Starting phenix.real_space_refine on Fri Feb 6 01:23:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c8d_45301/02_2026/9c8d_45301.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c8d_45301/02_2026/9c8d_45301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c8d_45301/02_2026/9c8d_45301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c8d_45301/02_2026/9c8d_45301.map" model { file = "/net/cci-nas-00/data/ceres_data/9c8d_45301/02_2026/9c8d_45301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c8d_45301/02_2026/9c8d_45301.cif" } resolution = 2.98 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= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 14112 2.51 5 N 3420 2.21 5 O 3804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21468 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "C" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "D" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "E" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "F" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "G" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "H" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "I" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "J" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "K" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1622 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "M" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "N" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "O" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "P" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "Q" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "R" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "S" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "T" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "U" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "V" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "W" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "X" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Time building chain proxies: 5.29, per 1000 atoms: 0.25 Number of scatterers: 21468 At special positions: 0 Unit cell: (162.708, 163.542, 76.7648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 3804 8.00 N 3420 7.00 C 14112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 82 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 82 " distance=2.03 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: 1.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5088 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 35.2% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 41 through 57 Processing helix chain 'A' and resid 117 through 124 removed outlier: 4.086A pdb=" N GLY A 124 " --> pdb=" O ASN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 230 through 246 removed outlier: 3.743A pdb=" N ALA A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 57 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 230 through 246 removed outlier: 3.662A pdb=" N CYS B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 236 " --> pdb=" O MET B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 230 through 246 Processing helix chain 'D' and resid 42 through 57 Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 164 through 170 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 230 through 246 Processing helix chain 'E' and resid 42 through 57 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 164 through 170 Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 230 through 246 removed outlier: 3.690A pdb=" N CYS E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 235 " --> pdb=" O PRO E 231 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE E 236 " --> pdb=" O MET E 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 57 Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 164 through 170 Processing helix chain 'F' and resid 224 through 230 Processing helix chain 'F' and resid 230 through 246 Processing helix chain 'G' and resid 42 through 57 Processing helix chain 'G' and resid 117 through 122 Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 164 through 170 Processing helix chain 'G' and resid 224 through 230 Processing helix chain 'G' and resid 230 through 246 removed outlier: 3.671A pdb=" N CYS G 234 " --> pdb=" O PHE G 230 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE G 236 " --> pdb=" O MET G 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 57 Processing helix chain 'H' and resid 117 through 122 Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 164 through 170 Processing helix chain 'H' and resid 224 through 230 Processing helix chain 'H' and resid 230 through 246 removed outlier: 3.650A pdb=" N CYS H 234 " --> pdb=" O PHE H 230 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA H 235 " --> pdb=" O PRO H 231 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE H 236 " --> pdb=" O MET H 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 57 Processing helix chain 'I' and resid 117 through 122 Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 164 through 170 Processing helix chain 'I' and resid 224 through 230 Processing helix chain 'I' and resid 230 through 246 removed outlier: 3.648A pdb=" N CYS I 234 " --> pdb=" O PHE I 230 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE I 236 " --> pdb=" O MET I 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 57 Processing helix chain 'J' and resid 117 through 122 Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 164 through 170 Processing helix chain 'J' and resid 224 through 230 Processing helix chain 'J' and resid 230 through 246 removed outlier: 3.596A pdb=" N CYS J 234 " --> pdb=" O PHE J 230 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA J 240 " --> pdb=" O PHE J 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 57 Processing helix chain 'K' and resid 117 through 122 Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 164 through 170 Processing helix chain 'K' and resid 224 through 230 Processing helix chain 'K' and resid 