Starting phenix.real_space_refine on Mon Sep 14 22:26:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rdy_4835/09_2026/6rdy_4835.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rdy_4835/09_2026/6rdy_4835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6rdy_4835/09_2026/6rdy_4835.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rdy_4835/09_2026/6rdy_4835.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rdy_4835/09_2026/6rdy_4835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rdy_4835/09_2026/6rdy_4835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rdy_4835/09_2026/6rdy_4835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rdy_4835/09_2026/6rdy_4835.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 275 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.61, per 1000 atoms: 0.22 Number of scatterers: 33891 At special positions: 0 Unit cell: (163.215, 134.784, 208.494, 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: 2.99 Conformation dependent library (CDL) restraints added in 1.5 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 27 sheets defined 51.5% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 55 through 68 removed outlier: 4.500A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.692A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.633A pdb=" N PHE A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.767A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.926A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 127 removed outlier: 3.789A pdb=" N LEU B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.097A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 90 removed outlier: 4.448A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.698A pdb=" N VAL C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.532A pdb=" N SER D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 4.081A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.840A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 66 removed outlier: 3.742A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 90 removed outlier: 3.647A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.560A pdb=" N ILE E 95 " --> pdb=" O ASN E 92 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 97 through 126 removed outlier: 4.249A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.972A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.014A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 127 removed outlier: 4.035A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.584A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 3.733A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.700A 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 69 through 92 removed outlier: 4.398A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.543A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 67 removed outlier: 3.974A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 3.798A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 Processing helix chain 'I' and resid 97 through 126 removed outlier: 3.615A pdb=" N GLY I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE I 126 " --> pdb=" O PHE I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.366A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 90 removed outlier: 3.782A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing helix chain 'J' and resid 95 through 127 removed outlier: 3.877A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 65 removed outlier: 3.648A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU P 56 " --> pdb=" O GLN P 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.691A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN P 76 " --> pdb=" O ASP P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'P' and resid 103 through 108 removed outlier: 5.160A pdb=" N SER P 106 " --> pdb=" O LYS P 103 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL P 108 " --> pdb=" O ILE P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 129 removed outlier: 3.645A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP P 127 " --> pdb=" O GLU P 123 " (cutoff:3.500A) removed outlier: 3.566A 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 144 removed outlier: 3.948A pdb=" N GLU P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 4.006A 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 40 removed outlier: 3.868A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 41 removed outlier: 4.269A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.782A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (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: 3.797A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 Processing helix chain 'S' and resid 41 through 69 removed outlier: 3.620A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.575A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 128 Processing helix chain 'S' and resid 143 through 151 removed outlier: 3.663A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 183 Processing helix chain 'S' and resid 212 through 222 removed outlier: 6.304A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 241 Processing helix chain 'S' and resid 242 through 312 removed outlier: 4.128A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.895A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 removed outlier: 3.655A pdb=" N THR T 159 " --> pdb=" O GLY T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 211 Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.809A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 removed outlier: 3.550A pdb=" N GLN T 278 " --> pdb=" O LYS T 274 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 285 Processing helix chain 'T' and resid 295 through 311 Proline residue: T 303 - end of helix Processing helix chain 'T' and resid 311 through 316 removed outlier: 3.539A pdb=" N THR T 316 " --> pdb=" O TYR T 312 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.701A pdb=" N ALA T 333 " --> pdb=" O LYS T 329 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.617A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU T 362 " --> pdb=" O HIS T 358 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 400 removed outlier: 3.513A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 409 through 415 removed outlier: 3.752A pdb=" N PHE T 413 " --> pdb=" O GLU T 409 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.889A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 430 through 435' Processing helix chain 'T' and resid 436 through 441 removed outlier: 4.212A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 450 Processing helix chain 'T' and resid 450 through 460 removed outlier: 4.185A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.723A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR T 481 " --> pdb=" O GLY T 477 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 499 removed outlier: 3.602A pdb=" N THR T 498 " --> pdb=" O ILE T 494 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 494 through 499' Processing helix chain 'T' and resid 501 through 506 Processing helix chain 'T' and resid 517 through 527 removed outlier: 4.451A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL T 524 " --> pdb=" O ALA T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 540 removed outlier: 3.818A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 552 removed outlier: 4.360A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 47 removed outlier: 3.801A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 50 No H-bonds generated for 'chain 'U' and resid 48 through 50' Processing helix chain 'U' and resid 58 through 71 removed outlier: 5.375A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.837A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.704A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU U 160 " --> pdb=" O PRO U 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 156 through 160' Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.589A pdb=" N VAL U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.917A 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 Processing helix chain 'U' and resid 295 through 315 Proline residue: U 303 - end of helix removed outlier: 3.999A 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 326 through 340 Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.537A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.888A 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: 4.056A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 485 removed outlier: 4.262A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 496 Processing helix chain 'U' and resid 497 through 506 removed outlier: 4.234A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.594A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 4.125A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 3.628A pdb=" N LEU U 554 " --> pdb=" O LEU U 550 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 Processing helix chain 'V' and resid 58 through 67 removed outlier: 4.214A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 4.224A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE V 138 " --> pdb=" O ASP V 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 134 through 138' Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.816A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.703A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 341 removed outlier: 3.548A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.610A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.609A pdb=" N LEU V 372 " --> pdb=" O SER V 369 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 369 through 373' Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 430 through 435 removed outlier: 3.685A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN V 435 " --> pdb=" O SER V 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 430 through 435' Processing helix chain 'V' and resid 438 through 456 removed outlier: 3.797A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 3.847A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 Processing helix chain 'V' and resid 513 through 517 removed outlier: 3.880A pdb=" N ASP V 516 " --> pdb=" O ARG V 513 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 513 through 517' Processing helix chain 'V' and resid 521 through 526 Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.563A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 removed outlier: 4.027A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.591A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 153 removed outlier: 3.596A 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: 4.839A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 230 removed outlier: 3.625A pdb=" N GLU X 229 " --> pdb=" O ARG X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 242 removed outlier: 3.500A pdb=" N ASN X 241 " --> pdb=" O GLU X 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 260 removed outlier: 3.659A pdb=" N ARG X 258 " --> pdb=" O PRO X 254 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA X 259 " --> pdb=" O PRO X 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG X 260 " --> pdb=" O GLY X 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 254 through 260' Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.786A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 298 removed outlier: 3.948A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (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 365 through 370 removed outlier: 3.675A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 421 removed outlier: 7.662A pdb=" N ALA X 394 " --> pdb=" O ASN X 390 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N GLU X 395 " --> pdb=" O VAL X 391 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS X 396 " --> pdb=" O ILE X 392 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 425 Processing helix chain 'X' and resid 426 through 442 removed outlier: 3.543A pdb=" N THR X 432 " --> pdb=" O GLU X 428 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 455 removed outlier: 3.683A pdb=" N THR X 454 " --> pdb=" O ALA X 450 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY X 455 " --> pdb=" O GLU X 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 450 through 455' Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 483 through 487 Processing helix chain 'X' and resid 491 through 505 removed outlier: 3.847A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 533 removed outlier: 3.545A pdb=" N LEU X 530 " --> pdb=" O SER X 526 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 526 through 533' Processing helix chain 'Y' and resid 114 through 118 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: 3.997A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 removed outlier: 3.556A pdb=" N ALA Y 259 " --> pdb=" O PRO Y 255 " (cutoff:3.500A) Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.639A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.791A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 4.038A 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 353 Processing helix chain 'Y' and resid 354 through 358 removed outlier: 3.971A pdb=" N LEU Y 358 " --> pdb=" O PHE Y 355 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 371 Processing helix chain 'Y' and resid 393 through 421 removed outlier: 3.726A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA Y 418 " --> pdb=" O GLN Y 414 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 443 removed outlier: 3.825A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) Processing helix chain 'Y' and resid 448 through 452 removed outlier: 4.134A pdb=" N VAL Y 452 " --> pdb=" O VAL Y 449 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 474 removed outlier: 3.600A pdb=" N GLY Y 472 " --> pdb=" O SER Y 468 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 508 removed outlier: 3.708A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 532 Processing helix chain 'Y' and resid 544 through 555 removed outlier: 4.221A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 removed outlier: 3.641A pdb=" N THR Z 117 " --> pdb=" O GLY Z 114 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU Z 118 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 114 through 118' Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 188 through 204 removed outlier: 3.532A pdb=" N LEU Z 192 " --> pdb=" O GLY Z 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 229 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.615A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 259 removed outlier: 3.646A pdb=" N ARG Z 258 " --> pdb=" O PRO Z 254 " (cutoff:3.500A) Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.500A pdb=" N THR Z 264 " --> pdb=" O ARG Z 260 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.510A pdb=" N LEU Z 301 " --> pdb=" O VAL Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 removed outlier: 4.418A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 355 Processing helix chain 'Z' and resid 367 through 372 Processing helix chain 'Z' and resid 388 through 393 removed outlier: 3.612A pdb=" N ILE Z 392 " --> pdb=" O ASN Z 388 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY Z 393 " --> pdb=" O PRO Z 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 388 through 393' Processing helix chain 'Z' and resid 393 through 412 Processing helix chain 'Z' and resid 426 through 440 removed outlier: 3.576A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 455 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.907A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 3.732A 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 502 removed outlier: 3.736A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 532 Processing sheet with id=AA1, first strand: chain 'Q' and resid 62 through 63 removed outlier: 7.097A pdb=" N GLN S 159 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL S 139 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA S 161 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER S 141 " --> pdb=" O ALA S 161 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ALA S 163 " --> pdb=" O SER S 141 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER S 100 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER S 189 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 85 through 86 removed outlier: 3.551A pdb=" N LYS R 86 " --> pdb=" O PHE R 70 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY R 132 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE R 108 " --> pdb=" O GLU S 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 96 through 100 removed outlier: 6.751A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.516A 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: 6.716A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS T 116 " --> pdb=" O PHE T 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 107 through 111 removed outlier: 6.894A pdb=" N LEU T 108 " --> pdb=" O THR T 147 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR T 147 " --> pdb=" O LEU T 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 121 through 122 removed outlier: 4.664A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AA8, first strand: chain 'T' and resid 163 through 164 removed outlier: 6.274A pdb=" N THR T 164 " --> pdb=" O SER T 289 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR T 378 " --> pdb=" O GLY T 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 382 through 384 removed outlier: 7.965A pdb=" N ILE T 383 " --> pdb=" O GLU T 221 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE T 223 " --> pdb=" O ILE T 383 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'X' and resid 62 through 65 removed outlier: 4.732A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'X' and resid 62 through 65 removed outlier: 4.732A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 37 through 44 current: chain 'U' and resid 94 through 99 removed outlier: 6.660A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AB4, first strand: chain 'U' and resid 163 through 164 removed outlier: 6.448A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR U 256 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE U 323 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL U 258 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP U 325 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL U 260 " --> pdb=" O ASP U 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR U 378 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU U 222 " --> pdb=" O GLY U 404 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'V' and resid 116 through 122 removed outlier: 3.815A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU Z 72 " --> pdb=" O VAL Z 65 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AB7, first strand: chain 'V' and resid 163 through 164 Processing sheet with id=AB8, first strand: chain 'X' and resid 110 through 113 Processing sheet with id=AB9, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.088A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.677A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 279 through 282 removed outlier: 6.220A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL X 339 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU X 181 " --> pdb=" O VAL X 339 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY X 180 " --> pdb=" O THR X 362 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC4, first strand: chain 'Y' and resid 110 through 113 removed outlier: 4.501A pdb=" N VAL Y 113 " --> pdb=" O ASP Y 139 