Starting phenix.real_space_refine on Thu Nov 20 11:37:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rdp_4826/11_2025/6rdp_4826.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rdp_4826/11_2025/6rdp_4826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rdp_4826/11_2025/6rdp_4826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rdp_4826/11_2025/6rdp_4826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rdp_4826/11_2025/6rdp_4826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rdp_4826/11_2025/6rdp_4826.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21541 2.51 5 N 5795 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 255 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: (159.003, 134.784, 207.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 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: 2.80 Conformation dependent library (CDL) restraints added in 1.7 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: 183 helices and 0 sheets defined 52.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 removed outlier: 4.684A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.867A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.587A 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 126 removed outlier: 3.570A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 4.387A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 92 removed outlier: 3.717A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 124 removed outlier: 4.374A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.787A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 90 removed outlier: 3.968A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 126 removed outlier: 3.884A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 removed outlier: 4.206A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.942A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.920A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.751A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 90 removed outlier: 4.139A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 110 through 126 removed outlier: 3.880A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 66 Processing helix chain 'F' and resid 69 through 92 removed outlier: 3.985A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 124 removed outlier: 3.915A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 removed outlier: 4.443A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS G 66 " --> pdb=" O VAL G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.818A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 127 removed outlier: 4.311A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.855A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 92 removed outlier: 4.072A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 111 removed outlier: 3.665A pdb=" N LEU H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 4.220A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 3.829A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 3.726A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 removed outlier: 3.526A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 93 through 96' Processing helix chain 'I' and resid 97 through 127 removed outlier: 3.699A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.210A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 90 removed outlier: 3.976A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 96 removed outlier: 3.584A pdb=" N ILE J 95 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 96' Processing helix chain 'J' and resid 97 through 109 removed outlier: 3.646A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 126 removed outlier: 3.601A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 60 removed outlier: 3.704A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU P 56 " --> pdb=" O GLN P 52 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.506A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.534A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 105 removed outlier: 3.850A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 125 removed outlier: 3.749A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 132 removed outlier: 4.543A pdb=" N SER P 132 " --> pdb=" O GLY P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 129 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 3.558A pdb=" N ALA P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 removed outlier: 3.561A pdb=" N TYR Q 19 " --> pdb=" O SER Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 4.210A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 44 removed outlier: 3.866A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 41 removed outlier: 4.364A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.725A 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: 4.125A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 Processing helix chain 'S' and resid 40 through 70 removed outlier: 3.841A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 removed outlier: 3.574A pdb=" N SER S 78 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 90 removed outlier: 4.342A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 128 removed outlier: 3.617A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 148 removed outlier: 3.644A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 143 through 148' Processing helix chain 'S' and resid 171 through 182 Processing helix chain 'S' and resid 227 through 231 removed outlier: 3.730A pdb=" N ALA S 230 " --> pdb=" O SER S 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.650A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 4.101A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE T 138 " --> pdb=" O ASP T 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 134 through 138' Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 213 removed outlier: 3.708A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.535A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 3.610A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 329 through 341 removed outlier: 3.525A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.734A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 415 removed outlier: 3.525A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 434 removed outlier: 3.866A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.774A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 460 removed outlier: 3.824A pdb=" N GLN T 452 " --> pdb=" O LEU T 448 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.949A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 506 removed outlier: 3.563A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 513 through 515 No H-bonds generated for 'chain 'T' and resid 513 through 515' Processing helix chain 'T' and resid 516 through 527 removed outlier: 4.929A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 540 removed outlier: 3.807A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU T 536 " --> pdb=" O VAL T 532 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 554 removed outlier: 3.920A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 47 removed outlier: 3.726A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 64 removed outlier: 3.574A pdb=" N VAL U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 72 Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.873A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.826A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.621A pdb=" N VAL U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 4.012A 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 284 Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.603A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 3.529A pdb=" N GLN U 330 " --> pdb=" O ASP U 326 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.797A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 400 removed outlier: 3.524A pdb=" N SER U 400 " --> pdb=" O THR U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 409 through 415 removed outlier: 3.839A pdb=" N LYS U 415 " --> pdb=" O GLU U 411 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 460 removed outlier: 4.000A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 469 through 485 removed outlier: 3.786A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.570A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.664A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.810A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'V' and resid 45 through 49 Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.973A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (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: 3.944A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 246 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.733A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 341 removed outlier: 3.528A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.583A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.598A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 