Starting phenix.real_space_refine on Mon Sep 14 21:47:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6red_4850/09_2026/6red_4850.cif Found real_map, /net/cci-nas-00/data/ceres_data/6red_4850/09_2026/6red_4850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6red_4850/09_2026/6red_4850.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6red_4850/09_2026/6red_4850.cif" model { file = "/net/cci-nas-00/data/ceres_data/6red_4850/09_2026/6red_4850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6red_4850/09_2026/6red_4850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6red_4850/09_2026/6red_4850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6red_4850/09_2026/6red_4850.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21545 2.51 5 N 5796 2.21 5 O 6424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 245 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33899 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: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} 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: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.30, per 1000 atoms: 0.22 Number of scatterers: 33899 At special positions: 0 Unit cell: (164.16, 135, 209.52, 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 6424 8.00 N 5796 7.00 C 21545 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: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 0 sheets defined 52.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 54 through 68 removed outlier: 4.337A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.776A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 119 removed outlier: 4.240A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.756A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.977A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 4.483A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.409A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.394A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 4.783A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.220A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.591A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 4.256A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.458A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 92 Processing helix chain 'E' and resid 95 through 126 removed outlier: 4.495A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 4.042A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 90 removed outlier: 3.569A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.507A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.985A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.680A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 3.571A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 66 removed outlier: 3.953A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.336A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 124 removed outlier: 4.206A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.539A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.234A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 4.235A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.904A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.238A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 126 removed outlier: 4.663A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 121 " --> pdb=" O SER J 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 62 Processing helix chain 'P' and resid 66 through 84 removed outlier: 4.047A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.797A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 removed outlier: 4.030A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.901A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 3.932A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 13 Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 40 removed outlier: 4.329A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN Q 40 " --> pdb=" O LYS Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 44 removed outlier: 3.783A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 41 through 44' Processing helix chain 'R' and resid 29 through 41 removed outlier: 3.730A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 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 156 through 168 removed outlier: 3.818A pdb=" N VAL R 160 " --> pdb=" O ASP R 156 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 removed outlier: 3.508A pdb=" N GLU R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.652A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 79 Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.466A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 128 removed outlier: 3.787A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 151 removed outlier: 3.501A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 183 Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.769A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 4.076A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 212 Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.735A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 removed outlier: 3.514A pdb=" N VAL T 269 " --> pdb=" O LYS T 265 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA T 270 " --> pdb=" O ARG T 266 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN T 271 " --> pdb=" O SER T 267 " (cutoff:3.500A) 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 315 Proline residue: T 303 - end of helix removed outlier: 4.168A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 removed outlier: 3.528A pdb=" N GLN T 330 " --> pdb=" O ASP T 326 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' Processing helix chain 'T' and resid 353 through 363 Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 410 through 415 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.879A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 430 through 435' Processing helix chain 'T' and resid 436 through 456 removed outlier: 3.723A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 458 through 462 Processing helix chain 'T' and resid 469 through 482 removed outlier: 3.968A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.635A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 522 through 528 Processing helix chain 'T' and resid 530 through 540 Processing helix chain 'T' and resid 543 through 556 removed outlier: 3.810A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 48 removed outlier: 3.639A pdb=" N LEU U 45 " --> pdb=" O ASP U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 73 removed outlier: 3.651A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 3.592A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 77 Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.940A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE U 138 " --> pdb=" O ASP U 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 134 through 138' Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.578A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 212 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.790A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 283 removed outlier: 3.727A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 280 through 283' Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.793A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 3.718A pdb=" N GLN U 330 " --> pdb=" O ASP U 326 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER U 331 " --> pdb=" O LEU U 327 