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP Y 139 " --> pdb=" O VAL Y 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.809A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N TYR Y 340 " --> pdb=" O VAL Y 284 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE Y 179 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL Y 339 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU Y 181 " --> pdb=" O VAL Y 339 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA Y 360 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR Y 383 " --> pdb=" O THR Y 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.314A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id=AC8, first strand: chain 'Z' and resid 178 through 181 removed outlier: 5.768A pdb=" N VAL Z 280 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL Z 336 " --> pdb=" O VAL Z 280 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU Z 282 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA Z 338 " --> pdb=" O LEU Z 282 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL Z 284 " --> pdb=" O ALA Z 338 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER Z 208 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL Z 247 " --> pdb=" O SER Z 208 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE Z 210 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY Z 249 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY Z 212 " --> pdb=" O GLY Z 249 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 559 through 561 1602 hydrogen bonds defined for protein. 4629 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: 7.02 Time building geometry restraints manager: 3.92 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: 9257 1.33 - 1.45: 5662 1.45 - 1.57: 19272 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34412 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.02e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.90e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C4 ATP T1001 " pdb=" N9 ATP T1001 " ideal model delta sigma weight residual 1.374 1.312 0.062 1.00e-02 1.00e+04 3.82e+01 bond pdb=" C5 ATP U1001 " pdb=" N7 ATP U1001 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.69e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 46303 4.34 - 8.68: 297 8.68 - 13.02: 32 13.02 - 17.36: 3 17.36 - 21.71: 3 Bond angle restraints: 46638 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 118.16 21.71 1.00e+00 1.00e+00 4.71e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 118.48 21.39 1.00e+00 1.00e+00 4.58e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 118.94 20.93 1.00e+00 1.00e+00 4.38e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 119.81 17.02 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 122.46 14.37 1.00e+00 1.00e+00 2.06e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 19706 26.67 - 53.35: 918 53.35 - 80.02: 83 80.02 - 106.69: 22 106.69 - 133.36: 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 -124.97 -55.03 0 5.00e+00 4.00e-02 1.21e+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 -126.66 -53.34 0 5.00e+00 4.00e-02 1.14e+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 -126.91 -53.09 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 20727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4237 0.070 - 0.141: 1127 0.141 - 0.211: 142 0.211 - 0.281: 10 0.281 - 0.352: 3 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB ILE D 95 " pdb=" CA ILE D 95 " pdb=" CG1 ILE D 95 " pdb=" CG2 ILE D 95 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE E 95 " pdb=" CA ILE E 95 " pdb=" CG1 ILE E 95 " pdb=" CG2 ILE E 95 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE J 95 " pdb=" CA ILE J 95 " pdb=" CG1 ILE J 95 " pdb=" CG2 ILE J 95 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+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 5.91e-02 3.50e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA X 350 " -0.060 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO X 351 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO X 351 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO X 351 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 203 " 0.025 2.00e-02 2.50e+03 2.53e-02 1.12e+01 pdb=" CG PHE U 203 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE U 203 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE U 203 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE U 203 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE U 203 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE U 203 " 0.002 2.00e-02 2.50e+03 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 492 2.62 - 3.19: 29366 3.19 - 3.76: 53955 3.76 - 4.33: 76062 4.33 - 4.90: 124893 Nonbonded interactions: 284768 Sorted by model distance: nonbonded pdb=" OE1 GLU Y 215 " pdb="MG MG Y 602 " model vdw 2.050 2.170 nonbonded pdb=" OE2 GLU X 215 " pdb="MG MG X 602 " model vdw 2.060 2.170 nonbonded pdb=" O2B ATP T1001 " pdb="MG MG T1002 " model vdw 2.138 2.170 nonbonded pdb=" O ALA S 125 " pdb=" OG1 THR S 129 " model vdw 2.241 3.040 nonbonded pdb=" O GLY V 225 " pdb=" OG1 THR V 385 " model vdw 2.243 3.040 ... (remaining 284763 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.930 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: 0.590 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 31.640 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.110 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 0.130 34412 Z= 0.471 Angle : 1.076 21.706 46638 Z= 0.619 Chirality : 0.062 0.352 5519 Planarity : 0.008 0.091 5997 Dihedral : 15.166 133.362 12570 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.96 % Favored : 93.77 % Rotamer: Outliers : 0.51 % Allowed : 11.84 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.10), residues: 4461 helix: -3.32 (0.07), residues: 2113 sheet: -2.07 (0.20), residues: 563 loop : -2.34 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 360 TYR 0.023 0.003 TYR Z 487 PHE 0.059 0.003 PHE U 203 TRP 0.028 0.003 TRP X 141 HIS 0.009 0.002 HIS Y 204 Details of bonding type rmsd/Z covalent geometry : bond 0.01070 / 0.47 (34412) covalent geometry : angle 1.07634 / 0.62 (46638) hydrogen bonds : bond 0.18471 / 12.33 ( 1590) hydrogen bonds : angle 8.27470 / 5.85 ( 4629) *********************** 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 838 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 820 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7761 (tp) cc_final: 0.7421 (mt) REVERT: A 61 MET cc_start: 0.8010 (mmt) cc_final: 0.7709 (mmt) REVERT: A 94 ASN cc_start: 0.7746 (m110) cc_final: 0.7432 (m-40) REVERT: A 124 ILE cc_start: 0.7979 (pt) cc_final: 0.7628 (pt) REVERT: C 111 GLU cc_start: 0.7482 (tp30) cc_final: 0.7123 (tt0) REVERT: E 60 LYS cc_start: 0.6622 (mtmt) cc_final: 0.6099 (mttp) REVERT: F 94 ASN cc_start: 0.8416 (m-40) cc_final: 0.8187 (t0) REVERT: G 94 ASN cc_start: 0.7792 (t0) cc_final: 0.7549 (t0) REVERT: H 61 MET cc_start: 0.7519 (mmt) cc_final: 0.7265 (mmt) REVERT: I 69 ILE cc_start: 0.7459 (mm) cc_final: 0.7243 (mm) REVERT: J 60 LYS cc_start: 0.6721 (mtmt) cc_final: 0.6308 (pttt) REVERT: P 136 GLU cc_start: 0.6593 (tt0) cc_final: 0.6152 (tt0) REVERT: Q 35 PHE cc_start: 0.7948 (m-80) cc_final: 0.7569 (m-10) REVERT: Q 42 ARG cc_start: 0.7054 (ptp90) cc_final: 0.6382 (mtm-85) REVERT: Q 52 TYR cc_start: 0.6047 (m-10) cc_final: 0.5636 (m-10) REVERT: R 31 LYS cc_start: 0.7180 (tmmt) cc_final: 0.6324 (mptt) REVERT: R 68 ASP cc_start: 0.5619 (m-30) cc_final: 0.5151 (m-30) REVERT: R 88 THR cc_start: 0.5944 (t) cc_final: 0.5476 (p) REVERT: S 62 MET cc_start: 0.7598 (ptm) cc_final: 0.7202 (ptt) REVERT: S 124 ARG cc_start: 0.8176 (ptm-80) cc_final: 0.7973 (ptm160) REVERT: T 101 LYS cc_start: 0.8599 (tptt) cc_final: 0.8374 (mttp) REVERT: T 271 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7431 (mt0) REVERT: T 357 LEU cc_start: 0.8842 (tp) cc_final: 0.8559 (tp) REVERT: T 453 TYR cc_start: 0.7269 (t80) cc_final: 0.6980 (t80) REVERT: T 502 TYR cc_start: 0.7565 (t80) cc_final: 0.7289 (t80) REVERT: T 506 LYS cc_start: 0.6415 (mmtp) cc_final: 0.6019 (mmtt) REVERT: T 515 GLN cc_start: 0.7589 (tt0) cc_final: 0.7384 (mm-40) REVERT: U 112 ASP cc_start: 0.7672 (t0) cc_final: 0.7414 (t0) REVERT: U 215 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8708 (mp) REVERT: U 384 GLU cc_start: 0.7218 (tt0) cc_final: 0.6820 (mt-10) REVERT: U 511 LYS cc_start: 0.7831 (tttt) cc_final: 0.7061 (mmtp) REVERT: V 94 ILE cc_start: 0.9377 (mm) cc_final: 0.9158 (tp) REVERT: V 98 TYR cc_start: 0.8424 (t80) cc_final: 0.8150 (t80) REVERT: V 165 ASP cc_start: 0.7840 (t0) cc_final: 0.7600 (t0) REVERT: V 316 THR cc_start: 0.6881 (p) cc_final: 0.6664 (p) REVERT: V 492 ILE cc_start: 0.8613 (mt) cc_final: 0.8103 (tt) REVERT: V 513 ARG cc_start: 0.6867 (mtm180) cc_final: 0.6466 (mtp180) REVERT: V 551 LYS cc_start: 0.7899 (tttp) cc_final: 0.7184 (mttt) REVERT: X 243 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8571 (mmtm) REVERT: X 573 LYS cc_start: 0.6372 (ttmt) cc_final: 0.6149 (mmmt) REVERT: Y 405 LYS cc_start: 0.8184 (tptt) cc_final: 0.7593 (ttpp) REVERT: Y 494 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7413 (tp30) REVERT: Y 550 LYS cc_start: 0.6223 (mmtt) cc_final: 0.5875 (pptt) REVERT: Z 222 ASP cc_start: 0.7366 (m-30) cc_final: 0.7149 (m-30) REVERT: Z 370 GLU cc_start: 0.6811 (mm-30) cc_final: 0.5918 (mm-30) REVERT: Z 385 ARG cc_start: 0.6870 (ttm-80) cc_final: 0.6426 (ttm170) REVERT: Z 547 GLU cc_start: 0.5487 (mp0) cc_final: 0.4744 (pm20) outliers start: 18 outliers final: 11 residues processed: 835 average time/residue: 0.2327 time to fit residues: 309.2574 Evaluate side-chains 539 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 527 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 215 ILE Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 ASN E 94 ASN F 98 GLN G 94 ASN G 98 GLN J 98 GLN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 ASN R 38 ASN R 73 ASN R 83 GLN S 195 ASN S 250 HIS S 262 ASN S 297 GLN ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 264 GLN T 497 GLN U 228 GLN U 241 HIS U 319 HIS U 386 GLN U 441 GLN U 529 ASN V 64 GLN V 169 GLN V 196 GLN V 242 GLN V 244 ASN V 271 GLN V 278 GLN V 486 GLN V 497 GLN V 539 ASN X 199 ASN X 337 GLN X 408 GLN X 412 ASN Y 174 GLN Y 514 ASN Z 199 ASN Z 252 ASN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 404 GLN Z 414 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117155 restraints weight = 58210.