414 removed outlier: 3.998A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 435 removed outlier: 4.050A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN V 435 " --> pdb=" O SER V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 456 removed outlier: 3.632A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 4.030A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) removed outlier: 3.681A 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 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 526 removed outlier: 4.228A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.609A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 removed outlier: 4.168A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.528A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 removed outlier: 4.679A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.733A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 275 removed outlier: 3.528A pdb=" N ARG X 260 " --> pdb=" O GLY X 256 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA X 262 " --> pdb=" O ARG X 258 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU X 263 " --> pdb=" O ALA X 259 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 300 removed outlier: 3.846A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU X 300 " --> pdb=" O GLU X 296 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 365 through 371 removed outlier: 3.547A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 421 removed outlier: 4.548A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 491 through 506 Processing helix chain 'X' and resid 526 through 533 removed outlier: 4.052A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) 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: 3.787A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 275 removed outlier: 3.616A pdb=" N ARG Y 260 " --> pdb=" O GLY Y 256 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.789A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 301 Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.707A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) Processing helix chain 'Y' and resid 356 through 358 No H-bonds generated for 'chain 'Y' and resid 356 through 358' Processing helix chain 'Y' and resid 365 through 371 Processing helix chain 'Y' and resid 388 through 393 Processing helix chain 'Y' and resid 393 through 418 removed outlier: 3.902A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 443 Processing helix chain 'Y' and resid 462 through 475 Processing helix chain 'Y' and resid 482 through 487 Processing helix chain 'Y' and resid 491 through 508 removed outlier: 3.795A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 533 Processing helix chain 'Y' and resid 544 through 555 Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 164 through 170 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.114A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.510A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 Processing helix chain 'Z' and resid 313 through 323 removed outlier: 4.080A 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 365 through 370 Processing helix chain 'Z' and resid 392 through 412 removed outlier: 4.282A pdb=" N HIS Z 396 " --> pdb=" O ILE Z 392 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 421 removed outlier: 4.079A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 426 through 443 Processing helix chain 'Z' and resid 447 through 449 No H-bonds generated for 'chain 'Z' and resid 447 through 449' Processing helix chain 'Z' and resid 450 through 455 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.615A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 487 removed outlier: 3.786A pdb=" N TYR Z 487 " --> pdb=" O MET Z 484 " (cutoff:3.500A) Processing helix chain 'Z' and resid 491 through 508 removed outlier: 3.683A pdb=" N VAL Z 495 " --> pdb=" O ASP Z 491 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 532 1413 hydrogen bonds defined for protein. 4119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8056 1.33 - 1.45: 7063 1.45 - 1.58: 19072 1.58 - 1.70: 21 1.70 - 1.83: 200 Bond restraints: 34412 Sorted by residual: 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 4.86e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.76e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.09e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.53e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.45e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 46149 3.82 - 7.63: 437 7.63 - 11.45: 42 11.45 - 15.26: 7 15.26 - 19.08: 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 139.87 120.79 19.08 1.00e+00 1.00e+00 3.64e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 120.87 19.00 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 121.99 17.88 1.00e+00 1.00e+00 3.20e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.69 15.14 1.00e+00 1.00e+00 2.29e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.61 13.22 1.00e+00 1.00e+00 1.75e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 19548 23.28 - 46.57: 1121 46.57 - 69.85: 113 69.85 - 93.14: 39 93.14 - 116.42: 2 Dihedral angle restraints: 20823 sinusoidal: 8066 harmonic: 12757 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual 180.00 -119.14 -60.86 0 5.00e+00 4.00e-02 1.48e+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 -120.34 -59.66 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -123.11 -56.89 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 20820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4868 0.098 - 0.196: 609 0.196 - 0.294: 39 0.294 - 0.391: 2 0.391 - 0.489: 1 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB VAL U 81 " pdb=" CA VAL U 81 " pdb=" CG1 VAL U 81 " pdb=" CG2 VAL U 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CG LEU U 202 " pdb=" CB LEU U 202 " pdb=" CD1 LEU U 202 " pdb=" CD2 LEU U 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.65e+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 5.88e-02 3.46e+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 U 296 " 0.058 5.00e-02 4.00e+02 8.68e-02 1.20e+01 pdb=" N PRO U 297 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO U 297 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO U 297 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP X 348 " 0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO X 349 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO X 349 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO X 349 " 0.046 5.00e-02 4.00e+02 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 375 2.60 - 3.17: 27998 3.17 - 3.75: 55164 3.75 - 4.32: 81117 4.32 - 4.90: 130964 Nonbonded interactions: 295618 Sorted by model distance: nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.023 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.115 2.170 nonbonded pdb=" O3G ATP V1001 " pdb="MG MG V1002 " model vdw 2.120 2.170 ... (remaining 295613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.310 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 0.122 34412 Z= 0.476 Angle : 1.067 19.079 46638 Z= 0.610 Chirality : 0.064 0.489 5519 Planarity : 0.008 0.087 5997 Dihedral : 14.804 116.422 12663 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.40 % Favored : 94.33 % Rotamer: Outliers : 0.65 % Allowed : 6.93 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.10), residues: 4461 helix: -3.04 (0.08), residues: 2160 sheet: -1.26 (0.21), residues: 579 loop : -1.93 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 217 TYR 0.021 0.003 TYR Q 52 PHE 0.043 0.003 PHE E 122 TRP 0.022 0.004 TRP Z 141 HIS 0.013 0.002 HIS S 250 Details of bonding type rmsd covalent geometry : bond 0.01109 (34412) covalent geometry : angle 1.06665 (46638) hydrogen bonds : bond 0.18315 ( 1413) hydrogen bonds : angle 7.80954 ( 4119) *********************** 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 626 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 603 time to evaluate : 1.332 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: D 61 MET cc_start: 0.4044 (mmp) cc_final: 0.3180 (mmt) REVERT: D 87 ASN cc_start: 0.7387 (m-40) cc_final: 0.7185 (m110) REVERT: D 92 ASN cc_start: 0.6686 (p0) cc_final: 0.6244 (t0) REVERT: E 123 LEU cc_start: 0.6295 (mm) cc_final: 0.5821 (tm) REVERT: H 78 LEU cc_start: 0.6149 (mp) cc_final: 0.5797 (mt) REVERT: P 63 LYS cc_start: 0.7718 (tppt) cc_final: 0.7318 (mtpp) REVERT: P 82 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7938 (mtmt) REVERT: P 88 ARG cc_start: 0.8760 (ptp90) cc_final: 0.8460 (ptp90) REVERT: P 120 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7802 (mmtp) REVERT: P 122 PHE cc_start: 0.7877 (m-10) cc_final: 0.7368 (m-80) REVERT: P 136 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7853 (mt-10) REVERT: P 140 ASN cc_start: 0.8785 (m110) cc_final: 0.8552 (m-40) REVERT: P 146 LEU cc_start: 0.8669 (tt) cc_final: 0.8408 (mt) REVERT: S 58 LYS cc_start: 0.7863 (tttt) cc_final: 0.7637 (tptm) REVERT: S 60 MET cc_start: 0.7308 (mtp) cc_final: 0.7045 (mtm) REVERT: S 144 ASP cc_start: 0.7913 (m-30) cc_final: 0.7695 (m-30) REVERT: S 149 GLN cc_start: 0.7445 (mt0) cc_final: 0.7243 (mt0) REVERT: S 154 GLU cc_start: 0.6565 (mt-10) cc_final: 0.5371 (tp30) REVERT: S 244 ARG cc_start: 0.7347 (tpp-160) cc_final: 0.6948 (tpp80) REVERT: T 471 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7445 (tp-100) REVERT: T 510 ASP cc_start: 0.7309 (m-30) cc_final: 0.6878 (m-30) REVERT: U 47 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6894 (mm-30) REVERT: U 287 MET cc_start: 0.8439 (tpt) cc_final: 0.8015 (tpp) REVERT: U 414 TYR cc_start: 0.7302 (t80) cc_final: 0.6917 (t80) REVERT: V 73 TRP cc_start: 0.8217 (m-10) cc_final: 0.7864 (m-10) REVERT: X 414 GLN cc_start: 0.7559 (mt0) cc_final: 0.7300 (mt0) REVERT: X 429 ASP cc_start: 0.7914 (m-30) cc_final: 0.7553 (m-30) REVERT: X 440 GLN cc_start: 0.8521 (mt0) cc_final: 0.8249 (mt0) REVERT: X 488 MET cc_start: 0.8840 (mmt) cc_final: 0.8629 (mmt) REVERT: X 517 VAL cc_start: 0.5541 (OUTLIER) cc_final: 0.5302 (m) REVERT: Y 371 LEU cc_start: 0.8357 (mp) cc_final: 0.8151 (mt) REVERT: Y 405 LYS cc_start: 0.8192 (tptt) cc_final: 0.7619 (ttpp) REVERT: Y 413 LEU cc_start: 0.7981 (mt) cc_final: 0.7775 (mt) REVERT: Y 437 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7434 (mtm-85) REVERT: Y 501 LYS cc_start: 0.7406 (tttm) cc_final: 0.6900 (mtpp) REVERT: Z 227 MET cc_start: 0.8876 (mtt) cc_final: 0.8560 (mtt) REVERT: Z 502 MET cc_start: 0.7096 (mtp) cc_final: 0.6670 (mtp) outliers start: 23 outliers final: 10 residues processed: 622 average time/residue: 0.7418 time to fit residues: 546.3499 Evaluate side-chains 402 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 391 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 504 LYS Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN D 94 ASN E 92 ASN P 52 GLN R 38 ASN R 73 ASN R 78 HIS R 85 GLN R 110 GLN S 45 GLN S 191 GLN S 293 ASN S 297 GLN T 104 GLN T 134 ASN T 149 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 422 ASN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 GLN U 121 ASN U 242 GLN U 246 ASN U 248 GLN U 319 HIS U 386 GLN U 405 GLN U 441 GLN U 461 GLN U 497 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS V 60 GLN V 64 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS V 134 ASN V 139 HIS V 149 GLN V 152 ASN V 196 GLN V 241 HIS V 244 ASN V 422 ASN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 408 GLN Y 322 GLN Y 398 ASN Y 440 GLN Z 132 GLN Z 199 ASN Z 278 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 574 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.162232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118215 restraints weight = 46519.520| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.93 r_work: 0.3265 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1726 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 : 0.602 12.188 46638 Z= 0.311 Chirality : 0.043 0.180 5519 Planarity : 0.005 0.062 5997 Dihedral : 7.191 97.662 4936 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.90 % Favored : 95.85 % Rotamer: Outliers : 2.72 % Allowed : 12.85 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.03 (0.12), residues: 4461 helix: -1.29 (0.10), residues: 2187 sheet: -0.86 (0.22), residues: 528 loop : -1.34 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 86 TYR 0.017 0.001 TYR U 502 PHE 0.034 0.001 PHE E 122 TRP 0.009 0.001 TRP R 37 HIS 0.005 0.001 HIS V 549 Details of bonding type rmsd covalent geometry : bond 0.00289 (34412) covalent geometry : angle 0.60186 (46638) hydrogen bonds : bond 0.04132 ( 1413) hydrogen bonds : angle 4.85741 ( 4119) *********************** 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 578 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 481 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.4166 (OUTLIER) cc_final: 0.3953 (mt) REVERT: A 81 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6306 (tpt) REVERT: A 119 LEU cc_start: 0.4738 (tt) cc_final: 0.4414 (tt) REVERT: D 61 MET cc_start: 0.3567 (mmp) cc_final: 0.2808 (mmt) REVERT: D 87 ASN cc_start: 0.6352 (m-40) cc_final: 0.5955 (m110) REVERT: D 92 ASN cc_start: 0.6800 (p0) cc_final: 0.6172 (t0) REVERT: D 98 GLN cc_start: 0.7338 (tp-100) cc_final: 0.7001 (tt0) REVERT: E 81 MET cc_start: 0.7840 (ttp) cc_final: 0.7618 (ttm) REVERT: E 123 LEU cc_start: 0.6651 (mm) cc_final: 0.6115 (tm) REVERT: F 81 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7198 (ptm) REVERT: F 84 SER cc_start: 0.6964 (OUTLIER) cc_final: 0.6754 (t) REVERT: H 56 LEU cc_start: 0.4298 (OUTLIER) cc_final: 0.3412 (tm) REVERT: H 81 MET cc_start: 0.6082 (ptt) cc_final: 0.5872 (ptm) REVERT: J 81 MET cc_start: 0.6662 (tmm) cc_final: 0.6232 (tpt) REVERT: P 88 ARG cc_start: 0.8684 (ptp90) cc_final: 0.8417 (ptp90) REVERT: P 122 PHE cc_start: 0.8241 (m-10) cc_final: 0.7563 (m-80) REVERT: P 141 TYR cc_start: 0.8940 (t80) cc_final: 0.8706 (t80) REVERT: S 58 LYS cc_start: 0.7968 (tttt) cc_final: 0.7645 (tptm) REVERT: S 178 ILE cc_start: 0.8889 (mt) cc_final: 0.8542 (mp) REVERT: S 244 ARG cc_start: 0.7549 (tpp-160) cc_final: 0.7317 (tpp80) REVERT: T 237 ASP cc_start: 0.8237 (m-30) cc_final: 0.8017 (m-30) REVERT: T 287 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8144 (tpp) REVERT: T 439 MET cc_start: 0.8503 (ttp) cc_final: 0.8074 (tpp) REVERT: T 475 GLU cc_start: 0.7954 (tp30) cc_final: 0.7560 (tp30) REVERT: U 45 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7932 (mt) REVERT: U 47 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7131 (mm-30) REVERT: U 414 TYR cc_start: 0.7969 (t80) cc_final: 0.7399 (t80) REVERT: U 474 LEU cc_start: 0.7804 (mt) cc_final: 0.7471 (tm) REVERT: V 46 ASP cc_start: 0.7814 (m-30) cc_final: 0.7389 (p0) REVERT: V 73 TRP cc_start: 0.8121 (m-10) cc_final: 0.7894 (m-10) REVERT: V 482 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: X 414 GLN cc_start: 0.7585 (mt0) cc_final: 0.7338 (mt0) REVERT: X 440 GLN cc_start: 0.8597 (mt0) cc_final: 0.8242 (mt0) REVERT: X 471 GLN cc_start: 0.8171 (tt0) cc_final: 0.7843 (tt0) REVERT: X 488 MET cc_start: 0.9139 (mmt) cc_final: 0.8797 (mmt) REVERT: X 504 LYS cc_start: 0.7978 (tttt) cc_final: 0.7417 (tmtt) REVERT: Y 55 GLU cc_start: 0.8262 (tp30) cc_final: 0.7932 (pt0) REVERT: Y 195 GLU cc_start: 0.7812 (tp30) cc_final: 0.7210 (tp30) REVERT: Y 204 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6035 (p-80) REVERT: Y 405 LYS cc_start: 0.8137 (tptt) cc_final: 0.7629 (ttpp) REVERT: Y 416 ILE cc_start: 0.6890 (tt) cc_final: 0.6386 (mp) REVERT: Y 437 ARG cc_start: 0.7672 (mtt-85) cc_final: 0.7240 (mtm-85) REVERT: Y 441 ARG cc_start: 0.8102 (mmt-90) cc_final: 0.7754 (tpp80) REVERT: Y 501 LYS cc_start: 0.7011 (tttm) cc_final: 0.6555 (mtpp) REVERT: Z 91 ASP cc_start: 0.8644 (t0) cc_final: 0.8420 (t70) outliers start: 97 outliers final: 19 residues processed: 538 average time/residue: 0.6887 time to fit residues: 444.5231 Evaluate side-chains 424 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 396 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 107 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 264 optimal weight: 3.9990 chunk 236 optimal weight: 0.4980 chunk 184 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 422 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 396 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN I 94 ASN P 52 GLN P 59 GLN P 140 ASN Q 40 GLN ** R 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN T 126 HIS T 134 ASN T 149 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 196 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 549 HIS U 121 ASN U 152 ASN U 228 GLN U 244 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 271 GLN ** V 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Z 414 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.160388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113791 restraints weight = 46720.609| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.98 r_work: 0.3179 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 34412 Z= 0.198 Angle : 0.617 9.860 46638 Z= 0.317 Chirality : 0.045 0.171 5519 Planarity : 0.005 0.080 5997 Dihedral : 7.085 89.161 4926 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.60 % Favored : 95.14 % Rotamer: Outliers : 3.59 % Allowed : 14.79 % Favored : 81.62 % 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: -1.32 (0.12), residues: 4461 helix: -0.58 (0.11), residues: 2190 sheet: -0.86 (0.22), residues: 522 loop : -1.07 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 145 TYR 0.018 0.002 TYR U 502 PHE 0.029 0.001 PHE E 122 TRP 0.014 0.001 TRP R 37 HIS 0.008 0.001 HIS V 549 Details of bonding type rmsd covalent geometry : bond 0.00464 (34412) covalent geometry : angle 0.61735 (46638) hydrogen bonds : bond 0.04205 ( 1413) hydrogen bonds : angle 4.55581 ( 4119) *********************** 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 544 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 416 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6209 (tpt) REVERT: D 61 MET cc_start: 0.3936 (mmp) cc_final: 0.2721 (mpp) REVERT: D 81 MET cc_start: 0.7331 (ttm) cc_final: 0.5777 (tpp) REVERT: D 87 ASN cc_start: 0.6265 (m-40) cc_final: 