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.788A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.897A 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 402 Processing helix chain 'U' and resid 412 through 416 removed outlier: 3.877A pdb=" N GLY U 416 " --> pdb=" O PHE U 413 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 455 removed outlier: 3.590A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 460 removed outlier: 3.725A pdb=" N ALA U 460 " --> pdb=" O ALA U 457 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 469 removed outlier: 4.385A pdb=" N ALA U 468 " --> pdb=" O ASP U 465 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 484 removed outlier: 4.107A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 501 Processing helix chain 'U' and resid 501 through 506 Processing helix chain 'U' and resid 513 through 515 No H-bonds generated for 'chain 'U' and resid 513 through 515' Processing helix chain 'U' and resid 516 through 528 removed outlier: 4.215A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA U 523 " --> pdb=" O ALA U 519 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL U 528 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 4.056A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 3.899A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 48 removed outlier: 3.732A pdb=" N GLU V 47 " --> pdb=" O ALA V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.683A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.664A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE V 138 " --> pdb=" O ASP V 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 134 through 138' Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.943A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 283 Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 4.385A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 removed outlier: 3.549A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 removed outlier: 3.517A pdb=" N ALA V 349 " --> pdb=" O GLY V 346 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.832A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.936A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 400 Processing helix chain 'V' and resid 409 through 414 Processing helix chain 'V' and resid 438 through 454 removed outlier: 3.617A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 470 through 485 removed outlier: 4.036A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (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 528 removed outlier: 3.536A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.803A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 545 through 555 removed outlier: 4.148A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 188 through 201 Processing helix chain 'X' and resid 216 through 229 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.114A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 Processing helix chain 'X' and resid 287 through 297 removed outlier: 3.737A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 342 through 345 Processing helix chain 'X' and resid 348 through 355 removed outlier: 3.608A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 370 removed outlier: 3.613A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 421 removed outlier: 3.523A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 443 removed outlier: 3.593A pdb=" N ALA X 436 " --> pdb=" O THR X 432 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 447 through 451 removed outlier: 3.864A pdb=" N GLU X 451 " --> pdb=" O GLN X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 482 through 487 removed outlier: 3.645A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 508 removed outlier: 4.005A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 533 Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 204 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.601A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 275 removed outlier: 5.091A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 301 Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.730A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 345 removed outlier: 3.721A pdb=" N ASP Y 344 " --> pdb=" O VAL Y 341 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 355 Processing helix chain 'Y' and resid 365 through 371 removed outlier: 3.611A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 412 removed outlier: 7.242A pdb=" N ALA Y 394 " --> pdb=" O ASN Y 390 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N GLU Y 395 " --> pdb=" O VAL Y 391 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) Processing helix chain 'Y' and resid 412 through 420 removed outlier: 4.065A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 427 through 442 removed outlier: 4.616A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 removed outlier: 3.959A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 504 removed outlier: 3.742A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) Processing helix chain 'Y' and resid 505 through 508 Processing helix chain 'Y' and resid 518 through 522 removed outlier: 3.589A pdb=" N LEU Y 521 " --> pdb=" O SER Y 518 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 554 removed outlier: 4.175A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.521A pdb=" N GLN Z 153 " --> pdb=" O PHE Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 removed outlier: 3.578A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 201 Processing helix chain 'Z' and resid 216 through 229 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.117A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 259 Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.587A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.855A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 348 through 355 removed outlier: 3.602A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 358 No H-bonds generated for 'chain 'Z' and resid 356 through 358' Processing helix chain 'Z' and resid 365 through 372 removed outlier: 3.527A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 412 removed outlier: 3.620A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 420 Processing helix chain 'Z' and resid 421 through 425 removed outlier: 4.077A pdb=" N GLU Z 424 " --> pdb=" O GLY Z 421 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Z 425 " --> pdb=" O MET Z 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 421 through 425' Processing helix chain 'Z' and resid 429 through 440 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.690A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 492 through 500 removed outlier: 3.641A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 500 through 508 removed outlier: 3.579A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 509 through 511 No H-bonds generated for 'chain 'Z' and resid 509 through 511' Processing helix chain 'Z' and resid 527 through 533 1434 hydrogen bonds defined for protein. 