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119070 restraints weight = 33006.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120041 restraints weight = 23640.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120595 restraints weight = 19009.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120849 restraints weight = 16275.625| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2076 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= 0.132 Angle : 0.626 12.734 46638 Z= 0.321 Chirality : 0.044 0.185 5519 Planarity : 0.005 0.096 5997 Dihedral : 6.713 110.752 4840 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.52 % Favored : 96.23 % Rotamer: Outliers : 2.53 % Allowed : 15.77 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.62 (0.12), residues: 4461 helix: -1.58 (0.10), residues: 2120 sheet: -1.66 (0.22), residues: 522 loop : -1.75 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 314 TYR 0.019 0.002 TYR Z 271 PHE 0.025 0.001 PHE V 489 TRP 0.009 0.001 TRP R 37 HIS 0.004 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (34412) covalent geometry : angle 0.62650 / 0.32 (46638) hydrogen bonds : bond 0.04084 / 2.69 ( 1590) hydrogen bonds : angle 5.31288 / 3.75 ( 4629) *********************** 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 758 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 668 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8086 (mmt) cc_final: 0.7712 (mmt) REVERT: A 94 ASN cc_start: 0.7511 (m110) cc_final: 0.7225 (m-40) REVERT: C 111 GLU cc_start: 0.7480 (tp30) cc_final: 0.6961 (tt0) REVERT: C 113 ILE cc_start: 0.8472 (mt) cc_final: 0.8114 (mm) REVERT: D 82 PHE cc_start: 0.7913 (m-10) cc_final: 0.7653 (m-10) REVERT: E 123 LEU cc_start: 0.8010 (mt) cc_final: 0.7320 (tt) REVERT: P 50 SER cc_start: 0.8072 (p) cc_final: 0.7661 (m) REVERT: P 73 GLU cc_start: 0.6028 (mt-10) cc_final: 0.5800 (mt-10) REVERT: P 143 GLU cc_start: 0.7696 (mm-30) cc_final: 0.6557 (tm-30) REVERT: P 145 MET cc_start: 0.7553 (ttm) cc_final: 0.7175 (tpp) REVERT: Q 35 PHE cc_start: 0.7794 (m-80) cc_final: 0.7416 (m-80) REVERT: Q 42 ARG cc_start: 0.6938 (ptp90) cc_final: 0.6237 (mtm-85) REVERT: R 31 LYS cc_start: 0.7029 (tmmt) cc_final: 0.6505 (mptt) REVERT: S 124 ARG cc_start: 0.8231 (ptm-80) cc_final: 0.8014 (ptm160) REVERT: T 304 TYR cc_start: 0.8627 (m-80) cc_final: 0.8412 (m-80) REVERT: T 329 LYS cc_start: 0.9133 (mttt) cc_final: 0.8856 (mttm) REVERT: T 389 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: T 439 MET cc_start: 0.7671 (tpp) cc_final: 0.7463 (tpp) REVERT: T 509 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7564 (mm) REVERT: T 547 ASP cc_start: 0.6710 (p0) cc_final: 0.6278 (t0) REVERT: U 112 ASP cc_start: 0.7838 (t0) cc_final: 0.7496 (t0) REVERT: U 511 LYS cc_start: 0.7585 (tttt) cc_final: 0.6993 (mmtp) REVERT: U 550 LEU cc_start: 0.8663 (mt) cc_final: 0.8153 (mt) REVERT: V 98 TYR cc_start: 0.8111 (t80) cc_final: 0.7595 (t80) REVERT: V 272 LEU cc_start: 0.8779 (tp) cc_final: 0.8560 (tp) REVERT: V 316 THR cc_start: 0.7119 (p) cc_final: 0.6778 (p) REVERT: V 492 ILE cc_start: 0.8467 (mt) cc_final: 0.7965 (tt) REVERT: V 551 LYS cc_start: 0.7934 (tttp) cc_final: 0.7263 (mttt) REVERT: X 56 LEU cc_start: 0.8730 (mp) cc_final: 0.8512 (mp) REVERT: X 243 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8361 (tttp) REVERT: X 456 THR cc_start: 0.8398 (m) cc_final: 0.8032 (p) REVERT: X 573 LYS cc_start: 0.5639 (ttmt) cc_final: 0.5344 (tptt) REVERT: Y 401 ARG cc_start: 0.7399 (mmm160) cc_final: 0.6465 (mmm-85) REVERT: Y 405 LYS cc_start: 0.8313 (tptt) cc_final: 0.7835 (tttm) REVERT: Y 489 VAL cc_start: 0.8309 (m) cc_final: 0.8075 (p) REVERT: Y 550 LYS cc_start: 0.6132 (mmtt) cc_final: 0.5802 (pptt) REVERT: Z 297 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.8996 (p) REVERT: Z 359 ASP cc_start: 0.8040 (m-30) cc_final: 0.7368 (m-30) REVERT: Z 438 LYS cc_start: 0.8005 (ptpp) cc_final: 0.6831 (mttp) REVERT: Z 547 GLU cc_start: 0.5535 (mp0) cc_final: 0.4803 (pm20) outliers start: 90 outliers final: 41 residues processed: 729 average time/residue: 0.2106 time to fit residues: 252.7805 Evaluate side-chains 576 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 532 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 564 GLU 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: 5.9990 chunk 62 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 344 optimal weight: 2.9990 chunk 422 optimal weight: 3.9990 chunk 307 optimal weight: 7.9990 chunk 396 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 ASN G 98 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN R 73 ASN R 171 GLN R 178 GLN S 191 GLN S 262 ASN T 104 GLN T 121 ASN T 126 HIS T 241 HIS T 271 GLN U 123 GLN U 134 ASN U 228 GLN U 246 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS V 169 GLN V 264 GLN X 412 ASN Y 144 HIS ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 471 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111109 restraints weight = 59169.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112269 restraints weight = 35669.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112782 restraints weight = 26582.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113036 restraints weight = 22105.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113185 restraints weight = 22028.671| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 34412 Z= 0.281 Angle : 0.723 12.062 46638 Z= 0.371 Chirality : 0.049 0.220 5519 Planarity : 0.005 0.057 5997 Dihedral : 6.819 109.967 4832 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.31 % Favored : 94.42 % Rotamer: Outliers : 4.15 % Allowed : 18.41 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -2.18 (0.12), residues: 4461 helix: -1.16 (0.11), residues: 2136 sheet: -1.55 (0.22), residues: 528 loop : -1.57 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 314 TYR 0.020 0.002 TYR B 102 PHE 0.022 0.002 PHE V 459 TRP 0.011 0.002 TRP X 141 HIS 0.010 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.28 (34412) covalent geometry : angle 0.72304 / 0.37 (46638) hydrogen bonds : bond 0.04478 / 2.96 ( 1590) hydrogen bonds : angle 5.26947 / 3.72 ( 4629) *********************** 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 713 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 565 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7655 (m110) cc_final: 0.7326 (m-40) REVERT: C 111 GLU cc_start: 0.7605 (tp30) cc_final: 0.7029 (tt0) REVERT: E 123 LEU cc_start: 0.8106 (mt) cc_final: 0.7456 (tt) REVERT: G 81 MET cc_start: 0.7684 (ttp) cc_final: 0.7431 (ttt) REVERT: H 61 MET cc_start: 0.7251 (mmt) cc_final: 0.6988 (mmt) REVERT: P 110 LYS cc_start: 0.6636 (mmmt) cc_final: 0.6382 (mmmm) REVERT: P 136 GLU cc_start: 0.6593 (tt0) cc_final: 0.6245 (tt0) REVERT: P 140 ASN cc_start: 0.8431 (m110) cc_final: 0.8193 (m110) REVERT: P 143 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7217 (tm-30) REVERT: Q 42 ARG cc_start: 0.6940 (ptp90) cc_final: 0.6231 (mtm-85) REVERT: R 31 LYS cc_start: 0.7316 (tmmt) cc_final: 0.6685 (mptt) REVERT: R 177 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6569 (mt-10) REVERT: S 68 MET cc_start: 0.8288 (ttp) cc_final: 0.7987 (ttt) REVERT: S 124 ARG cc_start: 0.8263 (ptm-80) cc_final: 0.8015 (ptm160) REVERT: S 248 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: T 304 TYR cc_start: 0.8825 (m-80) cc_final: 0.8505 (m-80) REVERT: T 389 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: T 509 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7799 (mm) REVERT: U 112 ASP cc_start: 0.7955 (t0) cc_final: 0.7608 (t0) REVERT: U 511 LYS cc_start: 0.7705 (tttt) cc_final: 0.6965 (mmtp) REVERT: U 550 LEU cc_start: 0.8677 (mt) cc_final: 0.8178 (mt) REVERT: U 551 LYS cc_start: 0.8024 (tptt) cc_final: 0.7754 (ttpt) REVERT: V 316 THR cc_start: 0.7178 (p) cc_final: 0.6934 (p) REVERT: V 384 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6514 (pp20) REVERT: V 492 ILE cc_start: 0.8529 (mt) cc_final: 0.7874 (tt) REVERT: V 551 LYS cc_start: 0.8027 (tttp) cc_final: 0.7335 (mttt) REVERT: X 484 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6655 (ppp) REVERT: X 573 LYS cc_start: 0.6100 (ttmt) cc_final: 0.5880 (tptt) REVERT: Y 405 LYS cc_start: 0.8260 (tptt) cc_final: 0.7757 (tttm) REVERT: Y 489 VAL cc_start: 0.8491 (m) cc_final: 0.8181 (p) REVERT: Y 550 LYS cc_start: 0.6166 (mmtt) cc_final: 0.5891 (pptt) REVERT: Z 370 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6396 (mm-30) REVERT: Z 438 LYS cc_start: 0.8271 (ptpp) cc_final: 0.7024 (mttp) outliers start: 148 outliers final: 104 residues processed: 668 average time/residue: 0.2102 time to fit residues: 233.6323 Evaluate side-chains 624 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 515 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 535 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 492 ILE Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 566 LYS Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 505 ASP Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 246 LEU Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 559 VAL Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 171 optimal weight: 0.9990 chunk 295 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 374 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 261 optimal weight: 0.0980 chunk 151 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 98 GLN P 76 GLN Q 49 GLN S 262 ASN T 358 HIS T 405 GLN T 422 ASN T 435 GLN U 134 ASN U 529 ASN U 549 HIS V 169 GLN Y 42 GLN Y 132 GLN Y 388 ASN Y 390 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 337 GLN Z 471 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114739 restraints weight = 57890.