0.5818 (m110) REVERT: D 92 ASN cc_start: 0.6956 (p0) cc_final: 0.6413 (t0) REVERT: D 99 LEU cc_start: 0.7023 (mt) cc_final: 0.6620 (pp) REVERT: E 81 MET cc_start: 0.7832 (ttp) cc_final: 0.7625 (ttm) REVERT: E 123 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6247 (tm) REVERT: F 81 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6958 (ptm) REVERT: G 61 MET cc_start: 0.7526 (mmt) cc_final: 0.7304 (mpp) REVERT: G 109 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5805 (tm) REVERT: H 56 LEU cc_start: 0.4373 (OUTLIER) cc_final: 0.3469 (tm) REVERT: J 81 MET cc_start: 0.6708 (tmm) cc_final: 0.6167 (tpt) REVERT: Q 40 GLN cc_start: 0.5917 (OUTLIER) cc_final: 0.5360 (mm110) REVERT: Q 66 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7361 (tm-30) REVERT: S 58 LYS cc_start: 0.7881 (tttt) cc_final: 0.7497 (tptm) REVERT: S 144 ASP cc_start: 0.8366 (m-30) cc_final: 0.7889 (m-30) REVERT: S 154 GLU cc_start: 0.6549 (mt-10) cc_final: 0.5130 (tp30) REVERT: S 234 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: S 244 ARG cc_start: 0.7760 (tpp-160) cc_final: 0.7300 (tpp80) REVERT: T 226 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8322 (t0) REVERT: T 287 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8235 (tpp) REVERT: T 439 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8161 (tpp) REVERT: T 475 GLU cc_start: 0.7965 (tp30) cc_final: 0.7414 (tp30) REVERT: U 45 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7932 (mt) REVERT: U 47 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7258 (mm-30) REVERT: U 414 TYR cc_start: 0.8096 (t80) cc_final: 0.7507 (t80) REVERT: U 527 GLN cc_start: 0.8148 (mt0) cc_final: 0.7865 (mt0) REVERT: V 476 ARG cc_start: 0.6948 (tpp80) cc_final: 0.6575 (tpp-160) REVERT: V 482 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: V 522 GLU cc_start: 0.7174 (pp20) cc_final: 0.6768 (tm-30) REVERT: V 549 HIS cc_start: 0.7398 (m90) cc_final: 0.6685 (m-70) REVERT: X 414 GLN cc_start: 0.7604 (mt0) cc_final: 0.7250 (mt0) REVERT: X 440 GLN cc_start: 0.8691 (mt0) cc_final: 0.8291 (mt0) REVERT: X 471 GLN cc_start: 0.8281 (tt0) cc_final: 0.7928 (tt0) REVERT: X 488 MET cc_start: 0.9178 (mmt) cc_final: 0.8923 (mmt) REVERT: X 504 LYS cc_start: 0.8093 (tttt) cc_final: 0.7424 (tmtt) REVERT: Y 83 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8351 (t0) REVERT: Y 194 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6454 (mpp) REVERT: Y 195 GLU cc_start: 0.7854 (tp30) cc_final: 0.7163 (tp30) REVERT: Y 204 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6393 (p-80) REVERT: Y 401 ARG cc_start: 0.7464 (mmm160) cc_final: 0.6434 (mmt90) REVERT: Y 405 LYS cc_start: 0.8110 (tptt) cc_final: 0.7438 (ttpp) REVERT: Y 416 ILE cc_start: 0.6885 (tt) cc_final: 0.6327 (mp) REVERT: Y 437 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7284 (mtm-85) REVERT: Y 501 LYS cc_start: 0.6961 (tttm) cc_final: 0.6496 (mtpp) REVERT: Z 91 ASP cc_start: 0.8748 (t0) cc_final: 0.8527 (t70) REVERT: Z 440 GLN cc_start: 0.8422 (tt0) cc_final: 0.8151 (mt0) outliers start: 128 outliers final: 45 residues processed: 491 average time/residue: 0.6822 time to fit residues: 402.4247 Evaluate side-chains 440 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 380 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 40 GLN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 423 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 194 MET Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 171 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 374 optimal weight: 2.9990 chunk 245 optimal weight: 0.0050 chunk 261 optimal weight: 0.3980 chunk 151 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN G 94 ASN P 52 GLN R 85 GLN T 134 ASN T 149 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 549 HIS U 121 ASN U 228 GLN U 264 GLN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN V 121 ASN V 134 ASN V 271 GLN V 471 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 294 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.162280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118347 restraints weight = 46374.095| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.16 r_work: 0.3243 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2360 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= 0.131 Angle : 0.562 9.321 46638 Z= 0.287 Chirality : 0.043 0.189 5519 Planarity : 0.004 0.060 5997 Dihedral : 6.663 82.483 4926 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.21 % Favored : 95.58 % Rotamer: Outliers : 3.51 % Allowed : 15.99 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 4461 helix: -0.10 (0.11), residues: 2208 sheet: -0.63 (0.23), residues: 532 loop : -0.96 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 437 TYR 0.023 0.001 TYR T 453 PHE 0.029 0.001 PHE E 122 TRP 0.019 0.002 TRP V 73 HIS 0.007 0.001 HIS R 78 Details of bonding type rmsd covalent geometry : bond 0.00298 (34412) covalent geometry : angle 0.56167 (46638) hydrogen bonds : bond 0.03738 ( 1413) hydrogen bonds : angle 4.28028 ( 4119) *********************** 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 534 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 409 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.3860 (mt) cc_final: 0.3231 (tm) REVERT: A 81 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6046 (tpt) REVERT: D 61 MET cc_start: 0.3887 (mmp) cc_final: 0.2645 (mpp) REVERT: D 81 MET cc_start: 0.7312 (ttm) cc_final: 0.5462 (tpp) REVERT: D 85 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7034 (mm) REVERT: D 87 ASN cc_start: 0.6260 (m-40) cc_final: 0.5743 (m110) REVERT: D 92 ASN cc_start: 0.6702 (p0) cc_final: 0.6303 (t0) REVERT: D 98 GLN cc_start: 0.7344 (tp-100) cc_final: 0.7088 (tt0) REVERT: D 99 LEU cc_start: 0.7133 (mt) cc_final: 0.6606 (pp) REVERT: E 81 MET cc_start: 0.7785 (ttp) cc_final: 0.7562 (ttt) REVERT: E 92 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6530 (p0) REVERT: E 123 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6158 (tm) REVERT: F 61 MET cc_start: 0.5521 (mmt) cc_final: 0.5101 (mtm) REVERT: F 81 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7061 (ptm) REVERT: G 109 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5800 (tm) REVERT: H 56 LEU cc_start: 0.4032 (OUTLIER) cc_final: 0.3457 (tm) REVERT: H 87 ASN cc_start: 0.7303 (m-40) cc_final: 0.7076 (t0) REVERT: J 61 MET cc_start: 0.3786 (OUTLIER) cc_final: 0.3308 (mmp) REVERT: J 81 MET cc_start: 0.6771 (tmm) cc_final: 0.6228 (tpt) REVERT: R 154 GLN cc_start: 0.7153 (pt0) cc_final: 0.6130 (pp30) REVERT: S 58 LYS cc_start: 0.7873 (tttt) cc_final: 0.7501 (tptm) REVERT: S 144 ASP cc_start: 0.8359 (m-30) cc_final: 0.7944 (m-30) REVERT: S 154 GLU cc_start: 0.6491 (mt-10) cc_final: 0.5100 (tp30) REVERT: S 234 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: S 244 ARG cc_start: 0.7715 (tpp-160) cc_final: 0.7389 (tpp80) REVERT: S 271 MET cc_start: 0.8859 (ttp) cc_final: 0.8528 (ptp) REVERT: T 226 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: T 287 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8176 (tpp) REVERT: T 439 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8161 (tpp) REVERT: T 475 GLU cc_start: 0.7933 (tp30) cc_final: 0.7391 (tp30) REVERT: U 47 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7282 (mm-30) REVERT: U 56 LYS cc_start: 0.7829 (ptpp) cc_final: 0.7483 (mttp) REVERT: U 414 TYR cc_start: 0.8055 (t80) cc_final: 0.7493 (t80) REVERT: U 546 LEU cc_start: 0.8910 (tp) cc_final: 0.8692 (tm) REVERT: V 73 TRP cc_start: 0.8238 (m-10) cc_final: 0.7912 (m-90) REVERT: V 418 ARG cc_start: 0.8348 (mtt180) cc_final: 0.7980 (mtt180) REVERT: V 482 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: V 522 GLU cc_start: 0.7129 (pp20) cc_final: 0.6785 (tm-30) REVERT: X 411 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8806 (ttmt) REVERT: X 414 GLN cc_start: 0.7529 (mt0) cc_final: 0.7254 (mt0) REVERT: X 440 GLN cc_start: 0.8686 (mt0) cc_final: 0.8300 (mt0) REVERT: X 488 MET cc_start: 0.9177 (mmt) cc_final: 0.8858 (mmt) REVERT: X 504 LYS cc_start: 0.8063 (tttt) cc_final: 0.7360 (tmtt) REVERT: X 550 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8408 (mttp) REVERT: Y 83 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8803 (t0) REVERT: Y 194 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6432 (mpp) REVERT: Y 195 GLU cc_start: 0.7850 (tp30) cc_final: 0.7196 (tp30) REVERT: Y 204 HIS cc_start: 0.6847 (OUTLIER) cc_final: 0.6219 (p-80) REVERT: Y 401 ARG cc_start: 0.7419 (mmm160) cc_final: 0.6501 (mmt180) REVERT: Y 405 LYS cc_start: 0.8146 (tptt) cc_final: 0.7632 (ttpp) REVERT: Y 437 ARG cc_start: 0.7689 (mtt-85) cc_final: 0.7227 (mtm-85) REVERT: Y 501 LYS cc_start: 0.6982 (tttm) cc_final: 0.6513 (mtpp) REVERT: Z 91 ASP cc_start: 0.8735 (t0) cc_final: 0.8514 (t70) REVERT: Z 440 GLN cc_start: 0.8354 (tt0) cc_final: 0.8126 (mt0) REVERT: Z 521 LEU cc_start: 0.5663 (OUTLIER) cc_final: 0.5379 (tt) outliers start: 125 outliers final: 42 residues processed: 491 average time/residue: 0.6777 time to fit residues: 402.1779 Evaluate side-chains 433 