4149 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: 5.71 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8626 1.33 - 1.45: 5919 1.45 - 1.57: 19654 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34420 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.84e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.74e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.54e+01 bond pdb=" C5 ATP V1001 " pdb=" N7 ATP V1001 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.67e+01 bond pdb=" C5 ATP T1001 " pdb=" N7 ATP T1001 " ideal model delta sigma weight residual 1.387 1.331 0.056 1.00e-02 1.00e+04 3.14e+01 ... (remaining 34415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 46080 3.53 - 7.07: 519 7.07 - 10.60: 35 10.60 - 14.14: 12 14.14 - 17.67: 3 Bond angle restraints: 46649 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 122.20 17.67 1.00e+00 1.00e+00 3.12e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.55 17.32 1.00e+00 1.00e+00 3.00e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 124.31 15.56 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.78 13.05 1.00e+00 1.00e+00 1.70e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 125.03 11.80 1.00e+00 1.00e+00 1.39e+02 ... (remaining 46644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.25: 20075 30.25 - 60.49: 611 60.49 - 90.74: 45 90.74 - 120.98: 0 120.98 - 151.23: 4 Dihedral angle restraints: 20735 sinusoidal: 7975 harmonic: 12760 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -122.78 -57.22 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -133.09 -46.91 0 5.00e+00 4.00e-02 8.80e+01 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 -134.41 -45.59 0 5.00e+00 4.00e-02 8.31e+01 ... (remaining 20732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4352 0.076 - 0.152: 1053 0.152 - 0.228: 101 0.228 - 0.304: 11 0.304 - 0.380: 3 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE Y 524 " pdb=" CA ILE Y 524 " pdb=" CG1 ILE Y 524 " pdb=" CG2 ILE Y 524 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+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 -2.28 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 5517 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.22e-02 3.86e+01 pdb=" C ALA Z 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.030 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" C ALA X 503 " 0.100 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.037 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL Z 341 " -0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO Z 342 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO Z 342 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Z 342 " -0.047 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1129 2.69 - 3.24: 32604 3.24 - 3.80: 57093 3.80 - 4.35: 76930 4.35 - 4.90: 126582 Nonbonded interactions: 294338 Sorted by model distance: nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.140 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.197 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.217 2.170 nonbonded pdb=" OG SER Q 15 " pdb=" OE1 GLU S 248 " model vdw 2.243 3.040 nonbonded pdb=" OG SER X 295 " pdb=" OE1 GLN X 311 " model vdw 2.268 3.040 ... (remaining 294333 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 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 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: 7.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.720 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0203 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.121 34420 Z= 0.511 Angle : 1.043 17.672 46649 Z= 0.595 Chirality : 0.064 0.380 5520 Planarity : 0.008 0.086 5999 Dihedral : 14.479 151.228 12573 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.73 % Favored : 95.16 % Rotamer: Outliers : 0.31 % Allowed : 6.82 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.10), residues: 4462 helix: -3.03 (0.08), residues: 2162 sheet: -1.38 (0.21), residues: 547 loop : -2.04 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 146 TYR 0.024 0.003 TYR Q 52 PHE 0.034 0.003 PHE R 74 TRP 0.025 0.004 TRP Y 141 HIS 0.011 0.002 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.01201 / 0.51 (34420) covalent geometry : angle 1.04295 / 0.59 (46649) hydrogen bonds : bond 0.16415 / 11.26 ( 1434) hydrogen bonds : angle 7.00222 / 5.04 ( 4149) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 323 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: -0.1054 (mmt) cc_final: -0.1572 (mtt) REVERT: G 99 LEU cc_start: 0.3804 (mt) cc_final: 0.3229 (mt) REVERT: S 183 ILE cc_start: -0.0113 (OUTLIER) cc_final: -0.0875 (mp) REVERT: T 367 LYS cc_start: 0.1617 (tptp) cc_final: 0.0687 (tttp) REVERT: T 501 VAL cc_start: -0.0756 (t) cc_final: -0.1086 (p) REVERT: U 118 MET cc_start: 0.1813 (ttt) cc_final: 0.0978 (mtt) REVERT: V 408 LEU cc_start: 0.2177 (mt) cc_final: 0.1179 (mp) REVERT: Y 52 PHE cc_start: 0.2508 (m-80) cc_final: 0.0540 (t80) REVERT: Y 64 GLU cc_start: 0.0628 (mm-30) cc_final: 0.0183 (mt-10) REVERT: Y 207 PHE cc_start: 0.2325 (m-80) cc_final: 0.1374 (m-80) REVERT: Y 386 MET cc_start: 0.2348 (mmp) cc_final: -0.1212 (mmm) REVERT: Y 422 MET cc_start: -0.2470 (ttt) cc_final: -0.3081 (mpp) REVERT: Z 80 MET cc_start: -0.0173 (mmm) cc_final: -0.0542 (ttt) REVERT: Z 251 MET cc_start: -0.1408 (ptp) cc_final: -0.1834 (mtt) REVERT: Z 411 LYS cc_start: 0.1479 (ttpt) cc_final: 0.0881 (tmtm) REVERT: Z 424 GLU cc_start: 0.3631 (pp20) cc_final: 0.2848 (tt0) REVERT: Z 486 PHE cc_start: 0.2418 (m-80) cc_final: 0.1585 (m-80) REVERT: Z 502 MET cc_start: 0.0073 (mtp) cc_final: -0.1533 (tpt) outliers start: 11 outliers final: 3 residues processed: 334 average time/residue: 0.5881 time to fit residues: 244.3746 Evaluate side-chains 209 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain V residue 137 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN C 87 ASN D 94 ASN E 94 ASN G 92 ASN G 94 ASN G 98 GLN P 52 GLN Q 46 HIS R 38 ASN R 53 ASN R 66 HIS R 73 ASN R 83 GLN R 85 GLN R 154 GLN S 98 ASN S 116 ASN S 174 GLN S 237 HIS T 386 GLN T 435 GLN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN U 228 GLN U 319 HIS U 386 GLN U 435 GLN U 497 GLN ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN V 278 GLN V 435 GLN V 486 GLN V 497 GLN X 241 ASN X 322 GLN X 390 ASN Y 157 GLN Y 199 ASN Y 278 GLN Y 286 ASN Y 388 ASN Y 404 GLN Z 42 GLN Z 68 HIS Z 199 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.280364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.240906 restraints weight = 59157.006| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 2.42 r_work: 0.4618 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0627 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34420 Z= 0.135 Angle : 0.629 9.551 46649 Z= 0.320 Chirality : 0.044 0.354 5520 Planarity : 0.005 0.058 5999 Dihedral : 6.805 153.555 4832 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.65 % Favored : 96.21 % Rotamer: Outliers : 1.71 % Allowed : 11.00 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.12), residues: 4462 helix: -1.30 (0.10), residues: 2164 sheet: -0.96 (0.22), residues: 505 loop : -1.47 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 260 TYR 0.022 0.002 TYR Z 340 PHE 0.029 0.002 PHE Y 288 TRP 0.008 0.001 TRP X 141 HIS 0.005 0.001 HIS V 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (34420) covalent geometry : angle 0.62864 / 0.32 (46649) hydrogen bonds : bond 0.03882 / 2.63 ( 1434) hydrogen bonds : angle 4.58913 / 3.28 ( 4149) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 231 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.4854 (OUTLIER) cc_final: 0.4440 (tpp) REVERT: E 95 ILE cc_start: 0.1173 (mm) cc_final: 0.0059 (tp) REVERT: H 55 VAL cc_start: 0.6456 (m) cc_final: 0.5941 (p) REVERT: H 56 LEU cc_start: 0.4870 (mm) cc_final: 0.4485 (tp) REVERT: S 172 PHE cc_start: 0.5762 (t80) cc_final: 0.5562 (p90) REVERT: S 223 VAL cc_start: -0.0201 (OUTLIER) cc_final: -0.0523 (t) REVERT: S 279 LYS cc_start: 0.3306 (ptmm) cc_final: 0.3016 (mmpt) REVERT: T 140 GLN cc_start: 0.4022 (mt0) cc_final: 0.2353 (tm130) REVERT: T 313 PHE cc_start: 0.2566 (m-10) cc_final: 0.1987 (m-10) REVERT: T 483 MET cc_start: 0.1168 (pp-130) cc_final: 0.0558 (ptt) REVERT: T 488 GLN cc_start: 0.3662 (OUTLIER) cc_final: 