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116914 restraints weight = 32902.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117578 restraints weight = 22664.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118250 restraints weight = 18012.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118497 restraints weight = 15713.723| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34412 Z= 0.124 Angle : 0.585 10.332 46638 Z= 0.298 Chirality : 0.044 0.234 5519 Planarity : 0.004 0.046 5997 Dihedral : 6.208 100.074 4832 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 3.45 % Allowed : 20.45 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.54 (0.12), residues: 4461 helix: -0.53 (0.11), residues: 2107 sheet: -1.41 (0.22), residues: 543 loop : -1.33 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 385 TYR 0.019 0.001 TYR B 102 PHE 0.026 0.001 PHE D 107 TRP 0.007 0.001 TRP V 73 HIS 0.005 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (34412) covalent geometry : angle 0.58490 / 0.30 (46638) hydrogen bonds : bond 0.03568 / 2.37 ( 1590) hydrogen bonds : angle 4.80236 / 3.38 ( 4629) *********************** 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 706 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 583 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7576 (m110) cc_final: 0.7319 (m-40) REVERT: E 123 LEU cc_start: 0.8058 (mt) cc_final: 0.7421 (tt) REVERT: H 61 MET cc_start: 0.7252 (mmt) cc_final: 0.6936 (mmt) REVERT: P 50 SER cc_start: 0.8193 (p) cc_final: 0.7879 (m) REVERT: Q 42 ARG cc_start: 0.6951 (ptp90) cc_final: 0.6350 (mtm-85) REVERT: R 31 LYS cc_start: 0.7199 (tmmt) cc_final: 0.6512 (mptt) REVERT: R 32 GLU cc_start: 0.7606 (tm-30) cc_final: 0.6760 (tt0) REVERT: S 124 ARG cc_start: 0.8246 (ptm-80) cc_final: 0.7984 (ptm160) REVERT: S 248 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: T 260 VAL cc_start: 0.9368 (t) cc_final: 0.9085 (p) REVERT: T 304 TYR cc_start: 0.8788 (m-80) cc_final: 0.8527 (m-80) REVERT: T 312 TYR cc_start: 0.8754 (t80) cc_final: 0.8505 (t80) REVERT: T 389 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: T 509 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7636 (mm) REVERT: U 112 ASP cc_start: 0.7940 (t0) cc_final: 0.7561 (t0) REVERT: U 203 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: U 371 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7228 (pm20) REVERT: U 483 MET cc_start: 0.7499 (tpp) cc_final: 0.7001 (tpp) REVERT: U 511 LYS cc_start: 0.7569 (tttt) cc_final: 0.6972 (mmtp) REVERT: V 272 LEU cc_start: 0.8782 (tp) cc_final: 0.8556 (tp) REVERT: V 316 THR cc_start: 0.7292 (p) cc_final: 0.7045 (p) REVERT: V 551 LYS cc_start: 0.7974 (tttp) cc_final: 0.7566 (mttm) REVERT: X 304 ILE cc_start: 0.8919 (mp) cc_final: 0.8534 (mm) REVERT: X 456 THR cc_start: 0.8441 (m) cc_final: 0.8038 (p) REVERT: X 573 LYS cc_start: 0.5597 (ttmt) cc_final: 0.5384 (tptt) REVERT: Y 296 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7331 (mt-10) REVERT: Y 401 ARG cc_start: 0.7260 (mmm160) cc_final: 0.6647 (mmm-85) REVERT: Y 405 LYS cc_start: 0.8260 (tptt) cc_final: 0.7748 (tttm) REVERT: Y 489 VAL cc_start: 0.8373 (m) cc_final: 0.8088 (p) REVERT: Z 359 ASP cc_start: 0.7973 (m-30) cc_final: 0.7453 (m-30) REVERT: Z 370 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6017 (mm-30) outliers start: 123 outliers final: 82 residues processed: 668 average time/residue: 0.2137 time to fit residues: 238.8978 Evaluate side-chains 609 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 522 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 500 ASP Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 241 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 424 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 406 optimal weight: 8.9990 chunk 273 optimal weight: 6.9990 chunk 300 optimal weight: 3.9990 chunk 278 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 GLN G 98 GLN J 98 GLN P 76 GLN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN T 121 ASN T 405 GLN T 435 GLN U 134 ASN U 264 GLN U 358 HIS ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 169 GLN Y 174 GLN Y 198 ASN Y 388 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110374 restraints weight = 59127.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111555 restraints weight = 35722.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112247 restraints weight = 25532.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112524 restraints weight = 21116.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112684 restraints weight = 20512.857| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 34412 Z= 0.267 Angle : 0.696 10.722 46638 Z= 0.356 Chirality : 0.048 0.253 5519 Planarity : 0.005 0.049 5997 Dihedral : 6.465 105.943 4832 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.38 % Favored : 94.35 % Rotamer: Outliers : 4.80 % Allowed : 20.85 % Favored : 74.35 % 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: -1.63 (0.12), residues: 4461 helix: -0.63 (0.11), residues: 2137 sheet: -1.42 (0.22), residues: 534 loop : -1.36 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 401 TYR 0.020 0.002 TYR T 334 PHE 0.039 0.002 PHE E 116 TRP 0.009 0.001 TRP V 73 HIS 0.006 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.27 (34412) covalent geometry : angle 0.69636 / 0.36 (46638) hydrogen bonds : bond 0.04181 / 2.76 ( 1590) hydrogen bonds : angle 5.03531 / 3.54 ( 4629) *********************** 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 697 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 526 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7588 (m110) cc_final: 0.7260 (m-40) REVERT: B 87 ASN cc_start: 0.7905 (m-40) cc_final: 0.7558 (m-40) REVERT: D 81 MET cc_start: 0.8203 (ttp) cc_final: 0.7796 (ttp) REVERT: D 122 PHE cc_start: 0.5957 (m-80) cc_final: 0.5734 (m-80) REVERT: E 123 LEU cc_start: 0.8039 (mt) cc_final: 0.7364 (tt) REVERT: H 61 MET cc_start: 0.7240 (mmt) cc_final: 0.6943 (mmt) REVERT: R 31 LYS cc_start: 0.7031 (tmmt) cc_final: 0.6363 (mptt) REVERT: R 32 GLU cc_start: 0.7700 (tm-30) cc_final: 0.6952 (tt0) REVERT: R 118 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7208 (mt) REVERT: R 177 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6534 (mt-10) REVERT: S 52 ASN cc_start: 0.7354 (t0) cc_final: 0.7125 (t0) REVERT: S 68 MET cc_start: 0.8279 (ttp) cc_final: 0.8034 (ttt) REVERT: S 124 ARG cc_start: 0.8244 (ptm-80) cc_final: 0.8000 (ptm160) REVERT: S 248 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: T 304 TYR cc_start: 0.8799 (m-80) cc_final: 0.8495 (m-80) REVERT: T 389 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: T 509 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7848 (mm) REVERT: U 112 ASP cc_start: 0.8020 (t0) cc_final: 0.7645 (t0) REVERT: U 203 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: V 121 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.7879 (m110) REVERT: V 316 THR cc_start: 0.7315 (p) cc_final: 0.7071 (p) REVERT: V 551 LYS cc_start: 0.8080 (tttp) cc_final: 0.7427 (mttt) REVERT: X 56 LEU cc_start: 0.8939 (mt) cc_final: 0.8468 (mp) REVERT: X 502 MET cc_start: 0.7020 (ptp) cc_final: 0.6752 (ptp) REVERT: X 573 LYS cc_start: 0.5809 (ttmt) cc_final: 0.5557 (tptt) REVERT: Y 152 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: Y 405 LYS cc_start: 0.8265 (tptt) cc_final: 0.7754 (tttm) REVERT: Z 196 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8944 (mt) REVERT: Z 248 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: Z 370 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6278 (mm-30) outliers start: 171 outliers final: 136 residues processed: 653 average time/residue: 0.2098 time to fit residues: 231.0075 Evaluate side-chains 643 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 497 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 284 MET Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 389 ASP Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 480 LEU Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 502 TYR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 121 ASN Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 80 MET Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 207 PHE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 291 THR Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 505 ASP Chi-restraints excluded: chain Y residue 534 ILE Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 191 VAL Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 248 TYR Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 500 ASP Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 127 optimal weight: 0.9980 chunk 269 optimal weight: 6.9990 chunk 407 optimal weight: 0.9980 chunk 426 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 237 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 382 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 98 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 GLN S 262 ASN S 267 HIS T 121 ASN T 405 GLN T 435 GLN U 134 ASN U 529 ASN Y 388 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114018 restraints weight = 58054.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116128 restraints weight = 32813.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116738 restraints weight = 23252.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117540 restraints weight = 18476.