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 372 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 423 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 482 GLU Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 411 LYS Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 550 LYS Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 154 SER Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 194 MET Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Z residue 194 MET Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 241 optimal weight: 0.9980 chunk 290 optimal weight: 0.0470 chunk 106 optimal weight: 1.9990 chunk 424 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 406 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 278 optimal weight: 0.2980 chunk 255 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Q 40 GLN S 191 GLN T 134 ASN T 149 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 244 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 386 GLN V 405 GLN V 471 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.162793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119069 restraints weight = 46498.476| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.16 r_work: 0.3286 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34412 Z= 0.112 Angle : 0.539 9.235 46638 Z= 0.274 Chirality : 0.042 0.171 5519 Planarity : 0.004 0.057 5997 Dihedral : 6.326 83.628 4926 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.01 % Favored : 95.83 % Rotamer: Outliers : 3.25 % Allowed : 17.09 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.44 (0.13), residues: 4461 helix: 0.28 (0.11), residues: 2210 sheet: -0.65 (0.23), residues: 542 loop : -0.76 (0.16), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 199 TYR 0.013 0.001 TYR U 502 PHE 0.027 0.001 PHE E 122 TRP 0.010 0.001 TRP R 37 HIS 0.005 0.001 HIS V 549 Details of bonding type rmsd covalent geometry : bond 0.00251 (34412) covalent geometry : angle 0.53943 (46638) hydrogen bonds : bond 0.03474 ( 1413) hydrogen bonds : angle 4.09732 ( 4119) *********************** 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 550 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 434 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6025 (tpt) REVERT: C 86 ILE cc_start: 0.5852 (mm) cc_final: 0.5646 (mm) REVERT: D 81 MET cc_start: 0.7264 (ttm) cc_final: 0.5435 (tpp) REVERT: D 85 LEU cc_start: 0.7598 (tm) cc_final: 0.7028 (mm) REVERT: D 87 ASN cc_start: 0.6162 (m-40) cc_final: 0.5655 (m110) REVERT: D 92 ASN cc_start: 0.6594 (p0) cc_final: 0.6246 (t0) REVERT: D 99 LEU cc_start: 0.7104 (mt) cc_final: 0.6479 (pp) REVERT: E 81 MET cc_start: 0.7767 (ttp) cc_final: 0.7544 (ttt) REVERT: E 123 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.5991 (tm) REVERT: F 61 MET cc_start: 0.5463 (mmt) cc_final: 0.5195 (mtm) REVERT: F 81 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7098 (ptm) REVERT: G 109 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5731 (tm) REVERT: H 56 LEU cc_start: 0.3787 (OUTLIER) cc_final: 0.3257 (tm) REVERT: H 61 MET cc_start: 0.2970 (ttp) cc_final: 0.2534 (mtt) REVERT: H 87 ASN cc_start: 0.7413 (m-40) cc_final: 0.7210 (t0) REVERT: J 81 MET cc_start: 0.6674 (tmm) cc_final: 0.6095 (tpt) REVERT: P 63 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7458 (mtpt) REVERT: P 142 GLU cc_start: 0.7431 (tp30) cc_final: 0.7174 (tp30) REVERT: R 154 GLN cc_start: 0.7144 (pt0) cc_final: 0.6162 (pp30) REVERT: S 58 LYS cc_start: 0.7859 (tttt) cc_final: 0.7486 (tptm) REVERT: S 144 ASP cc_start: 0.8348 (m-30) cc_final: 0.7900 (m-30) REVERT: S 154 GLU cc_start: 0.6468 (mt-10) cc_final: 0.5072 (tp30) REVERT: S 178 ILE cc_start: 0.8771 (mt) cc_final: 0.8442 (mp) REVERT: S 234 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: S 244 ARG cc_start: 0.7736 (tpp-160) cc_final: 0.7352 (tpp80) REVERT: T 226 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: T 287 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8078 (tpp) REVERT: T 407 PHE cc_start: 0.7980 (t80) cc_final: 0.7686 (m-80) REVERT: T 439 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8212 (tpp) REVERT: T 475 GLU cc_start: 0.7856 (tp30) cc_final: 0.7312 (tp30) REVERT: T 516 ASP cc_start: 0.7393 (p0) cc_final: 0.7029 (p0) REVERT: U 47 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7259 (mm-30) REVERT: U 56 LYS cc_start: 0.7849 (ptpp) cc_final: 0.7379 (mtmm) REVERT: U 414 TYR cc_start: 0.7992 (t80) cc_final: 0.7456 (t80) REVERT: V 73 TRP cc_start: 0.8303 (m-10) cc_final: 0.7743 (m-90) REVERT: V 418 ARG cc_start: 0.8438 (mtt180) cc_final: 0.8074 (mtt180) REVERT: V 476 ARG cc_start: 0.6890 (tpp80) cc_final: 0.6523 (tpp-160) REVERT: V 522 GLU cc_start: 0.7217 (pp20) cc_final: 0.6877 (tm-30) REVERT: V 549 HIS cc_start: 0.7672 (m90) cc_final: 0.7035 (m-70) REVERT: X 414 GLN cc_start: 0.7447 (mt0) cc_final: 0.7166 (mt0) REVERT: X 440 GLN cc_start: 0.8627 (mt0) cc_final: 0.8255 (mt0) REVERT: X 471 GLN cc_start: 0.8358 (tt0) cc_final: 0.8080 (tt0) REVERT: X 488 MET cc_start: 0.9202 (mmt) cc_final: 0.8864 (mmt) REVERT: X 504 LYS cc_start: 0.8101 (tttt) cc_final: 0.7427 (tmtt) REVERT: Y 194 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6511 (mpp) REVERT: Y 195 GLU cc_start: 0.7817 (tp30) cc_final: 0.7167 (tp30) REVERT: Y 401 ARG cc_start: 0.7484 (mmm160) cc_final: 0.6543 (mmt180) REVERT: Y 405 LYS cc_start: 0.8129 (tptt) cc_final: 0.7644 (ttpp) REVERT: Y 437 ARG cc_start: 0.7693 (mtt-85) cc_final: 0.7306 (mmm-85) REVERT: Y 501 LYS cc_start: 0.6968 (tttm) cc_final: 0.6556 (mtpp) REVERT: Z 91 ASP cc_start: 0.8731 (t0) cc_final: 0.8514 (t70) REVERT: Z 521 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5289 (tt) outliers start: 116 outliers final: 45 residues processed: 515 average time/residue: 0.6500 time to fit residues: 404.2526 Evaluate side-chains 443 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 386 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 63 LYS Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 222 ASP Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain T residue 120 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 154 SER Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 194 MET Chi-restraints excluded: chain Z residue 194 MET Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 127 optimal weight: 1.9990 chunk 269 optimal weight: 7.9990 chunk 407 optimal weight: 1.9990 chunk 426 optimal weight: 3.9990 chunk 186 optimal weight: 0.0870 chunk 2 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 382 optimal weight: 6.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 52 GLN Q 40 GLN S 191 GLN T 134 ASN T 149 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN T 529 ASN U 228 GLN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN ** V 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 529 ASN ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.159947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113523 restraints weight = 46099.471| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.93 r_work: 0.3226 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34412 Z= 0.185 Angle : 0.593 10.212 46638 Z= 0.302 Chirality : 0.045 0.154 5519 Planarity : 0.004 0.057 5997 Dihedral : 6.630 90.272 4924 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.39 % Favored : 95.38 % Rotamer: Outliers : 3.40 % Allowed : 17.70 % Favored : 78.90 % 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: -0.38 (0.13), residues: 4461 helix: 0.33 (0.11), residues: 2213 sheet: -0.56 (0.23), residues: 534 loop : -0.76 (0.16), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 454 TYR 0.016 0.002 TYR V 414 PHE 0.025 0.001 PHE E 122 TRP 0.013 0.001 TRP R 37 HIS 0.006 0.001 HIS R 78 Details of bonding type rmsd covalent geometry : bond 0.00435 (34412) covalent geometry : angle 0.59271 (46638) hydrogen bonds : bond 0.03891 ( 1413) hydrogen bonds : angle 4.20148 ( 4119) *********************** 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 504 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 383 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.4355 (mm) cc_final: 0.3603 (tm) REVERT: A 81 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6553 (tpp) REVERT: D 81 MET cc_start: 0.7371 (ttm) cc_final: 0.6770 (ttt) REVERT: D 85 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7027 (mm) REVERT: D 92 ASN cc_start: 0.6554 (p0) cc_final: 0.6328 (t0) REVERT: E 81 MET cc_start: 0.7672 (ttp) cc_final: 0.7412 (ttm) REVERT: E 123 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.5960 (tm) REVERT: F 61 MET cc_start: 0.5699 (mmt) cc_final: 0.5345 (mtm) REVERT: F 81 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7011 (ptm) REVERT: G 109 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5756 (tm) REVERT: H 56 LEU cc_start: 0.3936 (OUTLIER) cc_final: 0.3203 (tm) REVERT: H 61 MET cc_start: 0.3236 (ttp) cc_final: 0.2862 (mtt) REVERT: H 81 MET cc_start: 0.6506 (ttm) cc_final: 0.6148 (tpt) REVERT: J 81 MET cc_start: 0.6715 (tmm) cc_final: 0.6092 (tpt) REVERT: Q 38 LYS cc_start: 0.7006 (ptmm) cc_final: 0.6742 (ptpt) REVERT: R 154 GLN cc_start: 0.7160 (pt0) cc_final: 0.6142 (pp30) REVERT: S 58 LYS cc_start: 0.7819 (tttt) cc_final: 0.7464 (tptm) REVERT: S 144 ASP cc_start: 0.8351 (m-30) cc_final: 0.7891 (m-30) REVERT: S 154 GLU cc_start: 0.6475 (mt-10) cc_final: 0.5073 (tp30) REVERT: S 178 ILE cc_start: 0.8843 (mt) cc_final: 0.8583 (mp) REVERT: S 234 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: S 244 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7395 (tpp80) REVERT: S 271 MET cc_start: 0.8849 (ttp) cc_final: 0.8643 (ptm) REVERT: T 226 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: T 287 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8247 (tpp) REVERT: T 439 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8141 (tpp) REVERT: T 474 LEU cc_start: 0.7927 (tt) cc_final: 0.7694 (tp) REVERT: T 475 GLU cc_start: 0.7945 (tp30) cc_final: 0.7293 (tp30) REVERT: T 516 ASP cc_start: 0.7447 (p0) cc_final: 0.7078 (p0) REVERT: U 47 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7295 (mm-30) REVERT: U 414 TYR cc_start: 0.8017 (t80) cc_final: 0.7471 (t80) REVERT: V 73 TRP cc_start: 0.8306 (m-10) cc_final: 0.7895 (m-90) REVERT: V 509 LEU cc_start: 0.7867 (mp) cc_final: 0.7666 (mp) REVERT: V 522 GLU cc_start: 0.7250 (pp20) cc_final: 0.6960 (tm-30) REVERT: V 549 HIS cc_start: 0.7465 (m90) cc_final: 0.6822 (m-70) REVERT: X 414 GLN cc_start: 0.7563 (mt0) cc_final: 0.7273 (mt0) REVERT: X 440 GLN cc_start: 0.8723 (mt0) cc_final: 0.8245 (mt0) REVERT: X 471 GLN cc_start: 0.8421 (tt0) cc_final: 0.8211 (tt0) REVERT: X 488 MET cc_start: 0.9194 (mmt) cc_final: 0.8949 (mmt) REVERT: Y 194 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6422 (mpp) REVERT: Y 195 GLU cc_start: 0.7843 (tp30) cc_final: 0.7139 (tp30) REVERT: Y 401 ARG cc_start: 0.7422 (mmm160) cc_final: 0.6644 (mmt180) REVERT: Y 405 LYS cc_start: 0.8149 (tptt) cc_final: 0.7674 (ttpp) REVERT: Y 437 ARG cc_start: 0.7694 (mtt-85) cc_final: 0.7292 (mmm-85) REVERT: Y 501 LYS cc_start: 0.6998 (tttm) cc_final: 0.6531 (mtpp) REVERT: Z 440 GLN cc_start: 0.7857 (mt0) cc_final: 0.7597 (mt0) REVERT: Z 521 LEU cc_start: 0.5406 (OUTLIER) cc_final: 0.5135 (tt) outliers start: 121 outliers final: 61 residues processed: 456 average time/residue: 0.6895 time to fit residues: 378.7324 Evaluate side-chains 439 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 366 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 191 GLN Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 291 ASP Chi-restraints excluded: chain T residue 120 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 423 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 46 ASP Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 513 ASP Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 154 SER Chi-restraints excluded: chain Y residue 156 GLU Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 194 MET Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 484 MET Chi-restraints excluded: chain Z residue 318 LEU Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 59 optimal weight: 0.9990 chunk 433 optimal weight: 1.9990 chunk 424 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 337 optimal weight: 1.9990 chunk 436 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 40 GLN S 191 GLN T 140 GLN T 149 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN ** V 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113541 restraints weight = 46246.540| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.91 r_work: 0.3205 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34412 Z= 0.182 Angle : 0.600 10.689 46638 Z= 0.304 Chirality : 0.045 0.184 5519 Planarity : 0.004 0.057 5997 Dihedral : 6.634 92.238 4924 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.39 % Favored : 95.38 % Rotamer: Outliers : 3.42 % Allowed : 18.18 % Favored : 78.40 % 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: -0.28 (0.13), residues: 4461 helix: 0.41 (0.11), residues: 2213 sheet: -0.57 (0.23), residues: 534 loop : -0.69 (0.16), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 429 TYR 0.014 0.002 TYR U 502 PHE 0.024 0.001 PHE S 92 TRP 0.013 0.001 TRP R 37 HIS 0.006 0.001 HIS V 549 Details of bonding type rmsd covalent geometry : bond 0.00428 (34412) covalent geometry : angle 0.59981 (46638) hydrogen bonds : bond 0.03876 ( 1413) hydrogen bonds : angle 4.21207 ( 4119) *********************** 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 497 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 375 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6600 (tpp) REVERT: D 81 MET cc_start: 0.7288 (ttm) cc_final: 0.6757 (ttt) REVERT: D 85 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7076 (mm) REVERT: D 98 GLN cc_start: 0.6469 (tt0) cc_final: 0.6015 (tp-100) REVERT: E 81 MET cc_start: 0.7666 (ttp) cc_final: 0.7395 (ttt) REVERT: F 81 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7032 (ptm) REVERT: G 109 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5727 (tm) REVERT: H 56 LEU cc_start: 0.3938 (OUTLIER) cc_final: 0.3163 (tm) REVERT: H 81 MET cc_start: 0.6601 (ttm) cc_final: 0.6216 (tpt) REVERT: J 81 MET cc_start: 0.6750 (tmm) cc_final: 0.6119 (tpt) REVERT: P 63 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7733 (mtpt) REVERT: Q 38 LYS cc_start: 0.7132 (ptmm) cc_final: 0.6874 (ptpt) REVERT: R 85 GLN cc_start: 0.7143 (mt0) cc_final: 0.6620 (mt0) REVERT: R 154 GLN cc_start: 0.7170 (pt0) cc_final: 0.6198 (pp30) REVERT: S 58 LYS cc_start: 0.7838 (tttt) cc_final: 0.7498 (tptm) REVERT: S 144 ASP cc_start: 0.8338 (m-30) cc_final: 0.7873 (m-30) REVERT: S 178 ILE cc_start: 0.8880 (mt) cc_final: 0.8644 (mp) REVERT: S 234 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: S 244 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.7495 (tpp80) REVERT: T 226 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8183 (m-30) REVERT: T 287 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8199 (tpp) REVERT: T 439 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8241 (tpp) REVERT: T 474 LEU cc_start: 0.7948 (tt) cc_final: 0.7729 (tp) REVERT: T 475 GLU cc_start: 0.8019 (tp30) cc_final: 0.7365 (tp30) REVERT: T 516 ASP cc_start: 0.7419 (p0) cc_final: 0.7037 (p0) REVERT: U 47 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7345 (mm-30) REVERT: U 283 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8281 (ttm170) REVERT: U 414 TYR cc_start: 0.7947 (t80) cc_final: 0.7437 (t80) REVERT: V 73 TRP cc_start: 0.8346 (m-10) cc_final: 0.7900 (m-90) REVERT: V 522 GLU cc_start: 0.7291 (pp20) cc_final: 0.6961 (tm-30) REVERT: V 549 HIS cc_start: 0.7535 (m90) cc_final: 0.6890 (m-70) REVERT: X 414 GLN cc_start: 0.7522 (mt0) cc_final: 0.7185 (mt0) REVERT: X 440 GLN cc_start: 0.8697 (mt0) cc_final: 0.8310 (mt0) REVERT: X 471 GLN cc_start: 0.8411 (tt0) cc_final: 0.8183 (tt0) REVERT: X 488 MET cc_start: 0.9195 (mmt) cc_final: 0.8927 (mmt) REVERT: Y 55 GLU cc_start: 0.7885 (pt0) cc_final: 0.7164 (pp20) REVERT: Y 195 GLU cc_start: 0.7895 (tp30) cc_final: 0.7654 (tp30) REVERT: Y 388 ASN cc_start: 0.7765 (t0) cc_final: 0.7356 (t0) REVERT: Y 401 ARG cc_start: 0.7688 (mmm160) cc_final: 0.6790 (mmt180) REVERT: Y 405 LYS cc_start: 0.8214 (tptt) cc_final: 0.7725 (ttpp) REVERT: Y 437 ARG cc_start: 0.7730 (mtt-85) cc_final: 0.7344 (mmm-85) REVERT: Y 501 LYS cc_start: 0.7022 (tttm) cc_final: 0.6552 (mtpp) REVERT: Z 91 ASP cc_start: 0.8753 (t0) cc_final: 0.8532 (t70) REVERT: Z 219 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8251 (mt-10) REVERT: Z 440 GLN cc_start: 0.7937 (mt0) cc_final: 0.7654 (mt0) outliers start: 122 outliers final: 60 residues processed: 452 average time/residue: 0.6983 time to fit residues: 380.8028 Evaluate side-chains 431 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 360 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 63 LYS Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 291 ASP Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 423 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 283 ARG Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 46 ASP Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 448 LEU Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 154 SER Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Z residue 318 LEU Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 554 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 41 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 379 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 21 ASN Q 40 GLN S 191 GLN T 149 GLN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN ** V 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114384 restraints weight = 46056.423| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.91 r_work: 0.3216 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34412 Z= 0.186 Angle : 0.600 9.680 46638 Z= 0.305 Chirality : 0.045 0.169 5519 Planarity : 0.004 0.058 5997 Dihedral : 6.658 93.974 4924 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.64 % Favored : 95.14 % Rotamer: Outliers : 3.37 % Allowed : 18.63 % Favored : 78.00 % 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: -0.26 (0.13), residues: 4461 helix: 0.43 (0.11), residues: 2213 sheet: -0.56 (0.23), residues: 536 loop : -0.69 (0.16), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG T 199 TYR 0.015 0.002 TYR T 502 PHE 0.026 0.001 PHE S 92 TRP 0.013 0.001 TRP R 37 HIS 0.006 0.001 HIS V 549 Details of bonding type rmsd covalent geometry : bond 0.00438 (34412) covalent geometry : angle 0.60012 (46638) hydrogen bonds : bond 0.03885 ( 1413) hydrogen bonds : angle 4.21639 ( 4119) *********************** 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 502 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 382 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.5345 (ttm) cc_final: 0.5085 (tmm) REVERT: A 81 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6564 (tpp) REVERT: C 81 MET cc_start: 0.6381 (ttt) cc_final: 0.5676 (tpp) REVERT: C 86 ILE cc_start: 0.6025 (mm) cc_final: 0.5733 (mp) REVERT: D 85 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6859 (mm) REVERT: E 81 MET cc_start: 0.7639 (ttp) cc_final: 0.7340 (ttt) REVERT: F 81 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6979 (ptm) REVERT: G 109 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5718 (tm) REVERT: H 56 LEU cc_start: 0.3935 (OUTLIER) cc_final: 0.2675 (pp) REVERT: H 61 MET cc_start: 0.3300 (mtt) cc_final: 0.3058 (ttt) REVERT: J 78 LEU cc_start: 0.6668 (mt) cc_final: 0.6262 (mt) REVERT: J 81 MET cc_start: 0.6669 (tmm) cc_final: 0.6440 (tmm) REVERT: P 142 GLU cc_start: 0.7672 (tp30) cc_final: 0.7461 (tp30) REVERT: Q 38 LYS cc_start: 0.7176 (ptmm) cc_final: 0.6876 (ptpt) REVERT: R 49 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7076 (mt-10) REVERT: R 85 GLN cc_start: 0.7135 (mt0) cc_final: 0.6917 (mt0) REVERT: R 154 GLN cc_start: 0.7180 (pt0) cc_final: 0.6210 (pp30) REVERT: S 58 LYS cc_start: 0.7854 (tttt) cc_final: 0.7531 (tptm) REVERT: S 87 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7933 (ptt180) REVERT: S 144 ASP cc_start: 0.8345 (m-30) cc_final: 0.7910 (m-30) REVERT: S 178 ILE cc_start: 0.8912 (mt) cc_final: 0.8686 (mp) REVERT: S 203 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7805 (p90) REVERT: S 220 LEU cc_start: 0.5804 (tt) cc_final: 0.5473 (tp) REVERT: S 234 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: S 244 ARG cc_start: 0.7714 (tpp-160) cc_final: 0.7442 (ttt90) REVERT: S 271 MET cc_start: 0.8846 (ttp) cc_final: 0.8641 (ptm) REVERT: T 226 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8185 (m-30) REVERT: T 287 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8219 (tpp) REVERT: T 439 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8280 (tpp) REVERT: T 474 LEU cc_start: 0.7950 (tt) cc_final: 0.7725 (tp) REVERT: T 475 GLU cc_start: 0.8041 (tp30) cc_final: 0.7418 (tp30) REVERT: T 516 ASP cc_start: 0.7389 (p0) cc_final: 0.7038 (p0) REVERT: U 47 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7380 (mm-30) REVERT: U 283 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8259 (ttm170) REVERT: U 414 TYR cc_start: 0.7953 (t80) cc_final: 0.7446 (t80) REVERT: V 73 TRP cc_start: 0.8306 (m-10) cc_final: 0.7869 (m-90) REVERT: V 522 GLU cc_start: 0.7316 (pp20) cc_final: 0.6964 (tm-30) REVERT: V 549 HIS cc_start: 0.7543 (m90) cc_final: 0.6845 (m-70) REVERT: X 414 GLN cc_start: 0.7591 (mt0) cc_final: 0.7237 (mt0) REVERT: X 440 GLN cc_start: 0.8710 (mt0) cc_final: 0.8352 (mt0) REVERT: X 471 GLN cc_start: 0.8422 (tt0) cc_final: 0.8175 (tt0) REVERT: X 488 MET cc_start: 0.9196 (mmt) cc_final: 0.8924 (mmt) REVERT: Y 55 GLU cc_start: 0.7890 (pt0) cc_final: 0.7130 (pp20) REVERT: Y 195 GLU cc_start: 0.7909 (tp30) cc_final: 0.7668 (tp30) REVERT: Y 388 ASN cc_start: 0.7880 (t0) cc_final: 0.7483 (t0) REVERT: Y 401 ARG cc_start: 0.7681 (mmm160) cc_final: 0.6808 (mmt180) REVERT: Y 405 LYS cc_start: 0.8222 (tptt) cc_final: 0.7712 (ttpp) REVERT: Y 437 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.7383 (mmm-85) REVERT: Y 501 LYS cc_start: 0.7054 (tttm) cc_final: 0.6571 (mtpp) REVERT: Y 546 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7775 (mt-10) REVERT: Z 91 ASP cc_start: 0.8685 (t0) cc_final: 0.8460 (t70) REVERT: Z 219 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8346 (mt-10) REVERT: Z 440 GLN cc_start: 0.7898 (mt0) cc_final: 0.7632 (mt0) REVERT: Z 521 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.5072 (tt) outliers start: 120 outliers final: 65 residues processed: 468 average time/residue: 0.6712 time to fit residues: 378.6555 Evaluate side-chains 449 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 371 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 291 ASP Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 423 VAL Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 283 ARG Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 46 ASP Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 154 SER Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 484 MET Chi-restraints excluded: chain Z residue 318 LEU Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 554 LEU Chi-restraints excluded: chain Z residue 573 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 307 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 438 optimal weight: 3.9990 chunk 397 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 433 optimal weight: 0.3980 chunk 241 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN F 98 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN T 149 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 152 ASN ** V 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.161102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115804 restraints weight = 45961.811| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.99 r_work: 0.3194 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34412 Z= 0.162 Angle : 0.596 14.573 46638 Z= 0.300 Chirality : 0.044 0.161 5519 Planarity : 0.004 0.057 5997 Dihedral : 6.541 93.725 4924 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.26 % Favored : 95.54 % Rotamer: Outliers : 2.81 % Allowed : 19.47 % Favored : 77.72 % 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: -0.19 (0.13), residues: 4461 helix: 0.49 (0.11), residues: 2227 sheet: -0.61 (0.22), residues: 542 loop : -0.64 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG T 199 TYR 0.018 0.001 TYR V 414 PHE 0.023 0.001 PHE E 122 TRP 0.012 0.001 TRP R 37 HIS 0.006 0.001 HIS V 549 Details of bonding type rmsd covalent geometry : bond 0.00379 (34412) covalent geometry : angle 0.59550 (46638) hydrogen bonds : bond 0.03761 ( 1413) hydrogen bonds : angle 4.18710 ( 4119) *********************** 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 484 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 384 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6530 (tpp) REVERT: C 61 MET cc_start: 0.0174 (ttp) cc_final: -0.0290 (tpt) REVERT: C 81 MET cc_start: 0.6427 (ttt) cc_final: 0.5676 (tpp) REVERT: C 86 ILE cc_start: 0.6180 (mm) cc_final: 0.5869 (mp) REVERT: D 81 MET cc_start: 0.7690 (ttp) cc_final: 0.7380 (ttp) REVERT: D 85 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6870 (mm) REVERT: D 87 ASN cc_start: 0.5752 (m-40) cc_final: 0.5316 (m110) REVERT: F 81 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7016 (ptm) REVERT: G 61 MET cc_start: 0.7174 (mmp) cc_final: 0.6105 (mtm) REVERT: G 109 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5766 (tm) REVERT: H 56 LEU cc_start: 0.3852 (OUTLIER) cc_final: 0.2449 (pp) REVERT: H 61 MET cc_start: 0.3634 (mtt) cc_final: 0.3363 (ttt) REVERT: H 105 LEU cc_start: 0.5580 (tt) cc_final: 0.4817 (mm) REVERT: H 109 LEU cc_start: 0.5683 (tm) cc_final: 0.5344 (tt) REVERT: J 81 MET cc_start: 0.6689 (tmm) cc_final: 0.6471 (tmm) REVERT: J 125 LEU cc_start: 0.3448 (OUTLIER) cc_final: 0.2898 (mt) REVERT: P 103 LYS cc_start: 0.8290 (tptm) cc_final: 0.7931 (mmpt) REVERT: P 141 TYR cc_start: 0.8988 (t80) cc_final: 0.8765 (t80) REVERT: P 142 GLU cc_start: 0.7634 (tp30) cc_final: 0.7416 (tp30) REVERT: Q 38 LYS cc_start: 0.7240 (ptmm) cc_final: 0.6952 (ptpt) REVERT: R 85 GLN cc_start: 0.7093 (mt0) cc_final: 0.6876 (mt0) REVERT: R 148 GLU cc_start: 0.7364 (tp30) cc_final: 0.7158 (tp30) REVERT: R 154 GLN cc_start: 0.7205 (pt0) cc_final: 0.6364 (pp30) REVERT: S 58 LYS cc_start: 0.7841 (tttt) cc_final: 0.7513 (tptm) REVERT: S 82 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7600 (m) REVERT: S 87 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7923 (ptt180) REVERT: S 144 ASP cc_start: 0.8352 (m-30) cc_final: 0.7915 (m-30) REVERT: S 178 ILE cc_start: 0.8883 (mt) cc_final: 0.8662 (mp) REVERT: S 203 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7696 (p90) REVERT: S 234 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: S 244 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7446 (ttt90) REVERT: S 271 MET cc_start: 0.8850 (ttp) cc_final: 0.8508 (ptp) REVERT: T 226 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8203 (m-30) REVERT: T 287 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8208 (tpp) REVERT: T 439 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8178 (tpp) REVERT: T 474 LEU cc_start: 0.7971 (tt) cc_final: 0.7694 (tp) REVERT: T 475 GLU