0.2680 (tt0) REVERT: U 84 LEU cc_start: -0.1557 (OUTLIER) cc_final: -0.1884 (mt) REVERT: U 118 MET cc_start: 0.2180 (ttt) cc_final: 0.1676 (mtt) REVERT: V 118 MET cc_start: 0.1367 (OUTLIER) cc_final: 0.0254 (ppp) REVERT: V 134 ASN cc_start: 0.0825 (p0) cc_final: 0.0501 (p0) REVERT: V 241 HIS cc_start: 0.0485 (t70) cc_final: -0.0004 (t70) REVERT: V 258 VAL cc_start: 0.5013 (t) cc_final: 0.4804 (t) REVERT: V 321 LEU cc_start: 0.2813 (OUTLIER) cc_final: 0.1226 (mp) REVERT: X 164 ILE cc_start: 0.5756 (pt) cc_final: 0.5552 (mt) REVERT: X 422 MET cc_start: 0.1229 (pp-130) cc_final: -0.0369 (ptt) REVERT: X 484 MET cc_start: 0.2554 (OUTLIER) cc_final: 0.2316 (pmm) REVERT: Y 52 PHE cc_start: 0.3032 (m-80) cc_final: 0.0908 (t80) REVERT: Y 194 MET cc_start: 0.1100 (mtm) cc_final: -0.1359 (pp-130) REVERT: Y 207 PHE cc_start: 0.3423 (m-80) cc_final: 0.1752 (m-80) REVERT: Y 246 LEU cc_start: 0.0871 (OUTLIER) cc_final: 0.0492 (mt) REVERT: Y 286 ASN cc_start: 0.0412 (OUTLIER) cc_final: -0.1058 (t0) REVERT: Y 386 MET cc_start: 0.1883 (mmp) cc_final: -0.0413 (mmp) REVERT: Y 422 MET cc_start: -0.3455 (ttt) cc_final: -0.3811 (mpt) REVERT: Z 80 MET cc_start: -0.0214 (mmm) cc_final: -0.0555 (ttt) REVERT: Z 224 TYR cc_start: 0.2114 (t80) cc_final: 0.0735 (t80) REVERT: Z 251 MET cc_start: -0.0037 (ptp) cc_final: -0.0863 (mtt) REVERT: Z 386 MET cc_start: 0.1661 (OUTLIER) cc_final: 0.1342 (ptp) REVERT: Z 422 MET cc_start: -0.0019 (tpp) cc_final: -0.0636 (tpp) REVERT: Z 424 GLU cc_start: 0.4379 (pp20) cc_final: 0.2501 (tt0) REVERT: Z 486 PHE cc_start: 0.2727 (m-80) cc_final: 0.2185 (m-80) REVERT: Z 502 MET cc_start: -0.0907 (mtp) cc_final: -0.2467 (tpt) outliers start: 61 outliers final: 23 residues processed: 270 average time/residue: 0.5551 time to fit residues: 189.1098 Evaluate side-chains 227 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 488 GLN Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 321 LEU Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 386 MET Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 422 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 396 optimal weight: 0.7980 chunk 243 optimal weight: 0.3980 chunk 277 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 425 optimal weight: 0.7980 chunk 384 optimal weight: 0.0670 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 98 GLN P 71 GLN S 195 ASN S 263 ASN ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 123 GLN U 228 GLN V 152 ASN V 242 GLN X 204 HIS ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN Y 204 HIS Z 144 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.281537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.243934 restraints weight = 59528.025| |-----------------------------------------------------------------------------| r_work (start): 0.4709 rms_B_bonded: 2.33 r_work: 0.4647 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4538 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0735 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 34420 Z= 0.116 Angle : 0.570 9.829 46649 Z= 0.288 Chirality : 0.042 0.291 5520 Planarity : 0.004 0.064 5999 Dihedral : 6.213 166.639 4828 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 2.16 % Allowed : 13.02 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.12), residues: 4462 helix: -0.41 (0.11), residues: 2154 sheet: -0.85 (0.22), residues: 532 loop : -1.12 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 476 TYR 0.020 0.001 TYR Y 487 PHE 0.018 0.001 PHE E 122 TRP 0.006 0.001 TRP Y 141 HIS 0.004 0.001 HIS X 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (34420) covalent geometry : angle 0.57030 / 0.29 (46649) hydrogen bonds : bond 0.03503 / 2.37 ( 1434) hydrogen bonds : angle 4.14727 / 2.96 ( 4149) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 214 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 ILE cc_start: 0.1371 (mm) cc_final: 0.0921 (mm) REVERT: F 81 MET cc_start: -0.0103 (OUTLIER) cc_final: -0.0515 (ptt) REVERT: H 56 LEU cc_start: 0.4914 (mm) cc_final: 0.4447 (tp) REVERT: H 61 MET cc_start: 0.5491 (OUTLIER) cc_final: 0.5104 (ttm) REVERT: I 81 MET cc_start: -0.1382 (ppp) cc_final: -0.1881 (ppp) REVERT: J 81 MET cc_start: 0.4527 (tmm) cc_final: 0.2589 (ptm) REVERT: Q 48 ARG cc_start: 0.4436 (OUTLIER) cc_final: 0.4023 (tmm-80) REVERT: R 178 GLN cc_start: 0.4859 (OUTLIER) cc_final: 0.4539 (tt0) REVERT: S 118 ASN cc_start: 0.3707 (m-40) cc_final: 0.3372 (p0) REVERT: S 172 PHE cc_start: 0.5948 (t80) cc_final: 0.5655 (p90) REVERT: S 223 VAL cc_start: -0.0642 (OUTLIER) cc_final: -0.0867 (t) REVERT: S 279 LYS cc_start: 0.3300 (ptmm) cc_final: 0.2996 (mmpt) REVERT: T 90 VAL cc_start: -0.0675 (OUTLIER) cc_final: -0.1046 (t) REVERT: T 313 PHE cc_start: 0.2656 (m-10) cc_final: 0.2112 (m-10) REVERT: T 483 MET cc_start: 0.1594 (pp-130) cc_final: 0.0667 (ptt) REVERT: T 488 GLN cc_start: 0.3842 (OUTLIER) cc_final: 0.2616 (mm-40) REVERT: V 118 MET cc_start: 0.1509 (OUTLIER) cc_final: 0.0435 (ppp) REVERT: V 134 ASN cc_start: 0.1397 (p0) cc_final: 0.0720 (p0) REVERT: V 240 ILE cc_start: 0.3711 (mt) cc_final: 0.2177 (tt) REVERT: V 241 HIS cc_start: 0.0727 (t70) cc_final: 0.0391 (t70) REVERT: X 422 MET cc_start: 0.0803 (pp-130) cc_final: -0.0658 (ptt) REVERT: Y 52 PHE cc_start: 0.2975 (m-80) cc_final: 0.0868 (t80) REVERT: Y 286 ASN cc_start: -0.0936 (OUTLIER) cc_final: -0.1644 (t0) REVERT: Y 386 MET cc_start: 0.2092 (mmp) cc_final: 0.0105 (mmp) REVERT: Y 422 MET cc_start: -0.3809 (ttt) cc_final: -0.4159 (mpt) REVERT: Y 456 THR cc_start: -0.0628 (OUTLIER) cc_final: -0.1017 (m) REVERT: Z 224 TYR cc_start: 0.2214 (t80) cc_final: 0.0921 (t80) REVERT: Z 324 ARG cc_start: 0.2150 (mtp180) cc_final: 0.1919 (mpt180) REVERT: Z 386 MET cc_start: 0.1696 (OUTLIER) cc_final: 0.1401 (ptp) REVERT: Z 422 MET cc_start: -0.0023 (tpp) cc_final: -0.0657 (tpp) REVERT: Z 424 GLU cc_start: 0.4371 (pp20) cc_final: 0.3078 (tt0) REVERT: Z 486 PHE cc_start: 0.2661 (m-80) cc_final: 0.2209 (m-80) REVERT: Z 502 MET cc_start: -0.1076 (mtp) cc_final: -0.2613 (tpt) outliers start: 77 outliers final: 35 residues processed: 264 average time/residue: 0.5632 time to fit residues: 187.1709 Evaluate side-chains 234 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 141 TYR Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 488 GLN Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 386 MET Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 62 optimal weight: 2.9990 chunk 360 optimal weight: 3.9990 chunk 279 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 410 optimal weight: 0.5980 chunk 321 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 423 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 409 optimal weight: 0.2980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 94 ASN T 140 GLN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 174 GLN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN Z 292 GLN Z 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.283619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.248979 restraints weight = 61010.783| |-----------------------------------------------------------------------------| r_work (start): 0.4748 rms_B_bonded: 2.34 r_work: 0.4686 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.4686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1089 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34420 Z= 0.142 Angle : 0.640 9.650 46649 Z= 0.323 Chirality : 0.044 0.307 5520 Planarity : 0.005 0.062 5999 Dihedral : 6.379 161.674 4828 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 2.66 % Allowed : 14.19 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.12), residues: 4462 