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117879 restraints weight = 15881.943| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34412 Z= 0.132 Angle : 0.598 11.408 46638 Z= 0.303 Chirality : 0.044 0.207 5519 Planarity : 0.004 0.045 5997 Dihedral : 6.055 97.691 4832 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.97 % Rotamer: Outliers : 4.21 % Allowed : 22.50 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.20 (0.13), residues: 4461 helix: -0.25 (0.11), residues: 2120 sheet: -1.27 (0.23), residues: 532 loop : -1.16 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 555 TYR 0.022 0.001 TYR T 312 PHE 0.038 0.001 PHE E 116 TRP 0.006 0.001 TRP V 73 HIS 0.005 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (34412) covalent geometry : angle 0.59772 / 0.30 (46638) hydrogen bonds : bond 0.03562 / 2.36 ( 1590) hydrogen bonds : angle 4.72340 / 3.32 ( 4629) *********************** 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 717 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 567 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7524 (m110) cc_final: 0.7294 (m-40) REVERT: B 87 ASN cc_start: 0.7865 (m-40) cc_final: 0.7479 (m-40) REVERT: C 94 ASN cc_start: 0.8008 (t0) cc_final: 0.7791 (t0) REVERT: D 81 MET cc_start: 0.8203 (ttp) cc_final: 0.7790 (ttp) REVERT: D 120 VAL cc_start: 0.7122 (OUTLIER) cc_final: 0.6860 (p) REVERT: D 122 PHE cc_start: 0.5853 (m-80) cc_final: 0.5633 (m-80) REVERT: E 100 VAL cc_start: 0.8763 (t) cc_final: 0.8527 (t) REVERT: E 123 LEU cc_start: 0.8177 (mt) cc_final: 0.7563 (tt) REVERT: F 105 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.5625 (mm) REVERT: H 61 MET cc_start: 0.7301 (mmt) cc_final: 0.6918 (mmt) REVERT: P 50 SER cc_start: 0.8159 (p) cc_final: 0.7691 (m) REVERT: Q 45 ILE cc_start: 0.7749 (mp) cc_final: 0.7487 (mt) REVERT: R 31 LYS cc_start: 0.7016 (tmmt) cc_final: 0.6381 (mptt) REVERT: R 32 GLU cc_start: 0.7467 (tm-30) cc_final: 0.6875 (tt0) REVERT: R 118 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7158 (mt) REVERT: R 177 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6597 (mt-10) REVERT: S 68 MET cc_start: 0.8236 (ttp) cc_final: 0.7947 (ttt) REVERT: S 124 ARG cc_start: 0.8203 (ptm-80) cc_final: 0.7939 (ptm160) REVERT: S 248 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: S 274 MET cc_start: 0.8041 (mmm) cc_final: 0.7761 (mmm) REVERT: T 260 VAL cc_start: 0.9369 (t) cc_final: 0.9100 (p) REVERT: T 304 TYR cc_start: 0.8747 (m-80) cc_final: 0.8524 (m-80) REVERT: T 509 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7687 (mm) REVERT: U 112 ASP cc_start: 0.7923 (t0) cc_final: 0.7540 (t0) REVERT: U 203 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: U 260 VAL cc_start: 0.9320 (t) cc_final: 0.8964 (m) REVERT: U 511 LYS cc_start: 0.7644 (tttt) cc_final: 0.6950 (mmtp) REVERT: V 121 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7786 (m110) REVERT: V 152 ASN cc_start: 0.8221 (m-40) cc_final: 0.7980 (m-40) REVERT: V 316 THR cc_start: 0.7315 (p) cc_final: 0.7065 (p) REVERT: V 551 LYS cc_start: 0.7973 (tttp) cc_final: 0.7402 (mttt) REVERT: X 456 THR cc_start: 0.8510 (m) cc_final: 0.8093 (p) REVERT: X 488 MET cc_start: 0.7818 (mmm) cc_final: 0.7507 (mmm) REVERT: X 502 MET cc_start: 0.6955 (ptp) cc_final: 0.6448 (ptp) REVERT: X 573 LYS cc_start: 0.5705 (ttmt) cc_final: 0.5499 (tptt) REVERT: Y 152 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: Y 194 MET cc_start: 0.8095 (tpp) cc_final: 0.7513 (mmm) REVERT: Y 296 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7407 (mt-10) REVERT: Y 401 ARG cc_start: 0.7276 (mmm160) cc_final: 0.6641 (mmm-85) REVERT: Y 405 LYS cc_start: 0.8387 (tptt) cc_final: 0.7889 (tttm) REVERT: Y 489 VAL cc_start: 0.8352 (m) cc_final: 0.8015 (p) REVERT: Z 196 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8881 (mt) REVERT: Z 248 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7706 (m-10) REVERT: Z 271 TYR cc_start: 0.8506 (t80) cc_final: 0.8226 (t80) REVERT: Z 359 ASP cc_start: 0.7986 (m-30) cc_final: 0.7569 (m-30) REVERT: Z 441 ARG cc_start: 0.8377 (mmt90) cc_final: 0.8176 (mmm-85) outliers start: 150 outliers final: 106 residues processed: 675 average time/residue: 0.2043 time to fit residues: 234.3399 Evaluate side-chains 636 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 519 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 480 LEU Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 121 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 158 GLU Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 191 VAL Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 248 TYR Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 500 ASP Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 59 optimal weight: 5.9990 chunk 433 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 255 optimal weight: 9.9990 chunk 337 optimal weight: 6.9990 chunk 436 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 98 GLN I 92 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 GLN S 262 ASN S 293 ASN U 134 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 497 GLN Y 174 GLN Y 388 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111165 restraints weight = 58796.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113182 restraints weight = 33023.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113880 restraints weight = 22756.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115014 restraints weight = 17736.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114869 restraints weight = 15254.528| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 34412 Z= 0.227 Angle : 0.664 10.384 46638 Z= 0.338 Chirality : 0.047 0.210 5519 Planarity : 0.005 0.045 5997 Dihedral : 6.231 103.382 4831 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.34 % Favored : 94.40 % Rotamer: Outliers : 5.13 % Allowed : 23.15 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.28 (0.13), residues: 4461 helix: -0.35 (0.11), residues: 2138 sheet: -1.33 (0.23), residues: 533 loop : -1.13 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 555 TYR 0.020 0.002 TYR T 502 PHE 0.040 0.002 PHE E 116 TRP 0.008 0.001 TRP V 73 HIS 0.005 0.001 HIS U 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (34412) covalent geometry : angle 0.66406 / 0.34 (46638) hydrogen bonds : bond 0.03954 / 2.60 ( 1590) hydrogen bonds : angle 4.90220 / 3.45 ( 4629) *********************** 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 707 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 524 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7581 (m110) cc_final: 0.7263 (m-40) REVERT: B 87 ASN cc_start: 0.7820 (m-40) cc_final: 0.7462 (m-40) REVERT: D 81 MET cc_start: 0.8294 (ttp) cc_final: 0.7946 (ttp) REVERT: D 120 VAL cc_start: 0.7202 (OUTLIER) cc_final: 0.6949 (p) REVERT: D 122 PHE cc_start: 0.5970 (m-80) cc_final: 0.5767 (m-80) REVERT: E 119 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5552 (tp) REVERT: E 123 LEU cc_start: 0.7960 (mt) cc_final: 0.7413 (tt) REVERT: F 105 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.5601 (mm) REVERT: H 61 MET cc_start: 0.7178 (mmt) cc_final: 0.6846 (mmt) REVERT: H 69 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6540 (pt) REVERT: Q 32 LYS cc_start: 0.7065 (mmmm) cc_final: 0.6044 (mttt) REVERT: R 31 LYS cc_start: 0.7193 (tmmt) cc_final: 0.6290 (mptt) REVERT: R 32 GLU cc_start: 0.7469 (tm-30) cc_final: 0.6857 (tt0) REVERT: R 118 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7132 (mt) REVERT: R 177 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6459 (mt-10) REVERT: S 68 MET cc_start: 0.8323 (ttp) cc_final: 0.8032 (ttt) REVERT: S 124 ARG cc_start: 0.8232 (ptm-80) cc_final: 0.7975 (ptm160) REVERT: S 248 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: S 274 MET cc_start: 0.8114 (mmm) cc_final: 0.7635 (mmm) REVERT: T 304 TYR cc_start: 0.8800 (m-80) cc_final: 0.8560 (m-80) REVERT: T 509 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7822 (mm) REVERT: U 112 ASP cc_start: 0.8046 (t0) cc_final: 0.7657 (t0) REVERT: U 203 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: V 121 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.7800 (m110) REVERT: V 316 THR cc_start: 0.7311 (p) cc_final: 0.7082 (p) REVERT: V 551 LYS cc_start: 0.8013 (tttp) cc_final: 0.7469 (mttt) REVERT: X 502 MET cc_start: 0.6860 (ptp) cc_final: 0.6569 (ptp) REVERT: X 573 LYS cc_start: 0.5795 (ttmt) cc_final: 0.5577 (tptt) REVERT: Y 152 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: Y 405 LYS cc_start: 0.8253 (tptt) cc_final: 0.7721 (tttm) REVERT: Z 248 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7816 (m-10) REVERT: Z 271 TYR cc_start: 0.8614 (t80) cc_final: 0.8357 (t80) REVERT: Z 359 ASP cc_start: 0.8109 (m-30) cc_final: 0.7592 (m-30) REVERT: Z 441 ARG cc_start: 0.8441 (mmt90) cc_final: 0.8240 (mmm-85) REVERT: Z 547 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5868 (pt0) outliers start: 183 outliers final: 140 residues processed: 660 average time/residue: 0.2041 time to fit residues: 228.9210 Evaluate side-chains 649 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 496 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 112 SER Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 257 ASN Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 284 MET Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 535 ILE Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 480 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 501 VAL Chi-restraints excluded: chain U residue 502 TYR Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain V residue 121 ASN Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 207 PHE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 474 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 534 ILE Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 158 GLU Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 191 VAL Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 248 TYR Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 500 ASP Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 547 GLU Chi-restraints excluded: chain Z residue 559 VAL Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 41 optimal weight: 2.9990 chunk 371 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 379 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 233 optimal weight: 0.0470 chunk 238 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN G 98 GLN I 92 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN S 262 ASN U 134 ASN U 140 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 174 GLN Y 388 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115395 restraints weight = 57910.