cc_start: 0.7965 (tp30) cc_final: 0.7299 (tp30) REVERT: U 47 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7347 (mm-30) REVERT: U 283 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8384 (ttp-110) REVERT: U 311 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7922 (mt-10) REVERT: U 414 TYR cc_start: 0.7914 (t80) cc_final: 0.7395 (t80) REVERT: V 73 TRP cc_start: 0.8262 (m-10) cc_final: 0.7880 (m-10) REVERT: V 522 GLU cc_start: 0.7369 (pp20) cc_final: 0.7015 (tm-30) REVERT: X 414 GLN cc_start: 0.7603 (mt0) cc_final: 0.7238 (mt0) REVERT: X 440 GLN cc_start: 0.8701 (mt0) cc_final: 0.8362 (mt0) REVERT: X 471 GLN cc_start: 0.8416 (tt0) cc_final: 0.8187 (tt0) REVERT: X 488 MET cc_start: 0.9196 (mmt) cc_final: 0.8925 (mmt) REVERT: X 502 MET cc_start: 0.7744 (mtp) cc_final: 0.7490 (mtp) REVERT: Y 55 GLU cc_start: 0.7908 (pt0) cc_final: 0.7127 (pp20) REVERT: Y 195 GLU cc_start: 0.7903 (tp30) cc_final: 0.7666 (tp30) REVERT: Y 388 ASN cc_start: 0.7871 (t0) cc_final: 0.7484 (t0) REVERT: Y 401 ARG cc_start: 0.7669 (mmm160) cc_final: 0.6777 (mmt180) REVERT: Y 405 LYS cc_start: 0.8208 (tptt) cc_final: 0.7690 (ttpp) REVERT: Y 437 ARG cc_start: 0.7727 (mtt-85) cc_final: 0.7344 (mmm-85) REVERT: Y 501 LYS cc_start: 0.7018 (tttm) cc_final: 0.6545 (mtpp) REVERT: Z 91 ASP cc_start: 0.8693 (t0) cc_final: 0.8480 (t70) REVERT: Z 219 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8401 (mt-10) REVERT: Z 440 GLN cc_start: 0.7931 (mt0) cc_final: 0.7652 (mt0) REVERT: Z 521 LEU cc_start: 0.5512 (OUTLIER) cc_final: 0.5179 (tt) outliers start: 100 outliers final: 54 residues processed: 454 average time/residue: 0.6980 time to fit residues: 380.7272 Evaluate side-chains 439 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 370 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 291 ASP Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 283 ARG Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 513 ASP Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 154 SER Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 573 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 109 optimal weight: 0.9980 chunk 102 optimal weight: 0.0970 chunk 325 optimal weight: 0.7980 chunk 404 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 313 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 336 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN T 149 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN ** V 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.162414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116029 restraints weight = 46149.465| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.82 r_work: 0.3232 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34412 Z= 0.127 Angle : 0.568 14.093 46638 Z= 0.286 Chirality : 0.043 0.196 5519 Planarity : 0.004 0.056 5997 Dihedral : 6.269 88.571 4924 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.26 % Favored : 95.54 % Rotamer: Outliers : 2.19 % Allowed : 20.23 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.13), residues: 4461 helix: 0.64 (0.11), residues: 2227 sheet: -0.54 (0.23), residues: 538 loop : -0.58 (0.16), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG T 199 TYR 0.015 0.001 TYR T 502 PHE 0.027 0.001 PHE S 92 TRP 0.010 0.001 TRP R 37 HIS 0.005 0.001 HIS V 549 Details of bonding type rmsd covalent geometry : bond 0.00293 (34412) covalent geometry : angle 0.56845 (46638) hydrogen bonds : bond 0.03534 ( 1413) hydrogen bonds : angle 4.10526 ( 4119) ********************** 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 466 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 388 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6539 (tpp) REVERT: C 61 MET cc_start: 0.0437 (OUTLIER) cc_final: -0.0172 (tpt) REVERT: C 81 MET cc_start: 0.6376 (ttt) cc_final: 0.5589 (tpp) REVERT: C 86 ILE cc_start: 0.6174 (mm) cc_final: 0.5864 (mp) REVERT: D 85 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6900 (mm) REVERT: D 87 ASN cc_start: 0.5606 (m-40) cc_final: 0.5150 (m110) REVERT: F 81 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7150 (ptm) REVERT: G 61 MET cc_start: 0.7242 (mmp) cc_final: 0.6184 (mtm) REVERT: G 71 LEU cc_start: 0.6377 (mt) cc_final: 0.5806 (tt) REVERT: G 109 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5794 (tm) REVERT: H 56 LEU cc_start: 0.3566 (OUTLIER) cc_final: 0.2332 (pp) REVERT: H 61 MET cc_start: 0.3764 (mtt) cc_final: 0.3515 (ttt) REVERT: H 105 LEU cc_start: 0.5474 (tt) cc_final: 0.4747 (mm) REVERT: H 109 LEU cc_start: 0.5651 (tm) cc_final: 0.5336 (tt) REVERT: J 81 MET cc_start: 0.6659 (tmm) cc_final: 0.6455 (tmm) REVERT: R 85 GLN cc_start: 0.7188 (mt0) cc_final: 0.6696 (mt0) REVERT: R 148 GLU cc_start: 0.7279 (tp30) cc_final: 0.7014 (tp30) REVERT: R 154 GLN cc_start: 0.7150 (pt0) cc_final: 0.6342 (pp30) REVERT: S 58 LYS cc_start: 0.7816 (tttt) cc_final: 0.7517 (tptm) REVERT: S 82 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7605 (m) REVERT: S 144 ASP cc_start: 0.8356 (m-30) cc_final: 0.7909 (m-30) REVERT: S 178 ILE cc_start: 0.8884 (mt) cc_final: 0.8674 (mp) REVERT: S 203 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7667 (p90) REVERT: S 244 ARG cc_start: 0.7665 (tpp-160) cc_final: 0.7418 (ttt90) REVERT: T 226 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8103 (m-30) REVERT: T 287 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8134 (tpp) REVERT: T 439 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8002 (tpp) REVERT: T 475 GLU cc_start: 0.7858 (tp30) cc_final: 0.7255 (tp30) REVERT: U 311 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7923 (mt-10) REVERT: U 414 TYR cc_start: 0.7960 (t80) cc_final: 0.7476 (t80) REVERT: V 73 TRP cc_start: 0.8226 (m-10) cc_final: 0.7882 (m-90) REVERT: V 476 ARG cc_start: 0.7046 (tpp80) cc_final: 0.6713 (tpp-160) REVERT: V 522 GLU cc_start: 0.7404 (pp20) cc_final: 0.7072 (tm-30) REVERT: V 549 HIS cc_start: 0.7894 (m90) cc_final: 0.7245 (m-70) REVERT: X 414 GLN cc_start: 0.7571 (mt0) cc_final: 0.7288 (mt0) REVERT: X 440 GLN cc_start: 0.8620 (mt0) cc_final: 0.8352 (mt0) REVERT: X 471 GLN cc_start: 0.8371 (tt0) cc_final: 0.8091 (tt0) REVERT: X 488 MET cc_start: 0.9066 (mmt) cc_final: 0.8723 (mmt) REVERT: X 502 MET cc_start: 0.7719 (mtp) cc_final: 0.7456 (mtp) REVERT: Y 55 GLU cc_start: 0.7863 (pt0) cc_final: 0.7119 (pp20) REVERT: Y 195 GLU cc_start: 0.7856 (tp30) cc_final: 0.7219 (tp30) REVERT: Y 388 ASN cc_start: 0.7796 (t0) cc_final: 0.7429 (t0) REVERT: Y 401 ARG cc_start: 0.7638 (mmm160) cc_final: 0.6757 (mmt180) REVERT: Y 405 LYS cc_start: 0.8177 (tptt) cc_final: 0.7695 (ttpp) REVERT: Y 437 ARG cc_start: 0.7759 (mtt-85) cc_final: 0.7373 (mmm-85) REVERT: Y 501 LYS cc_start: 0.6919 (tttm) cc_final: 0.6479 (mtpp) REVERT: Z 91 ASP cc_start: 0.8646 (t0) cc_final: 0.8429 (t70) REVERT: Z 219 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8293 (mt-10) REVERT: Z 440 GLN cc_start: 0.7870 (mt0) cc_final: 0.7618 (mt0) REVERT: Z 521 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.5174 (tt) outliers start: 78 outliers final: 48 residues processed: 444 average time/residue: 0.6958 time to fit residues: 371.1111 Evaluate side-chains 428 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 368 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 226 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 154 SER Chi-restraints excluded: chain Y residue 178 LYS Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 32 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 404 optimal weight: 0.9980 chunk 357 optimal weight: 0.8980 chunk 101 optimal weight: 0.0050 chunk 149 optimal weight: 1.9990 chunk 396 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 354 optimal weight: 0.8980 chunk 297 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 GLN Q 40 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN ** V 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 390 ASN Y 322 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.162982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116699 restraints weight = 46053.412| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.80 r_work: 0.3290 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3199 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 : 0.563 13.784 46638 Z= 0.283 Chirality : 0.043 0.198 5519 Planarity : 0.004 0.056 5997 Dihedral : 6.075 82.824 4924 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.33 % Favored : 95.52 % Rotamer: Outliers : 2.10 % Allowed : 20.68 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4461 helix: 0.73 (0.11), residues: 2229 sheet: -0.49 (0.23), residues: 538 loop : -0.56 (0.16), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG T 199 TYR 0.018 0.001 TYR V 414 PHE 0.023 0.001 PHE E 122 TRP 0.011 0.001 TRP R 37 HIS 0.005 0.001 HIS V 549 Details of bonding type rmsd covalent geometry : bond 0.00273 (34412) covalent geometry : angle 0.56318 (46638) hydrogen bonds : bond 0.03446 ( 1413) hydrogen bonds : angle 4.02558 ( 4119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15352.27 seconds wall clock time: 261 minutes 5.52 seconds (15665.52 seconds total)