230 through 246 removed outlier: 3.593A pdb=" N CYS K 234 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE K 236 " --> pdb=" O MET K 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 57 Processing helix chain 'L' and resid 117 through 122 Processing helix chain 'L' and resid 153 through 164 Processing helix chain 'L' and resid 164 through 170 Processing helix chain 'L' and resid 224 through 230 Processing helix chain 'L' and resid 230 through 246 Processing helix chain 'M' and resid 11 through 18 Processing helix chain 'M' and resid 19 through 23 Processing helix chain 'N' and resid 11 through 18 removed outlier: 3.509A pdb=" N LEU N 17 " --> pdb=" O THR N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 23 Processing helix chain 'O' and resid 11 through 16 Processing helix chain 'O' and resid 19 through 23 Processing helix chain 'P' and resid 11 through 18 removed outlier: 3.557A pdb=" N LEU P 17 " --> pdb=" O THR P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 23 Processing helix chain 'Q' and resid 11 through 18 Processing helix chain 'Q' and resid 19 through 23 Processing helix chain 'R' and resid 11 through 19 removed outlier: 3.527A pdb=" N LEU R 17 " --> pdb=" O THR R 13 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE R 19 " --> pdb=" O SER R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 23 Processing helix chain 'S' and resid 11 through 18 Processing helix chain 'S' and resid 19 through 23 Processing helix chain 'T' and resid 11 through 19 Processing helix chain 'T' and resid 20 through 23 Processing helix chain 'U' and resid 11 through 19 removed outlier: 3.561A pdb=" N PHE U 19 " --> pdb=" O SER U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 23 Processing helix chain 'V' and resid 11 through 19 removed outlier: 3.685A pdb=" N LEU V 17 " --> pdb=" O THR V 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE V 19 " --> pdb=" O SER V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 23 Processing helix chain 'W' and resid 11 through 19 removed outlier: 3.511A pdb=" N PHE W 19 " --> pdb=" O SER W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 23 Processing helix chain 'X' and resid 11 through 19 removed outlier: 3.647A pdb=" N LEU X 17 " --> pdb=" O THR X 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE X 19 " --> pdb=" O SER X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 23 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 3.651A pdb=" N HIS A 62 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 216 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY A 211 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 113 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 217 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL A 108 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER A 185 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU A 110 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU A 183 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 112 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A 181 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU A 114 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU A 179 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 removed outlier: 4.072A pdb=" N GLY A 197 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 126 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER A 146 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 128 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 144 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 130 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR A 142 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS A 132 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 66 removed outlier: 3.710A pdb=" N SER B 64 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B 212 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY B 211 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 217 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL B 108 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SER B 185 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU B 110 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU B 183 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 112 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 181 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU B 114 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU B 179 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.853A pdb=" N GLY B 197 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE B 126 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER B 146 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 128 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER B 144 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B 130 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 142 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS B 132 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 65 removed outlier: 3.963A pdb=" N GLY C 211 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS C 217 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL C 108 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER C 185 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU C 110 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU C 183 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU C 112 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL C 181 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU C 114 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU C 179 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 90 removed outlier: 3.862A pdb=" N GLY C 197 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE C 126 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER C 146 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 128 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER C 144 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL C 130 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR C 142 