helix: -0.24 (0.11), residues: 2160 sheet: -0.72 (0.23), residues: 480 loop : -1.09 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 429 TYR 0.070 0.002 TYR P 141 PHE 0.024 0.002 PHE U 380 TRP 0.008 0.001 TRP V 73 HIS 0.006 0.001 HIS T 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (34420) covalent geometry : angle 0.64000 / 0.32 (46649) hydrogen bonds : bond 0.03724 / 2.51 ( 1434) hydrogen bonds : angle 4.20546 / 3.00 ( 4149) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 212 time to evaluate : 1.244 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: B 81 MET cc_start: 0.3337 (tmm) cc_final: 0.3103 (tmm) REVERT: H 56 LEU cc_start: 0.5085 (mm) cc_final: 0.4443 (tp) REVERT: J 81 MET cc_start: 0.4395 (tmm) cc_final: 0.2736 (ptm) REVERT: J 123 LEU cc_start: 0.1567 (tp) cc_final: 0.1213 (pp) REVERT: Q 48 ARG cc_start: 0.4516 (OUTLIER) cc_final: 0.4042 (tmm-80) REVERT: S 118 ASN cc_start: 0.3479 (m-40) cc_final: 0.3248 (p0) REVERT: S 172 PHE cc_start: 0.6161 (t80) cc_final: 0.5813 (p90) REVERT: S 223 VAL cc_start: -0.1088 (OUTLIER) cc_final: -0.1289 (t) REVERT: S 279 LYS cc_start: 0.3106 (ptmm) cc_final: 0.2895 (mmpt) REVERT: T 483 MET cc_start: 0.0943 (pp-130) cc_final: 0.0434 (tpt) REVERT: V 241 HIS cc_start: 0.0966 (t70) cc_final: 0.0469 (t70) REVERT: X 422 MET cc_start: 0.0945 (pp-130) cc_final: -0.0340 (ptt) REVERT: Y 52 PHE cc_start: 0.3491 (m-80) cc_final: 0.1305 (t80) REVERT: Y 194 MET cc_start: -0.0075 (mtm) cc_final: -0.0451 (mtm) REVERT: Y 422 MET cc_start: -0.3755 (ttt) cc_final: -0.4529 (mpt) REVERT: Z 52 PHE cc_start: 0.1171 (m-80) cc_final: 0.0920 (m-80) REVERT: Z 224 TYR cc_start: 0.2950 (t80) cc_final: 0.1307 (t80) REVERT: Z 251 MET cc_start: -0.1291 (OUTLIER) cc_final: -0.1656 (ptp) REVERT: Z 324 ARG cc_start: 0.3356 (mtp180) cc_final: 0.2217 (mpt-90) REVERT: Z 422 MET cc_start: 0.0323 (tpp) cc_final: -0.0535 (tpp) REVERT: Z 502 MET cc_start: -0.0528 (mtp) cc_final: -0.2245 (tpt) outliers start: 95 outliers final: 47 residues processed: 282 average time/residue: 0.5479 time to fit residues: 194.9510 Evaluate side-chains 246 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 253 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Z residue 80 MET Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 251 MET Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 128 optimal weight: 5.9990 chunk 390 optimal weight: 40.0000 chunk 256 optimal weight: 0.9990 chunk 433 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 183 optimal weight: 0.8980 chunk 324 optimal weight: 0.0980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 71 GLN S 174 GLN ** T 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 GLN Y 286 ASN Z 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.284141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.250519 restraints weight = 60830.770| |-----------------------------------------------------------------------------| r_work (start): 0.4765 rms_B_bonded: 2.44 r_work: 0.4702 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1130 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34420 Z= 0.123 Angle : 0.596 9.129 46649 Z= 0.297 Chirality : 0.043 0.235 5520 Planarity : 0.004 0.056 5999 Dihedral : 6.183 152.961 4828 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.85 % Rotamer: Outliers : 2.55 % Allowed : 15.26 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4462 helix: 0.08 (0.11), residues: 2162 sheet: -0.87 (0.23), residues: 492 loop : -0.97 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 364 TYR 0.033 0.002 TYR U 256 PHE 0.041 0.002 PHE S 203 TRP 0.009 0.001 TRP V 73 HIS 0.005 0.001 HIS X 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (34420) covalent geometry : angle 0.59584 / 0.30 (46649) hydrogen bonds : bond 0.03381 / 2.27 ( 1434) hydrogen bonds : angle 4.04001 / 2.86 ( 4149) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 218 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: -0.2877 (mtt) cc_final: -0.3524 (mmp) REVERT: G 123 LEU cc_start: 0.5418 (OUTLIER) cc_final: 0.4910 (pp) REVERT: H 56 LEU cc_start: 0.5042 (mm) cc_final: 0.4437 (tt) REVERT: J 61 MET cc_start: 0.2210 (tmt) cc_final: 0.1087 (ptm) REVERT: J 81 MET cc_start: 0.3868 (tmm) cc_final: 0.2491 (ptm) REVERT: J 123 LEU cc_start: 0.1285 (tp) cc_final: 0.0892 (pp) REVERT: Q 48 ARG cc_start: 0.4545 (OUTLIER) cc_final: 0.4179 (tmm-80) REVERT: R 178 GLN cc_start: 0.4694 (OUTLIER) cc_final: 0.4242 (tp40) REVERT: S 92 PHE cc_start: 0.0767 (m-80) cc_final: 0.0566 (m-80) REVERT: S 118 ASN cc_start: 0.3559 (m-40) cc_final: 0.3188 (p0) REVERT: S 172 PHE cc_start: 0.6234 (t80) cc_final: 0.5838 (OUTLIER) REVERT: S 259 MET cc_start: 0.2661 (mmt) cc_final: 0.1214 (tmt) REVERT: T 278 GLN cc_start: -0.2355 (OUTLIER) cc_final: -0.2900 (mm-40) REVERT: T 313 PHE cc_start: 0.2518 (m-10) cc_final: 0.2195 (m-10) REVERT: T 483 MET cc_start: 0.0795 (pp-130) cc_final: 0.0311 (tpt) REVERT: T 559 LEU cc_start: -0.1396 (OUTLIER) cc_final: -0.1680 (pt) REVERT: U 60 GLN cc_start: 0.2551 (pp30) cc_final: 0.2230 (pm20) REVERT: V 240 ILE cc_start: 0.3844 (mt) cc_final: 0.1874 (tt) REVERT: V 241 HIS cc_start: 0.1143 (t70) cc_final: 0.0667 (t70) REVERT: V 282 MET cc_start: 0.0993 (tpt) cc_final: -0.0549 (tpt) REVERT: X 194 MET cc_start: 0.0556 (OUTLIER) cc_final: -0.0491 (mpp) REVERT: X 386 MET cc_start: 0.1521 (tpp) cc_final: 0.1152 (mmt) REVERT: X 422 MET cc_start: 0.0943 (pp-130) cc_final: -0.0398 (ptt) REVERT: Y 52 PHE cc_start: 0.3264 (m-80) cc_final: 0.1213 (t80) REVERT: Y 194 MET cc_start: 0.0029 (mtm) cc_final: -0.0173 (mtm) REVERT: Y 286 ASN cc_start: 0.1030 (OUTLIER) cc_final: -0.0237 (t0) REVERT: Y 422 MET cc_start: -0.3542 (ttt) cc_final: -0.4444 (mpp) REVERT: Z 52 PHE cc_start: 0.1084 (m-80) cc_final: 0.0800 (m-80) REVERT: Z 80 MET cc_start: -0.1335 (ttt) cc_final: -0.2831 (ppp) REVERT: Z 224 TYR cc_start: 0.2912 (t80) cc_final: 0.1371 (t80) REVERT: Z 251 MET cc_start: -0.0964 (mmt) cc_final: -0.1392 (ptp) REVERT: Z 324 ARG cc_start: 0.3412 (mtp180) cc_final: 0.2274 (mpt180) REVERT: Z 502 MET cc_start: -0.0870 (mtp) cc_final: -0.2579 (tpt) outliers start: 91 outliers final: 54 residues processed: 286 average time/residue: 0.5321 time to fit residues: 191.3136 Evaluate side-chains 260 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 383 ILE Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 196 LEU Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 339 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 183 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 324 optimal weight: 0.8980 chunk 397 optimal weight: 0.0010 chunk 125 optimal weight: 7.9990 chunk 266 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 231 optimal weight: 0.8980 chunk 308 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 438 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN T 104 GLN T 336 GLN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 GLN ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 271 GLN V 121 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 250 GLN Z 79 HIS Z 250 GLN Z 278 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.284805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.252510 restraints weight = 60493.837| |-----------------------------------------------------------------------------| r_work (start): 0.4793 rms_B_bonded: 2.47 r_work: 0.4722 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1205 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34420 Z= 0.119 Angle : 0.593 10.428 46649 Z= 0.295 Chirality : 0.043 0.253 5520 Planarity : 0.004 0.050 5999 Dihedral : 6.122 166.125 4828 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 