cc_start: 0.7292 (tt0) cc_final: 0.6907 (tp30) REVERT: T 516 ASP cc_start: 0.8347 (t70) cc_final: 0.7506 (t0) REVERT: T 541 LYS cc_start: 0.7435 (ttpp) cc_final: 0.6903 (tttp) REVERT: U 45 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7811 (mm) REVERT: U 60 GLN cc_start: 0.7812 (mt0) cc_final: 0.7519 (tt0) REVERT: U 118 MET cc_start: 0.9037 (ttt) cc_final: 0.8379 (tmm) REVERT: U 322 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8836 (tp) REVERT: U 439 MET cc_start: 0.8751 (tpp) cc_final: 0.8379 (tpt) REVERT: U 449 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6731 (mt-10) REVERT: U 529 ASN cc_start: 0.7786 (t0) cc_final: 0.7337 (t0) REVERT: V 253 GLN cc_start: 0.8922 (tt0) cc_final: 0.8665 (tt0) REVERT: V 476 ARG cc_start: 0.7282 (tpp80) cc_final: 0.6953 (tpp80) REVERT: V 489 PHE cc_start: 0.6595 (m-80) cc_final: 0.6340 (m-80) REVERT: V 539 ASN cc_start: 0.7954 (m-40) cc_final: 0.7679 (t0) REVERT: V 549 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7072 (m-70) REVERT: V 551 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7573 (ttpp) REVERT: V 555 ARG cc_start: 0.6664 (mtt90) cc_final: 0.6211 (mmt180) REVERT: X 49 ASP cc_start: 0.7815 (m-30) cc_final: 0.7561 (m-30) REVERT: X 178 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8604 (mttm) REVERT: X 195 GLU cc_start: 0.8652 (tp30) cc_final: 0.8310 (tp30) REVERT: X 557 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6447 (mm-30) REVERT: Y 405 LYS cc_start: 0.7809 (tptt) cc_final: 0.7010 (ttmt) REVERT: Y 409 ASP cc_start: 0.7592 (m-30) cc_final: 0.6990 (m-30) REVERT: Y 437 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.7600 (mtt90) REVERT: Z 365 SER cc_start: 0.8678 (t) cc_final: 0.8327 (m) outliers start: 106 outliers final: 84 residues processed: 507 average time/residue: 0.2161 time to fit residues: 178.9829 Evaluate side-chains 508 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 412 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 14 MET Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 37 TRP Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 202 SER Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 282 MET Chi-restraints excluded: chain U residue 322 ILE Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 518 VAL Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 332 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 279 ASP Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 198 ASN Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 391 VAL Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 42 GLN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 292 GLN Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 109 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 325 optimal weight: 0.9990 chunk 404 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 315 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 98 GLN P 76 GLN S 185 HIS ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 61 HIS ** V 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 486 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 390 ASN Y 414 GLN Z 42 GLN Z 78 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.162918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127563 restraints weight = 48756.258| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.66 r_work: 0.3353 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34412 Z= 0.119 Angle : 0.563 13.587 46638 Z= 0.284 Chirality : 0.043 0.179 5519 Planarity : 0.004 0.054 5997 Dihedral : 5.445 86.047 4833 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.03 % Rotamer: Outliers : 2.75 % Allowed : 20.12 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.13 (0.13), residues: 4461 helix: 0.59 (0.12), residues: 2189 sheet: -0.48 (0.22), residues: 544 loop : -0.70 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 42 TYR 0.050 0.001 TYR Q 19 PHE 0.020 0.001 PHE U 300 TRP 0.030 0.002 TRP R 37 HIS 0.004 0.001 HIS S 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (34412) covalent geometry : angle 0.56337 / 0.28 (46638) hydrogen bonds : bond 0.03210 / 2.10 ( 1668) hydrogen bonds : angle 4.27721 / 2.98 ( 4833) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 428 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5419 (mmm) cc_final: 0.4910 (ptp) REVERT: B 95 ILE cc_start: 0.4048 (OUTLIER) cc_final: 0.3080 (mm) REVERT: D 81 MET cc_start: 0.6678 (mmm) cc_final: 0.6374 (mmt) REVERT: G 61 MET cc_start: 0.4830 (mtm) cc_final: 0.3882 (tpp) REVERT: G 122 PHE cc_start: 0.3733 (OUTLIER) cc_final: 0.3283 (m-80) REVERT: I 95 ILE cc_start: 0.4915 (OUTLIER) cc_final: 0.4556 (mp) REVERT: J 56 LEU cc_start: 0.4058 (OUTLIER) cc_final: 0.3156 (pp) REVERT: J 109 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6703 (mt) REVERT: P 49 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7214 (m) REVERT: Q 10 ARG cc_start: 0.6178 (tpp-160) cc_final: 0.5809 (ttt-90) REVERT: Q 14 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5212 (tmm) REVERT: Q 40 GLN cc_start: 0.5492 (tp-100) cc_final: 0.5259 (mp10) REVERT: R 32 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6680 (tp30) REVERT: R 177 GLU cc_start: 0.6992 (mp0) cc_final: 0.6157 (tp30) REVERT: S 101 VAL cc_start: 0.5702 (t) cc_final: 0.5479 (t) REVERT: S 196 LYS cc_start: 0.8131 (tptt) cc_final: 0.7559 (tptm) REVERT: S 256 TYR cc_start: 0.8964 (t80) cc_final: 0.8739 (t80) REVERT: S 271 MET cc_start: 0.8230 (ttp) cc_final: 0.7927 (tmm) REVERT: T 300 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8795 (t80) REVERT: T 335 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8449 (ttt180) REVERT: T 447 LYS cc_start: 0.8144 (ptpt) cc_final: 0.7585 (tttm) REVERT: T 449 GLU cc_start: 0.7283 (tt0) cc_final: 0.6922 (tp30) REVERT: T 516 ASP cc_start: 0.8350 (t70) cc_final: 0.7496 (t0) REVERT: T 541 LYS cc_start: 0.7480 (ttpp) cc_final: 0.7016 (ttmm) REVERT: U 45 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7797 (mm) REVERT: U 47 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6581 (mm-30) REVERT: U 60 GLN cc_start: 0.7815 (mt0) cc_final: 0.7583 (tt0) REVERT: U 118 MET cc_start: 0.9019 (ttt) cc_final: 0.8371 (tmm) REVERT: U 439 MET cc_start: 0.8728 (tpp) cc_final: 0.8346 (tpt) REVERT: U 449 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6726 (mt-10) REVERT: U 502 TYR cc_start: 0.8699 (t80) cc_final: 0.8319 (t80) REVERT: V 253 GLN cc_start: 0.8906 (tt0) cc_final: 0.8615 (tt0) REVERT: V 476 ARG cc_start: 0.7267 (tpp80) cc_final: 0.6982 (tpp80) REVERT: V 489 PHE cc_start: 0.6609 (m-80) cc_final: 0.6360 (m-80) REVERT: V 539 ASN cc_start: 0.7960 (m-40) cc_final: 0.7693 (t0) REVERT: V 549 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.7143 (m-70) REVERT: V 551 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7581 (ttpp) REVERT: V 555 ARG cc_start: 0.6664 (mtt90) cc_final: 0.6214 (mmt180) REVERT: X 49 ASP cc_start: 0.7777 (m-30) cc_final: 0.7526 (m-30) REVERT: X 178 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8595 (mttm) REVERT: X 195 GLU cc_start: 0.8639 (tp30) cc_final: 0.8312 (tp30) REVERT: X 557 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6502 (mm-30) REVERT: Y 405 LYS cc_start: 0.7846 (tptt) cc_final: 0.7084 (ttmt) REVERT: Y 409 ASP cc_start: 0.7586 (m-30) cc_final: 0.6993 (m-30) REVERT: Y 437 ARG cc_start: 0.7942 (mtt-85) cc_final: 0.7658 (mtt90) REVERT: Z 365 SER cc_start: 0.8665 (t) cc_final: 0.8356 (m) outliers start: 98 outliers final: 80 residues processed: 499 average time/residue: 0.2149 time to fit residues: 175.2424 Evaluate side-chains 503 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 411 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 14 MET Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 37 TRP Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 202 SER Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 335 ARG Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 282 MET Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 518 VAL Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 332 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 466 LEU Chi-restraints excluded: chain V residue 486 GLN Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 549 HIS Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 198 ASN Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 291 THR Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 391 VAL Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 292 GLN Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 404 optimal weight: 0.9980 chunk 357 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 396 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 354 optimal weight: 0.8980 chunk 297 optimal weight: 0.0970 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 76 GLN Q 21 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 486 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.162930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.128256 restraints weight = 48587.692| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.82 r_work: 0.3333 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34412 Z= 0.120 Angle : 0.563 13.557 46638 Z= 0.284 Chirality : 0.043 0.175 5519 Planarity : 0.004 0.050 5997 Dihedral : 5.402 85.659 4833 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.83 % Rotamer: Outliers : 2.75 % Allowed : 20.34 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.07 (0.13), residues: 4461 helix: 0.66 (0.12), residues: 2189 sheet: -0.45 (0.22), residues: 546 loop : -0.69 (0.16), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 42 TYR 0.049 0.001 TYR Q 19 PHE 0.020 0.001 PHE U 300 TRP 0.029 0.002 TRP R 37 HIS 0.003 0.001 HIS V 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (34412) covalent geometry : angle 0.56326 / 0.28 (46638) hydrogen bonds : bond 0.03208 / 2.10 ( 1668) hydrogen bonds : angle 4.24559 / 2.96 ( 4833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10688.12 seconds wall clock time: 183 minutes 9.67 seconds (10989.67 seconds total)