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117704 restraints weight = 32555.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118353 restraints weight = 22190.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119043 restraints weight = 17621.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119309 restraints weight = 15375.434| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34412 Z= 0.120 Angle : 0.601 14.591 46638 Z= 0.302 Chirality : 0.044 0.169 5519 Planarity : 0.004 0.043 5997 Dihedral : 5.842 94.429 4831 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.83 % Rotamer: Outliers : 3.93 % Allowed : 24.38 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.97 (0.13), residues: 4461 helix: -0.05 (0.12), residues: 2140 sheet: -1.27 (0.22), residues: 553 loop : -1.02 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 555 TYR 0.021 0.001 TYR T 502 PHE 0.029 0.001 PHE D 107 TRP 0.014 0.001 TRP R 37 HIS 0.005 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (34412) covalent geometry : angle 0.60055 / 0.30 (46638) hydrogen bonds : bond 0.03440 / 2.27 ( 1590) hydrogen bonds : angle 4.61830 / 3.24 ( 4629) *********************** 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 712 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 572 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7436 (m110) cc_final: 0.7220 (m-40) REVERT: B 87 ASN cc_start: 0.7752 (m-40) cc_final: 0.7340 (m-40) REVERT: C 60 LYS cc_start: 0.6637 (tptt) cc_final: 0.5887 (mmtt) REVERT: D 81 MET cc_start: 0.8227 (ttp) cc_final: 0.7846 (ttp) REVERT: D 120 VAL cc_start: 0.7079 (OUTLIER) cc_final: 0.6820 (p) REVERT: D 122 PHE cc_start: 0.5914 (m-80) cc_final: 0.5686 (m-80) REVERT: E 119 LEU cc_start: 0.6226 (tp) cc_final: 0.5663 (mt) REVERT: E 123 LEU cc_start: 0.8098 (mt) cc_final: 0.7681 (tt) REVERT: F 105 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5477 (mm) REVERT: H 61 MET cc_start: 0.7251 (mmt) cc_final: 0.6963 (mmt) REVERT: I 111 GLU cc_start: 0.8328 (tp30) cc_final: 0.8120 (tp30) REVERT: J 81 MET cc_start: 0.7884 (tmm) cc_final: 0.7665 (tmm) REVERT: P 50 SER cc_start: 0.8108 (p) cc_final: 0.7838 (m) REVERT: P 77 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8022 (t80) REVERT: P 110 LYS cc_start: 0.6147 (mmmt) cc_final: 0.5929 (mmmm) REVERT: Q 45 ILE cc_start: 0.7812 (mp) cc_final: 0.7600 (mt) REVERT: R 31 LYS cc_start: 0.7036 (tmmt) cc_final: 0.6204 (mptt) REVERT: R 118 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7011 (mt) REVERT: R 177 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6270 (mt-10) REVERT: S 183 ILE cc_start: 0.8355 (mt) cc_final: 0.7946 (mt) REVERT: S 248 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: S 274 MET cc_start: 0.7942 (mmm) cc_final: 0.7500 (mmm) REVERT: T 260 VAL cc_start: 0.9363 (t) cc_final: 0.9100 (p) REVERT: T 304 TYR cc_start: 0.8736 (m-80) cc_final: 0.8525 (m-80) REVERT: T 329 LYS cc_start: 0.8914 (mttm) cc_final: 0.8649 (mttt) REVERT: T 509 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7770 (mm) REVERT: U 112 ASP cc_start: 0.7944 (t0) cc_final: 0.7562 (t0) REVERT: U 203 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: U 260 VAL cc_start: 0.9275 (t) cc_final: 0.8919 (m) REVERT: U 483 MET cc_start: 0.7109 (tpp) cc_final: 0.6864 (tpp) REVERT: U 511 LYS cc_start: 0.7677 (tttt) cc_final: 0.6961 (mmtp) REVERT: V 121 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.7755 (m110) REVERT: V 152 ASN cc_start: 0.8130 (m-40) cc_final: 0.7928 (m-40) REVERT: V 309 MET cc_start: 0.8804 (mtt) cc_final: 0.8441 (mtt) REVERT: V 316 THR cc_start: 0.7322 (p) cc_final: 0.7084 (p) REVERT: V 551 LYS cc_start: 0.7964 (tttp) cc_final: 0.7429 (mttt) REVERT: X 456 THR cc_start: 0.8443 (m) cc_final: 0.8043 (p) REVERT: X 488 MET cc_start: 0.7775 (mmm) cc_final: 0.7478 (mmm) REVERT: X 502 MET cc_start: 0.6840 (ptp) cc_final: 0.6400 (ptp) REVERT: X 573 LYS cc_start: 0.5694 (ttmt) cc_final: 0.5472 (tptt) REVERT: Y 152 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: Y 194 MET cc_start: 0.8029 (tpp) cc_final: 0.7459 (mmm) REVERT: Y 296 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7429 (mt-10) REVERT: Y 401 ARG cc_start: 0.7300 (mmm160) cc_final: 0.6651 (mmm-85) REVERT: Y 405 LYS cc_start: 0.8383 (tptt) cc_final: 0.7895 (tttm) REVERT: Y 489 VAL cc_start: 0.8343 (m) cc_final: 0.8069 (p) REVERT: Z 58 SER cc_start: 0.8867 (m) cc_final: 0.8651 (m) REVERT: Z 196 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8880 (mt) REVERT: Z 271 TYR cc_start: 0.8521 (t80) cc_final: 0.8171 (t80) REVERT: Z 294 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8654 (m-40) REVERT: Z 359 ASP cc_start: 0.8031 (m-30) cc_final: 0.7467 (m-30) outliers start: 140 outliers final: 102 residues processed: 668 average time/residue: 0.2066 time to fit residues: 233.0451 Evaluate side-chains 651 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 537 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 466 LEU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 535 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 502 TYR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 121 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 505 ASP Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 158 GLU Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 294 ASN Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 500 ASP Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 307 optimal weight: 0.9980 chunk 238 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 438 optimal weight: 1.9990 chunk 397 optimal weight: 0.7980 chunk 254 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 433 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 98 GLN P 65 ASN P 76 GLN R 64 GLN S 262 ASN U 134 ASN U 529 ASN Y 174 GLN Y 388 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115957 restraints weight = 57764.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118172 restraints weight = 32914.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118660 restraints weight = 22794.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119424 restraints weight = 18613.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119928 restraints weight = 15820.149| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34412 Z= 0.124 Angle : 0.607 14.290 46638 Z= 0.304 Chirality : 0.044 0.178 5519 Planarity : 0.004 0.045 5997 Dihedral : 5.600 91.104 4830 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 3.56 % Allowed : 25.03 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.80 (0.13), residues: 4461 helix: 0.08 (0.12), residues: 2140 sheet: -1.12 (0.23), residues: 537 loop : -0.95 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 555 TYR 0.020 0.001 TYR T 502 PHE 0.031 0.001 PHE D 107 TRP 0.010 0.001 TRP R 37 HIS 0.005 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (34412) covalent geometry : angle 0.60687 / 0.30 (46638) hydrogen bonds : bond 0.03397 / 2.24 ( 1590) hydrogen bonds : angle 4.53888 / 3.19 ( 4629) *********************** 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 692 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 565 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ASN cc_start: 0.7719 (m-40) cc_final: 0.7250 (m-40) REVERT: C 60 LYS cc_start: 0.6553 (tptt) cc_final: 0.5386 (mtpt) REVERT: C 94 ASN cc_start: 0.8085 (t0) cc_final: 0.7856 (t0) REVERT: D 81 MET cc_start: 0.8243 (ttp) cc_final: 0.7890 (ttp) REVERT: D 120 VAL cc_start: 0.7012 (OUTLIER) cc_final: 0.6759 (p) REVERT: D 122 PHE cc_start: 0.5996 (m-80) cc_final: 0.5764 (m-80) REVERT: E 119 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5710 (mt) REVERT: E 123 LEU cc_start: 0.8046 (mt) cc_final: 0.7704 (tt) REVERT: F 105 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.5537 (mm) REVERT: H 61 MET cc_start: 0.7221 (mmt) cc_final: 0.6797 (mmt) REVERT: J 81 MET cc_start: 0.8062 (tmm) cc_final: 0.7823 (tmm) REVERT: P 77 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8010 (t80) REVERT: P 110 LYS cc_start: 0.6456 (mmmt) cc_final: 0.6143 (mmmm) REVERT: Q 32 LYS cc_start: 0.6837 (mmmm) cc_final: 0.6113 (mttt) REVERT: Q 45 ILE cc_start: 0.7651 (mp) cc_final: 0.7441 (mt) REVERT: R 31 LYS cc_start: 0.6820 (tmmt) cc_final: 0.6193 (mptt) REVERT: R 32 GLU cc_start: 0.7504 (tm-30) cc_final: 0.6519 (tt0) REVERT: R 118 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7055 (mt) REVERT: R 177 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6117 (mt-10) REVERT: S 68 MET cc_start: 0.8242 (ttp) cc_final: 0.7994 (ttt) REVERT: S 87 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7156 (ptt180) REVERT: S 183 ILE cc_start: 0.8356 (mt) cc_final: 0.7998 (mt) REVERT: S 248 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: S 274 MET cc_start: 0.7850 (mmm) cc_final: 0.7435 (mmm) REVERT: T 260 VAL cc_start: 0.9360 (t) cc_final: 0.9108 (p) REVERT: T 304 TYR cc_start: 0.8712 (m-80) cc_final: 0.8512 (m-80) REVERT: T 329 LYS cc_start: 0.8921 (mttm) cc_final: 0.8634 (mttt) REVERT: T 509 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7753 (mm) REVERT: U 77 TYR