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS C 132 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 66 removed outlier: 4.169A pdb=" N ALA D 212 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 211 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS D 217 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL D 108 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER D 185 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU D 110 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU D 183 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU D 112 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL D 181 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU D 114 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU D 179 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 90 removed outlier: 4.117A pdb=" N GLY D 197 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE D 126 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER D 146 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 128 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER D 144 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL D 130 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR D 142 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS D 132 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 62 through 66 removed outlier: 3.543A pdb=" N HIS E 62 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE E 216 " --> pdb=" O HIS E 62 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA E 212 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY E 211 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS E 217 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TYR E 106 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER E 185 " --> pdb=" O TYR E 106 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL E 108 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 181 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 86 through 90 removed outlier: 3.787A pdb=" N GLY E 197 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE E 126 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER E 146 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL E 128 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER E 144 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 130 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR E 142 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS E 132 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 61 through 65 removed outlier: 4.007A pdb=" N GLY F 211 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS F 217 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL F 108 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SER F 185 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU F 110 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU F 183 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU F 112 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL F 181 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU F 114 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU F 179 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 90 removed outlier: 3.911A pdb=" N GLY F 197 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE F 126 " --> pdb=" O SER F 146 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER F 146 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL F 128 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER F 144 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL F 130 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR F 142 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N CYS F 132 " --> pdb=" O ILE F 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 61 through 65 removed outlier: 3.957A pdb=" N GLY G 211 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS G 217 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL G 108 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER G 185 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU G 110 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU G 183 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU G 112 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL G 181 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU G 114 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU G 179 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 86 through 90 removed outlier: 3.857A pdb=" N GLY G 197 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE G 126 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER G 146 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL G 128 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER G 144 " --> pdb=" O VAL G 128 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL G 130 " --> pdb=" O THR G 142 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR G 142 " --> pdb=" O VAL G 130 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS G 132 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 61 through 66 removed outlier: 3.716A pdb=" N SER H 64 " --> pdb=" O LEU H 214 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA H 212 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY H 211 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS H 217 " --> pdb=" O ARG H 107 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL H 108 " --> pdb=" O SER H 185 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER H 185 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU H 110 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU H 183 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU H 112 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL H 181 " --> pdb=" O LEU H 112 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU H 114 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU H 179 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 86 through 90 removed outlier: 3.890A pdb=" N GLY H 197 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE H 126 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER H 146 