2.83 % Allowed : 16.19 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 4462 helix: 0.28 (0.11), residues: 2167 sheet: -0.91 (0.24), residues: 486 loop : -0.86 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 429 TYR 0.014 0.001 TYR U 393 PHE 0.033 0.002 PHE B 82 TRP 0.010 0.001 TRP V 73 HIS 0.005 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (34420) covalent geometry : angle 0.59266 / 0.30 (46649) hydrogen bonds : bond 0.03330 / 2.24 ( 1434) hydrogen bonds : angle 3.96237 / 2.80 ( 4149) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 216 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 110 THR cc_start: 0.6780 (m) cc_final: 0.6468 (p) REVERT: G 123 LEU cc_start: 0.5242 (tm) cc_final: 0.4709 (pp) REVERT: H 56 LEU cc_start: 0.5272 (mm) cc_final: 0.4511 (tt) REVERT: J 61 MET cc_start: 0.2193 (tmt) cc_final: 0.1070 (ptm) REVERT: R 100 VAL cc_start: -0.0255 (OUTLIER) cc_final: -0.0738 (p) REVERT: R 101 LYS cc_start: 0.3775 (mmtt) cc_final: 0.3144 (mmmm) REVERT: R 178 GLN cc_start: 0.4255 (OUTLIER) cc_final: 0.3864 (tp40) REVERT: S 92 PHE cc_start: 0.0691 (m-80) cc_final: 0.0451 (m-80) REVERT: S 118 ASN cc_start: 0.3212 (m-40) cc_final: 0.2924 (p0) REVERT: S 172 PHE cc_start: 0.6255 (t80) cc_final: 0.5919 (OUTLIER) REVERT: S 259 MET cc_start: 0.2468 (mmt) cc_final: 0.1092 (tmt) REVERT: T 278 GLN cc_start: -0.2370 (OUTLIER) cc_final: -0.2852 (mm-40) REVERT: T 313 PHE cc_start: 0.2878 (m-10) cc_final: 0.2607 (m-10) REVERT: T 439 MET cc_start: 0.1767 (mtt) cc_final: -0.0398 (ptp) REVERT: T 483 MET cc_start: 0.1036 (pp-130) cc_final: 0.0591 (tpt) REVERT: T 559 LEU cc_start: -0.1209 (OUTLIER) cc_final: -0.1512 (pt) REVERT: U 60 GLN cc_start: 0.2670 (pp30) cc_final: 0.2146 (pm20) REVERT: U 282 MET cc_start: -0.0158 (mmm) cc_final: -0.1308 (mmt) REVERT: U 513 ARG cc_start: 0.3412 (tpp-160) cc_final: 0.3044 (tpt170) REVERT: V 187 VAL cc_start: -0.0768 (OUTLIER) cc_final: -0.1234 (t) REVERT: V 241 HIS cc_start: 0.1432 (t70) cc_final: 0.0845 (t70) REVERT: V 282 MET cc_start: 0.1004 (tpt) cc_final: -0.0548 (tpt) REVERT: X 194 MET cc_start: 0.0566 (OUTLIER) cc_final: -0.0265 (mpp) REVERT: X 251 MET cc_start: 0.2064 (OUTLIER) cc_final: 0.1704 (mtm) REVERT: X 422 MET cc_start: 0.0932 (pp-130) cc_final: -0.0406 (ptt) REVERT: Y 52 PHE cc_start: 0.3181 (m-80) cc_final: 0.1122 (t80) REVERT: Y 422 MET cc_start: -0.3487 (ttt) cc_final: -0.4514 (mpt) REVERT: Z 52 PHE cc_start: 0.1213 (m-80) cc_final: 0.0948 (m-80) REVERT: Z 80 MET cc_start: -0.0846 (ttt) cc_final: -0.2559 (ppp) REVERT: Z 224 TYR cc_start: 0.2964 (t80) cc_final: 0.1439 (t80) REVERT: Z 251 MET cc_start: -0.1207 (mmt) cc_final: -0.1435 (ptp) REVERT: Z 324 ARG cc_start: 0.3439 (mtp180) cc_final: 0.2227 (mpt180) REVERT: Z 422 MET cc_start: 0.1344 (mpp) cc_final: 0.0304 (tpp) REVERT: Z 502 MET cc_start: -0.1135 (mtp) cc_final: -0.2801 (tpt) outliers start: 101 outliers final: 68 residues processed: 290 average time/residue: 0.5030 time to fit residues: 186.6001 Evaluate side-chains 271 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 197 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 383 ILE Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 196 LEU Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 79 HIS Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 227 MET Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 404 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 266 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 429 optimal weight: 0.9980 chunk 340 optimal weight: 0.0870 chunk 352 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 441 optimal weight: 0.1980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN Y 294 ASN ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.284742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.252996 restraints weight = 61387.785| |-----------------------------------------------------------------------------| r_work (start): 0.4789 rms_B_bonded: 2.48 r_work: 0.4720 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1174 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 34420 Z= 0.106 Angle : 0.576 14.225 46649 Z= 0.285 Chirality : 0.042 0.199 5520 Planarity : 0.004 0.047 5999 Dihedral : 5.969 163.935 4828 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 2.66 % Allowed : 16.72 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.13), residues: 4462 helix: 0.50 (0.12), residues: 2176 sheet: -0.98 (0.24), residues: 475 loop : -0.77 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 429 TYR 0.012 0.001 TYR T 304 PHE 0.034 0.001 PHE S 203 TRP 0.017 0.001 TRP Y 141 HIS 0.005 0.001 HIS Z 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (34420) covalent geometry : angle 0.57641 / 0.28 (46649) hydrogen bonds : bond 0.03172 / 2.12 ( 1434) hydrogen bonds : angle 3.86508 / 2.73 ( 4149) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 203 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.5494 (ppp) cc_final: 0.5070 (ppp) REVERT: D 61 MET cc_start: 0.4260 (mmt) cc_final: 0.3978 (tmm) REVERT: D 94 ASN cc_start: 0.3364 (OUTLIER) cc_final: 0.3164 (p0) REVERT: G 110 THR cc_start: 0.6810 (m) cc_final: 0.6480 (p) REVERT: G 123 LEU cc_start: 0.5110 (tm) cc_final: 0.4773 (pp) REVERT: H 56 LEU cc_start: 0.5284 (mm) cc_final: 0.4433 (tp) REVERT: J 61 MET cc_start: 0.2096 (tmt) cc_final: 0.1132 (ptm) REVERT: J 81 MET cc_start: 0.4164 (tmm) cc_final: 0.2867 (ptm) REVERT: J 123 LEU cc_start: 0.1299 (tp) cc_final: 0.0872 (pp) REVERT: P 74 LEU cc_start: 0.2393 (mt) cc_final: 0.2168 (mt) REVERT: R 70 PHE cc_start: 0.0642 (p90) cc_final: 0.0401 (p90) REVERT: R 100 VAL cc_start: -0.0184 (OUTLIER) cc_final: -0.0892 (p) REVERT: R 101 LYS cc_start: 0.3726 (mmtt) cc_final: 0.3087 (mmmm) REVERT: R 178 GLN cc_start: 0.3944 (OUTLIER) cc_final: 0.3596 (tp40) REVERT: S 118 ASN cc_start: 0.3290 (m-40) cc_final: 0.2956 (p0) REVERT: S 172 PHE cc_start: 0.6226 (t80) cc_final: 0.5921 (p90) REVERT: S 259 MET cc_start: 0.2412 (mmt) cc_final: 0.1075 (tmt) REVERT: T 278 GLN cc_start: -0.2435 (OUTLIER) cc_final: -0.2859 (mm-40) REVERT: T 313 PHE cc_start: 0.2849 (m-10) cc_final: 0.2618 (m-10) REVERT: T 483 MET cc_start: 0.1049 (pp-130) cc_final: 0.0605 (tpt) REVERT: T 559 LEU cc_start: -0.1217 (OUTLIER) cc_final: -0.1495 (pt) REVERT: U 282 MET cc_start: 0.0153 (mmm) cc_final: -0.1040 (mmt) REVERT: U 483 MET cc_start: 0.2207 (OUTLIER) cc_final: 0.0660 (tmm) REVERT: V 241 HIS cc_start: 0.1111 (t70) cc_final: 0.0633 (t70) REVERT: V 282 MET cc_start: 0.0863 (tpt) cc_final: -0.0905 (tpt) REVERT: X 164 ILE cc_start: 0.4872 (OUTLIER) cc_final: 0.4436 (pp) REVERT: X 194 MET cc_start: 0.0414 (tpt) cc_final: -0.0534 (mpp) REVERT: X 251 MET cc_start: 0.2338 (OUTLIER) cc_final: 0.1985 (mtm) REVERT: X 290 PHE cc_start: -0.0748 (OUTLIER) cc_final: -0.2234 (t80) REVERT: X 422 MET cc_start: 0.0874 (OUTLIER) cc_final: -0.0400 (ptt) REVERT: Y 52 PHE cc_start: 0.3096 (m-80) cc_final: 0.1045 (t80) REVERT: Y 286 ASN cc_start: 0.0446 (OUTLIER) cc_final: -0.0206 (t0) REVERT: Y 422 MET cc_start: -0.3309 (ttt) cc_final: -0.4463 (mpt) REVERT: Y 442 PHE cc_start: -0.0255 (OUTLIER) cc_final: -0.0793 (t80) REVERT: Z 52 PHE cc_start: 0.1119 (m-80) cc_final: 0.0826 (m-80) REVERT: Z 80 MET cc_start: -0.0962 (ttt) cc_final: -0.2615 (ppp) REVERT: Z 224 TYR cc_start: 0.2843 (t80) cc_final: 0.1356 (t80) REVERT: Z 251 MET cc_start: -0.1252 (mmt) cc_final: -0.1462 (ptp) REVERT: Z 324 ARG cc_start: 0.3473 (mtp180) cc_final: 0.2521 (mpt180) REVERT: Z 422 MET cc_start: 0.1489 (mpp) cc_final: 0.0520 (tpp) REVERT: Z 486 PHE cc_start: 0.1777 (m-80) cc_final: 0.0733 (m-80) REVERT: Z 502 MET cc_start: -0.1470 (mtp) cc_final: -0.3093 (tpt) outliers start: 95 outliers final: 58 residues processed: 273 average time/residue: 0.5254 time to fit residues: 182.5603 Evaluate side-chains 264 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 194 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain V residue 483 MET Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 196 LEU Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 339 VAL Chi-restraints excluded: chain X residue 422 MET Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 194 MET Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 442 PHE Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 141 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 339 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 366 optimal weight: 0.9990 chunk 390 optimal weight: 0.6980 chunk 242 optimal weight: 0.0770 chunk 267 optimal weight: 0.6980 chunk 302 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN T 241 HIS ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 204 HIS ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.285160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.253539 restraints weight = 60519.533| |-----------------------------------------------------------------------------| r_work (start): 0.4796 rms_B_bonded: 2.89 r_work: 0.4718 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1230 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 34420 Z= 0.110 Angle : 0.593 13.944 46649 Z= 0.291 Chirality : 0.043 0.210 5520 Planarity : 0.004 0.048 5999 Dihedral : 5.939 170.221 4828 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 2.50 % Allowed : 17.28 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4462 helix: 0.60 (0.12), residues: 2166 sheet: -0.97 (0.24), residues: 467 loop : -0.73 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 289 TYR 0.013 0.001 TYR T 304 PHE 0.028 0.001 PHE S 203 TRP 0.010 0.001 TRP Y 141 HIS 0.004 0.001 HIS Y 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (34420) covalent geometry : angle 0.59281 / 0.29 (46649) hydrogen bonds : bond 0.03223 / 2.15 ( 1434) hydrogen bonds : angle 3.86019 / 2.72 ( 4149) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 210 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2473 (tmm) cc_final: 0.2089 (tmm) REVERT: C 61 MET cc_start: -0.3661 (mtt) cc_final: -0.4070 (tpp) REVERT: D 61 MET cc_start: 0.4142 (mmt) cc_final: 0.3863 (tmm) REVERT: D 94 ASN cc_start: 0.3365 (OUTLIER) cc_final: 0.3157 (p0) REVERT: G 123 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5222 (pp) REVERT: H 56 LEU cc_start: 0.5442 (mm) cc_final: 0.4551 (tp) REVERT: J 61 MET cc_start: 0.2164 (tmt) cc_final: 0.1279 (ptm) REVERT: J 81 MET cc_start: 0.4323 (tmm) cc_final: 0.2877 (ptm) REVERT: R 178 GLN cc_start: 0.4082 (OUTLIER) cc_final: 0.3695 (tp40) REVERT: S 172 PHE cc_start: 0.6268 (t80) cc_final: 0.5926 (p90) REVERT: S 259 MET cc_start: 0.2428 (mmt) cc_final: 0.1063 (tmt) REVERT: T 207 LYS cc_start: 0.0100 (OUTLIER) cc_final: -0.0608 (pttm) REVERT: T 278 GLN cc_start: -0.2488 (OUTLIER) cc_final: -0.2891 (mm-40) REVERT: T 313 PHE cc_start: 0.2831 (m-10) cc_final: 0.2585 (m-10) REVERT: T 439 MET cc_start: 0.1555 (mtt) cc_final: -0.0346 (ptp) REVERT: T 483 MET cc_start: 0.0958 (pp-130) cc_final: 0.0595 (tpt) REVERT: T 559 LEU cc_start: -0.1114 (OUTLIER) cc_final: -0.1405 (pt) REVERT: U 282 MET cc_start: -0.0095 (mmm) cc_final: -0.1192 (mmt) REVERT: V 187 VAL cc_start: -0.0876 (OUTLIER) cc_final: -0.1230 (t) REVERT: V 241 HIS cc_start: 0.1280 (t70) cc_final: 0.0734 (t70) REVERT: V 282 MET cc_start: 0.0925 (tpt) cc_final: -0.0858 (tpt) REVERT: X 164 ILE cc_start: 0.4620 (OUTLIER) cc_final: 0.4250 (pp) REVERT: X 194 MET cc_start: 0.0425 (tpt) cc_final: -0.0497 (mpp) REVERT: X 251 MET cc_start: 0.2485 (OUTLIER) cc_final: 0.2075 (mtm) REVERT: X 290 PHE cc_start: -0.0787 (OUTLIER) cc_final: -0.2364 (t80) REVERT: X 422 MET cc_start: 0.1056 (pp-130) cc_final: -0.0370 (ptt) REVERT: Y 52 PHE cc_start: 0.3165 (m-80) cc_final: 0.0981 (t80) REVERT: Y 422 MET cc_start: -0.2938 (ttt) cc_final: -0.4320 (mpp) REVERT: Z 52 PHE cc_start: 0.1026 (m-80) cc_final: 0.0724 (m-80) REVERT: Z 80 MET cc_start: -0.0603 (ttt) cc_final: -0.2402 (ppp) REVERT: Z 224 TYR cc_start: 0.2830 (t80) cc_final: 0.1373 (t80) REVERT: Z 251 MET cc_start: -0.0945 (mmt) cc_final: -0.1311 (ptp) REVERT: Z 324 ARG cc_start: 0.3552 (mtp180) cc_final: 0.2353 (mpt-90) REVERT: Z 422 MET cc_start: 0.1245 (mpp) cc_final: 0.0862 (tpp) REVERT: Z 502 MET cc_start: -0.1512 (mtp) cc_final: -0.2840 (tpt) outliers start: 89 outliers final: 60 residues processed: 275 average time/residue: 0.5701 time to fit residues: 198.2092 Evaluate side-chains 263 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 207 LYS Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 383 ILE Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 196 LEU Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 339 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 141 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 115 optimal weight: 0.9980 chunk 351 optimal weight: 0.0980 chunk 182 optimal weight: 0.8980 chunk 278 optimal weight: 0.9980 chunk 438 optimal weight: 0.0020 chunk 241 optimal weight: 4.9990 chunk 257 optimal weight: 0.5980 chunk 246 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 259 optimal weight: 0.8980 chunk 408 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 174 GLN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.285382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.253888 restraints weight = 60594.208| |-----------------------------------------------------------------------------| r_work (start): 0.4812 rms_B_bonded: 2.48 r_work: 0.4742 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1202 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34420 Z= 0.103 Angle : 0.577 12.766 46649 Z= 0.283 Chirality : 0.042 0.185 5520 Planarity : 0.004 0.050 5999 Dihedral : 5.784 176.367 4828 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.85 % Favored : 96.01 % Rotamer: Outliers : 1.94 % Allowed : 18.49 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4462 helix: 0.76 (0.12), residues: 2167 sheet: -0.89 (0.24), residues: 465 loop : -0.67 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 429 TYR 0.023 0.001 TYR P 75 PHE 0.023 0.001 PHE I 82 TRP 0.009 0.001 TRP V 73 HIS 0.003 0.001 HIS T 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (34420) covalent geometry : angle 0.57692 / 0.28 (46649) hydrogen bonds : bond 0.03110 / 2.07 ( 1434) hydrogen bonds : angle 3.78292 / 2.66 ( 4149) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2554 (tmm) cc_final: 0.2209 (tmm) REVERT: C 61 MET cc_start: -0.3666 (mtt) cc_final: -0.4075 (tpp) REVERT: C 81 MET cc_start: 0.5558 (ppp) cc_final: 0.5080 (ppp) REVERT: D 61 MET cc_start: 0.4264 (mmt) cc_final: 0.3918 (tmm) REVERT: D 94 ASN cc_start: 0.3664 (OUTLIER) cc_final: 0.3436 (p0) REVERT: G 110 THR cc_start: 0.6707 (m) cc_final: 0.6403 (p) REVERT: G 123 LEU cc_start: 0.5231 (OUTLIER) cc_final: 0.4913 (pp) REVERT: H 56 LEU cc_start: 0.5553 (mm) cc_final: 0.4654 (tp) REVERT: J 61 MET cc_start: 0.2075 (tmt) cc_final: 0.1126 (ptm) REVERT: J 81 MET cc_start: 0.4296 (tmm) cc_final: 0.2915 (ptm) REVERT: R 178 GLN cc_start: 0.4116 (OUTLIER) cc_final: 0.3737 (tp40) REVERT: S 62 MET cc_start: 0.1521 (tmt) cc_final: 0.1231 (tmm) REVERT: S 172 PHE cc_start: 0.6315 (t80) cc_final: 0.6003 (p90) REVERT: S 259 MET cc_start: 0.2439 (mmt) cc_final: 0.1077 (tmt) REVERT: T 313 PHE cc_start: 0.2866 (m-10) cc_final: 0.2665 (m-10) REVERT: T 439 MET cc_start: 0.1052 (mtt) cc_final: -0.0276 (ptp) REVERT: T 483 MET cc_start: 0.0836 (pp-130) cc_final: 0.0528 (tpt) REVERT: T 559 LEU cc_start: -0.1132 (OUTLIER) cc_final: -0.1401 (pt) REVERT: U 282 MET cc_start: -0.0041 (mmm) cc_final: -0.1191 (mmt) REVERT: U 411 GLU cc_start: 0.0579 (OUTLIER) cc_final: -0.1179 (mt-10) REVERT: V 241 HIS cc_start: 0.1335 (t70) cc_final: 0.0758 (t70) REVERT: V 282 MET cc_start: 0.0788 (tpt) cc_final: -0.1176 (tpt) REVERT: X 164 ILE cc_start: 0.4459 (OUTLIER) cc_final: 0.4150 (pp) REVERT: X 194 MET cc_start: 0.0468 (OUTLIER) cc_final: -0.0518 (mpp) REVERT: X 290 PHE cc_start: -0.0771 (OUTLIER) cc_final: -0.2382 (t80) REVERT: X 422 MET cc_start: 0.1082 (pp-130) cc_final: -0.0363 (ptt) REVERT: Y 52 PHE cc_start: 0.3052 (m-80) cc_final: 0.0879 (t80) REVERT: Y 80 MET cc_start: -0.1014 (mmm) cc_final: -0.2971 (pmm) REVERT: Y 422 MET cc_start: -0.2898 (ttt) cc_final: -0.4327 (mpt) REVERT: Z 52 PHE cc_start: 0.1081 (m-80) cc_final: 0.0720 (m-80) REVERT: Z 80 MET cc_start: -0.0764 (ttt) cc_final: -0.2508 (ppp) REVERT: Z 224 TYR cc_start: 0.2806 (t80) cc_final: 0.1347 (t80) REVERT: Z 251 MET cc_start: -0.1024 (mmt) cc_final: -0.1313 (ptp) REVERT: Z 324 ARG cc_start: 0.3707 (mtp180) cc_final: 0.2316 (mpt-90) REVERT: Z 486 PHE cc_start: 0.1742 (m-80) cc_final: 0.0587 (m-80) REVERT: Z 488 MET cc_start: 0.1111 (mmt) cc_final: -0.0341 (ptm) REVERT: Z 502 MET cc_start: -0.0845 (mtp) cc_final: -0.2569 (tpt) outliers start: 69 outliers final: 50 residues processed: 254 average time/residue: 0.5886 time to fit residues: 188.4000 Evaluate side-chains 253 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 253 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 267 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 404 optimal weight: 0.9990 chunk 412 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 380 optimal weight: 0.9990 chunk 305 optimal weight: 0.8980 chunk 287 optimal weight: 0.0980 chunk 225 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.285924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.255970 restraints weight = 61072.199| |-----------------------------------------------------------------------------| r_work (start): 0.4832 rms_B_bonded: 2.46 r_work: 0.4761 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1340 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34420 Z= 0.120 Angle : 0.624 17.050 46649 Z= 0.306 Chirality : 0.043 0.202 5520 Planarity : 0.004 0.048 5999 Dihedral : 5.844 169.757 4828 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.36 % Rotamer: Outliers : 2.05 % Allowed : 18.68 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4462 helix: 0.75 (0.12), residues: 2146 sheet: -1.03 (0.24), residues: 462 loop : -0.71 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 86 TYR 0.016 0.001 TYR U 77 PHE 0.050 0.002 PHE R 70 TRP 0.010 0.001 TRP P 58 HIS 0.004 0.001 HIS V 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (34420) covalent geometry : angle 0.62445 / 0.31 (46649) hydrogen bonds : bond 0.03272 / 2.18 ( 1434) hydrogen bonds : angle 3.87980 / 2.73 ( 4149) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 210 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2785 (tmm) cc_final: 0.2454 (tmm) REVERT: C 61 MET cc_start: -0.3370 (mtt) cc_final: -0.3907 (tpp) REVERT: C 81 MET cc_start: 0.5704 (ppp) cc_final: 0.5249 (ppp) REVERT: D 61 MET cc_start: 0.4508 (mmt) cc_final: 0.3951 (tmm) REVERT: G 110 THR cc_start: 0.6748 (m) cc_final: 0.6449 (p) REVERT: G 123 LEU cc_start: 0.5317 (OUTLIER) cc_final: 0.4981 (pp) REVERT: H 56 LEU cc_start: 0.6058 (mm) cc_final: 0.5432 (pp) REVERT: J 61 MET cc_start: 0.2065 (tmt) cc_final: 0.1121 (ptm) REVERT: P 146 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6631 (mm) REVERT: S 62 MET cc_start: 0.1628 (tmt) cc_final: 0.1231 (tmm) REVERT: S 172 PHE cc_start: 0.6177 (t80) cc_final: 0.5946 (p90) REVERT: S 259 MET cc_start: 0.2417 (mmt) cc_final: 0.0969 (tmt) REVERT: T 313 PHE cc_start: 0.2901 (m-10) cc_final: 0.2668 (m-10) REVERT: T 439 MET cc_start: 0.1321 (mtt) cc_final: 0.0148 (mtt) REVERT: T 483 MET cc_start: 0.1012 (pp-130) cc_final: 0.0667 (tpt) REVERT: T 559 LEU cc_start: -0.0956 (OUTLIER) cc_final: -0.1239 (pt) REVERT: U 282 MET cc_start: 0.0002 (mmm) cc_final: -0.1086 (mmt) REVERT: U 411 GLU cc_start: 0.0698 (OUTLIER) cc_final: -0.1137 (mt-10) REVERT: V 126 HIS cc_start: 0.3017 (p90) cc_final: 0.2740 (p90) REVERT: V 240 ILE cc_start: 0.4018 (mt) cc_final: 0.3400 (pt) REVERT: V 241 HIS cc_start: 0.1664 (t70) cc_final: 0.1067 (t70) REVERT: V 282 MET cc_start: 0.1190 (tpt) cc_final: -0.0846 (tpt) REVERT: X 164 ILE cc_start: 0.4144 (OUTLIER) cc_final: 0.3798 (pp) REVERT: X 194 MET cc_start: 0.0268 (tpt) cc_final: -0.0662 (mpp) REVERT: X 290 PHE cc_start: -0.0431 (OUTLIER) cc_final: -0.2237 (t80) REVERT: X 383 THR cc_start: 0.4081 (OUTLIER) cc_final: 0.3815 (p) REVERT: X 422 MET cc_start: 0.1239 (pp-130) cc_final: -0.0350 (ptt) REVERT: Y 52 PHE cc_start: 0.3236 (m-80) cc_final: 0.0989 (t80) REVERT: Y 80 MET cc_start: -0.0832 (mmm) cc_final: -0.2979 (pmm) REVERT: Y 286 ASN cc_start: 0.1033 (OUTLIER) cc_final: 0.0561 (t0) REVERT: Y 422 MET cc_start: -0.2745 (ttt) cc_final: -0.4098 (mpt) REVERT: Y 488 MET cc_start: 0.5413 (pp-130) cc_final: 0.5086 (mtm) REVERT: Z 80 MET cc_start: -0.0661 (ttt) cc_final: -0.2456 (ppp) REVERT: Z 224 TYR cc_start: 0.3201 (t80) cc_final: 0.1684 (t80) REVERT: Z 251 MET cc_start: -0.0889 (mmt) cc_final: -0.1171 (pmm) REVERT: Z 253 GLU cc_start: 0.3327 (OUTLIER) cc_final: 0.0892 (tp30) REVERT: Z 324 ARG cc_start: 0.3811 (mtp180) cc_final: 0.2419 (mpt-90) REVERT: Z 422 MET cc_start: 0.1079 (tpp) cc_final: -0.0090 (mmt) REVERT: Z 486 PHE cc_start: 0.1933 (m-80) cc_final: 0.0794 (m-80) REVERT: Z 502 MET cc_start: -0.0832 (mtp) cc_final: -0.2494 (tpt) outliers start: 73 outliers final: 50 residues processed: 263 average time/residue: 0.5860 time to fit residues: 194.1112 Evaluate side-chains 255 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 383 ILE Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 253 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 368 optimal weight: 4.9990 chunk 270 optimal weight: 0.0030 chunk 101 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 265 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 325 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 418 optimal weight: 0.0980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.286055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.256283 restraints weight = 61582.582| |-----------------------------------------------------------------------------| r_work (start): 0.4813 rms_B_bonded: 2.90 r_work: 0.4737 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1260 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34420 Z= 0.105 Angle : 0.600 13.183 46649 Z= 0.293 Chirality : 0.042 0.206 5520 Planarity : 0.004 0.050 5999 Dihedral : 5.566 154.065 4828 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.17 % Rotamer: Outliers : 1.77 % Allowed : 19.24 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 4462 helix: 0.81 (0.12), residues: 2140 sheet: -0.88 (0.25), residues: 458 loop : -0.69 (0.15), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 429 TYR 0.016 0.001 TYR P 75 PHE 0.032 0.001 PHE I 82 TRP 0.009 0.001 TRP V 73 HIS 0.004 0.001 HIS X 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (34420) covalent geometry : angle 0.59954 / 0.29 (46649) hydrogen bonds : bond 0.03140 / 2.09 ( 1434) hydrogen bonds : angle 3.82470 / 2.70 ( 4149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11600.19 seconds wall clock time: 198 minutes 36.81 seconds (11916.81 seconds total)