cc_start: 0.7410 (m-80) cc_final: 0.7196 (m-10) REVERT: U 112 ASP cc_start: 0.7975 (t0) cc_final: 0.7570 (t0) REVERT: U 203 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: U 210 ASP cc_start: 0.7846 (m-30) cc_final: 0.7544 (m-30) REVERT: U 260 VAL cc_start: 0.9274 (t) cc_final: 0.8902 (m) REVERT: U 511 LYS cc_start: 0.7728 (tttt) cc_final: 0.6940 (mmtp) REVERT: V 152 ASN cc_start: 0.8154 (m-40) cc_final: 0.7935 (m-40) REVERT: V 309 MET cc_start: 0.8771 (mtt) cc_final: 0.8449 (mtt) REVERT: V 316 THR cc_start: 0.7360 (p) cc_final: 0.7119 (p) REVERT: V 551 LYS cc_start: 0.7902 (tttp) cc_final: 0.7402 (mttt) REVERT: X 456 THR cc_start: 0.8455 (m) cc_final: 0.8036 (p) REVERT: X 502 MET cc_start: 0.6852 (ptp) cc_final: 0.6420 (ptp) REVERT: Y 152 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: Y 194 MET cc_start: 0.8052 (tpp) cc_final: 0.7494 (mmm) REVERT: Y 296 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7513 (mt-10) REVERT: Y 401 ARG cc_start: 0.7331 (mmm160) cc_final: 0.6634 (mmm-85) REVERT: Y 405 LYS cc_start: 0.8394 (tptt) cc_final: 0.7917 (tttm) REVERT: Y 489 VAL cc_start: 0.8440 (m) cc_final: 0.8171 (p) REVERT: Z 58 SER cc_start: 0.8792 (m) cc_final: 0.8583 (m) REVERT: Z 196 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8866 (mt) REVERT: Z 271 TYR cc_start: 0.8438 (t80) cc_final: 0.8089 (t80) REVERT: Z 294 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8609 (m-40) REVERT: Z 359 ASP cc_start: 0.7845 (m-30) cc_final: 0.7403 (m-30) outliers start: 127 outliers final: 102 residues processed: 652 average time/residue: 0.2061 time to fit residues: 227.9585 Evaluate side-chains 648 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 533 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 502 TYR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 403 ASP Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 158 GLU Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 294 ASN Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 500 ASP Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 109 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 325 optimal weight: 0.6980 chunk 404 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 315 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 336 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 98 GLN J 94 ASN P 65 ASN R 64 GLN S 262 ASN U 134 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN Y 388 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116001 restraints weight = 58142.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118018 restraints weight = 33049.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119178 restraints weight = 22634.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119623 restraints weight = 17749.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119864 restraints weight = 15513.674| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34412 Z= 0.130 Angle : 0.614 13.535 46638 Z= 0.309 Chirality : 0.045 0.204 5519 Planarity : 0.004 0.048 5997 Dihedral : 5.543 90.160 4830 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 3.79 % Allowed : 25.08 % Favored : 71.13 % Cbeta Deviations : 0.00 % 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: -0.69 (0.13), residues: 4461 helix: 0.16 (0.12), residues: 2131 sheet: -1.10 (0.23), residues: 537 loop : -0.85 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 48 TYR 0.020 0.001 TYR V 312 PHE 0.031 0.001 PHE D 107 TRP 0.015 0.001 TRP V 73 HIS 0.005 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (34412) covalent geometry : angle 0.61411 / 0.31 (46638) hydrogen bonds : bond 0.03427 / 2.27 ( 1590) hydrogen bonds : angle 4.52999 / 3.18 ( 4629) ********************** 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 683 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 548 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ASN cc_start: 0.7705 (m-40) cc_final: 0.7252 (m-40) REVERT: C 60 LYS cc_start: 0.6632 (tptt) cc_final: 0.5419 (mtpt) REVERT: C 94 ASN cc_start: 0.8071 (t0) cc_final: 0.7826 (t0) REVERT: D 81 MET cc_start: 0.8265 (ttp) cc_final: 0.7934 (ttp) REVERT: D 120 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6783 (p) REVERT: D 122 PHE cc_start: 0.6150 (m-80) cc_final: 0.5906 (m-80) REVERT: E 123 LEU cc_start: 0.8018 (mt) cc_final: 0.7688 (tt) REVERT: F 105 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5531 (mm) REVERT: H 61 MET cc_start: 0.7200 (mmt) cc_final: 0.6912 (mmt) REVERT: J 81 MET cc_start: 0.7965 (tmm) cc_final: 0.7742 (tmm) REVERT: P 50 SER cc_start: 0.8199 (p) cc_final: 0.7908 (m) REVERT: P 77 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8013 (t80) REVERT: P 110 LYS cc_start: 0.6436 (mmmt) cc_final: 0.6144 (mmmm) REVERT: Q 32 LYS cc_start: 0.6820 (mmmm) cc_final: 0.6127 (mttt) REVERT: Q 65 LEU cc_start: 0.5429 (mp) cc_final: 0.5228 (tp) REVERT: R 31 LYS cc_start: 0.6820 (tmmt) cc_final: 0.6192 (mptt) REVERT: R 32 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6512 (tt0) REVERT: R 118 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7068 (mt) REVERT: R 177 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6153 (mt-10) REVERT: S 68 MET cc_start: 0.8278 (ttp) cc_final: 0.7953 (ttp) REVERT: S 87 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7148 (ptt180) REVERT: S 183 ILE cc_start: 0.8348 (mt) cc_final: 0.8001 (mt) REVERT: S 248 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: T 260 VAL cc_start: 0.9356 (t) cc_final: 0.9113 (p) REVERT: T 329 LYS cc_start: 0.8919 (mttm) cc_final: 0.8647 (mttt) REVERT: T 509 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7800 (mm) REVERT: U 112 ASP cc_start: 0.8020 (t0) cc_final: 0.7597 (t0) REVERT: U 203 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6233 (m-80) REVERT: U 260 VAL cc_start: 0.9276 (t) cc_final: 0.8905 (m) REVERT: U 511 LYS cc_start: 0.7711 (tttt) cc_final: 0.6936 (mmtp) REVERT: V 152 ASN cc_start: 0.8146 (m-40) cc_final: 0.7935 (m-40) REVERT: V 309 MET cc_start: 0.8770 (mtt) cc_final: 0.8467 (mtt) REVERT: V 316 THR cc_start: 0.7362 (p) cc_final: 0.7120 (p) REVERT: V 551 LYS cc_start: 0.7896 (tttp) cc_final: 0.7374 (mttt) REVERT: X 456 THR cc_start: 0.8528 (m) cc_final: 0.8110 (p) REVERT: X 502 MET cc_start: 0.6856 (ptp) cc_final: 0.6415 (ptp) REVERT: Y 152 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7692 (pm20) REVERT: Y 194 MET cc_start: 0.8106 (tpp) cc_final: 0.7543 (mmm) REVERT: Y 276 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6817 (mt-10) REVERT: Y 296 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7455 (mt-10) REVERT: Y 359 ASP cc_start: 0.7268 (p0) cc_final: 0.6942 (t0) REVERT: Y 405 LYS cc_start: 0.8396 (tptt) cc_final: 0.7888 (tttm) REVERT: Y 489 VAL cc_start: 0.8426 (m) cc_final: 0.8146 (p) REVERT: Z 196 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8874 (mt) REVERT: Z 271 TYR cc_start: 0.8418 (t80) cc_final: 0.8062 (t80) REVERT: Z 294 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8620 (m-40) REVERT: Z 359 ASP cc_start: 0.7844 (m-30) cc_final: 0.7531 (m-30) outliers start: 135 outliers final: 112 residues processed: 643 average time/residue: 0.2018 time to fit residues: 220.4007 Evaluate side-chains 650 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 525 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 188 GLN Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 257 ASN Chi-restraints excluded: chain S residue 262 ASN Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 502 TYR Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 403 ASP Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 513 ARG Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 228 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 276 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 291 THR Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 158 GLU Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 233 ILE Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 294 ASN Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 500 ASP Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 404 optimal weight: 3.9990 chunk 357 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 396 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 354 optimal weight: 0.6980 chunk 297 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN G 98 GLN J 94 ASN P 65 ASN S 262 ASN U 123 GLN U 134 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 174 GLN Y 388 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117322 restraints weight = 57790.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119318 restraints weight = 32717.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119990 restraints weight = 23455.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120715 restraints weight = 18551.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121220 restraints weight = 16008.557| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34412 Z= 0.119 Angle : 0.611 12.573 46638 Z= 0.306 Chirality : 0.044 0.246 5519 Planarity : 0.004 0.055 5997 Dihedral : 5.464 88.221 4830 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.76 % Rotamer: Outliers : 3.73 % Allowed : 25.48 % Favored : 70.79 % Cbeta Deviations : 0.00 % 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: -0.60 (0.13), residues: 4461 helix: 0.23 (0.12), residues: 2137 sheet: -1.06 (0.23), residues: 533 loop : -0.81 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 435 TYR 0.020 0.001 TYR V 312 PHE 0.032 0.001 PHE D 107 TRP 0.020 0.001 TRP V 73 HIS 0.005 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (34412) covalent geometry : angle 0.61140 / 0.31 (46638) hydrogen bonds : bond 0.03355 / 2.23 ( 1590) hydrogen bonds : angle 4.47402 / 3.14 ( 4629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6678.59 seconds wall clock time: 116 minutes 16.71 seconds (6976.71 seconds total)