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL H 128 " --> pdb=" O SER H 144 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER H 144 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL H 130 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR H 142 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS H 132 " --> pdb=" O ILE H 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 61 through 66 removed outlier: 4.238A pdb=" N ALA I 212 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY I 211 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS I 217 " --> pdb=" O ARG I 107 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL I 108 " --> pdb=" O SER I 185 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER I 185 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU I 110 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU I 183 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU I 112 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL I 181 " --> pdb=" O LEU I 112 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU I 114 " --> pdb=" O LEU I 179 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU I 179 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 86 through 90 removed outlier: 3.859A pdb=" N GLY I 197 " --> pdb=" O TYR I 133 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE I 126 " --> pdb=" O SER I 146 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER I 146 " --> pdb=" O PHE I 126 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 128 " --> pdb=" O SER I 144 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER I 144 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL I 130 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR I 142 " --> pdb=" O VAL I 130 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS I 132 " --> pdb=" O ILE I 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 61 through 65 removed outlier: 3.522A pdb=" N HIS J 62 " --> pdb=" O ILE J 216 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE J 216 " --> pdb=" O HIS J 62 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY J 211 " --> pdb=" O GLU J 113 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS J 217 " --> pdb=" O ARG J 107 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR J 106 " --> pdb=" O SER J 185 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER J 185 " --> pdb=" O TYR J 106 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL J 108 " --> pdb=" O LEU J 183 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL J 181 " --> pdb=" O LEU J 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 86 through 90 removed outlier: 3.828A pdb=" N GLY J 197 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE J 126 " --> pdb=" O SER J 146 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER J 146 " --> pdb=" O PHE J 126 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL J 128 " --> pdb=" O SER J 144 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER J 144 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL J 130 " --> pdb=" O THR J 142 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR J 142 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS J 132 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 61 through 66 removed outlier: 3.747A pdb=" N SER K 64 " --> pdb=" O LEU K 214 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA K 212 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY K 211 " --> pdb=" O GLU K 113 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS K 217 " --> pdb=" O ARG K 107 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL K 108 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER K 185 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU K 110 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU K 183 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU K 112 " --> pdb=" O VAL K 181 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL K 181 " --> pdb=" O LEU K 112 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU K 114 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU K 179 " --> pdb=" O LEU K 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 86 through 90 removed outlier: 3.857A pdb=" N GLY K 197 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE K 126 " --> pdb=" O SER K 146 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER K 146 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL K 128 " --> pdb=" O SER K 144 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER K 144 " --> pdb=" O VAL K 128 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL K 130 " --> pdb=" O THR K 142 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR K 142 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N CYS K 132 " --> pdb=" O ILE K 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 61 through 65 removed outlier: 3.983A pdb=" N GLY L 211 " --> pdb=" O GLU L 113 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS L 217 " --> pdb=" O ARG L 107 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR L 106 " --> pdb=" O SER L 185 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER L 185 " --> pdb=" O TYR L 106 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL L 108 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL L 181 " --> pdb=" O LEU L 110 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 86 through 90 removed outlier: 3.828A pdb=" N GLY L 197 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE L 126 " --> pdb=" O SER L 146 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER L 146 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL L 128 " --> pdb=" O SER L 144 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER L 144 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL L 130 " --> pdb=" O THR L 142 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR L 142 " --> pdb=" O VAL L 130 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS L 132 " --> pdb=" O ILE L 140 " (cutoff:3.500A) 806 hydrogen bonds defined for protein. 2334 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: 3.08 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6468 1.34 - 1.46: 5848 1.46 - 1.58: 9536 1.58 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 22056 Sorted by residual: bond pdb=" C LEU P 23 " pdb=" N PRO P 24 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.25e-02 6.40e+03 2.77e+00 bond pdb=" C GLU D 116 " pdb=" N SER D 117 " ideal model delta sigma weight residual 1.329 1.299 0.030 1.86e-02 2.89e+03 2.54e+00 bond pdb=" C GLU F 116 " pdb=" N SER F 117 " ideal model delta sigma weight residual 1.331 1.289 0.042 2.83e-02 1.25e+03 2.23e+00 bond pdb=" C GLU L 116 " pdb=" N SER L 117 " ideal model delta sigma weight residual 1.331 1.295 0.036 2.83e-02 1.25e+03 1.64e+00 bond pdb=" C GLU C 116 " pdb=" N SER C 117 " ideal model delta sigma weight residual 1.331 1.297 0.034 2.83e-02 1.25e+03 1.43e+00 ... (remaining 22051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 29602 2.04 - 4.08: 355 4.08 - 6.12: 64 6.12 - 8.16: 5 8.16 - 10.20: 10 Bond angle restraints: 30036 Sorted by residual: angle pdb=" N ALA E 87 " pdb=" CA ALA E 87 " pdb=" C ALA E 87 " ideal model delta sigma weight residual 107.93 113.38 -5.45 1.65e+00 3.67e-01 1.09e+01 angle pdb=" N ALA F 87 " pdb=" CA ALA F 87 " pdb=" C ALA F 87 " ideal model delta sigma weight residual 108.32 113.58 -5.26 1.64e+00 3.72e-01 1.03e+01 angle pdb=" N ALA H 87 " pdb=" CA ALA H 87 " pdb=" C ALA H 87 " ideal model delta sigma weight residual 108.32 113.43 -5.11 1.64e+00 3.72e-01 9.71e+00 angle pdb=" N ALA L 87 " pdb=" CA ALA L 87 " pdb=" C ALA L 87 " ideal model delta sigma weight residual 108.32 113.41 -5.09 1.64e+00 3.72e-01 9.64e+00 angle pdb=" N ALA A 87 " pdb=" CA ALA A 87 " pdb=" C ALA A 87 " ideal model delta sigma weight residual 108.32 113.40 -5.08 1.64e+00 3.72e-01 9.58e+00 ... (remaining 30031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 11927 17.69 - 35.38: 775 35.38 - 53.06: 82 53.06 - 70.75: 27 70.75 - 88.44: 11 Dihedral angle restraints: 12822 sinusoidal: 4914 harmonic: 7908 Sorted by residual: dihedral pdb=" CA TYR G 70 " pdb=" C TYR G 70 " pdb=" N ARG G 71 " pdb=" CA ARG G 71 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR K 70 " pdb=" C TYR K 70 " pdb=" N ARG K 71 " pdb=" CA ARG K 71 " ideal model delta harmonic sigma weight residual 180.00 161.66 18.34 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TYR H 70 " pdb=" C TYR H 70 " pdb=" N ARG H 71 " pdb=" CA ARG H 71 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 12819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3212 0.076 - 0.152: 264 0.152 - 0.228: 0 0.228 - 0.303: 1 0.303 - 0.379: 3 Chirality restraints: 3480 Sorted by residual: chirality pdb=" CB ILE A 207 " pdb=" CA ILE A 207 " pdb=" CG1 ILE A 207 " pdb=" CG2 ILE A 207 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CB ILE J 207 " pdb=" CA ILE J 207 " pdb=" CG1 ILE J 207 " pdb=" CG2 ILE J 207 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CB ILE L 207 " pdb=" CA ILE L 207 " pdb=" CG1 ILE L 207 " pdb=" CG2 ILE L 207 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 3477 not shown) Planarity restraints: 3672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 114 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO A 115 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 84 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 85 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 114 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO G 115 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 115 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 115 " -0.022 5.00e-02 4.00e+02 ... (remaining 3669 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4277 2.78 - 3.31: 19837 3.31 - 3.84: 33191 3.84 - 4.37: 38832 4.37 - 4.90: 66946 Nonbonded interactions: 163083 Sorted by model distance: nonbonded pdb=" OE1 GLN D 121 " pdb=" NE2 GLN D 157 " model vdw 2.249 3.120 nonbonded pdb=" OE1 GLN J 121 " pdb=" NE2 GLN J 157 " model vdw 2.255 3.120 nonbonded pdb=" NE2 GLN F 121 " pdb=" OE1 GLN F 157 " model vdw 2.304 3.120 nonbonded pdb=" OH TYR H 102 " pdb=" O SER H 191 " model vdw 2.305 3.040 nonbonded pdb=" NE2 GLN L 121 " pdb=" OE1 GLN L 157 " model vdw 2.310 3.120 ... (remaining 163078 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: 0.01 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' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 0.010 Normalize map: mean=0, sd=1: 5.500 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.330 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5601 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 : 0.003 0.042 22058 Z= 0.138 Angle : 0.624 10.199 30040 Z= 0.334 Chirality : 0.041 0.379 3480 Planarity : 0.004 0.042 3672 Dihedral : 12.167 88.439 7728 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.59 (0.17), residues: 2592 helix: 1.50 (0.18), residues: 780 sheet: 0.35 (0.20), residues: 684 loop : -2.36 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 206 TYR 0.012 0.001 TYR K 70 PHE 0.023 0.001 PHE O 19 TRP 0.017 0.002 TRP D 43 HIS 0.014 0.001 HIS E 219 Details of bonding type rmsd covalent geometry : bond 0.00283 (22056) covalent geometry : angle 0.62419 (30036) SS BOND : bond 0.00251 ( 2) SS BOND : angle 0.65994 ( 4) hydrogen bonds : bond 0.16991 ( 806) hydrogen bonds : angle 6.12116 ( 2334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.6178 (tt0) cc_final: 0.5953 (tt0) REVERT: A 126 PHE cc_start: 0.7824 (p90) cc_final: 0.7591 (p90) REVERT: A 201 GLU cc_start: 0.7433 (tt0) cc_final: 0.7183 (tt0) REVERT: B 113 GLU cc_start: 0.6382 (tt0) cc_final: 0.6127 (tt0) REVERT: B 204 SER cc_start: 0.8267 (t) cc_final: 0.8015 (t) REVERT: C 116 GLU cc_start: 0.7113 (tt0) cc_final: 0.6784 (tt0) REVERT: C 204 SER cc_start: 0.8385 (t) cc_final: 0.8153 (t) REVERT: D 62 HIS cc_start: 0.6252 (p-80) cc_final: 0.5947 (p-80) REVERT: D 113 GLU cc_start: 0.6055 (tt0) cc_final: 0.5792 (tt0) REVERT: D 116 GLU cc_start: 0.7106 (tt0) cc_final: 0.6733 (tt0) REVERT: D 126 PHE cc_start: 0.7881 (p90) cc_final: 0.7548 (p90) REVERT: D 204 SER cc_start: 0.8304 (t) cc_final: 0.8062 (t) REVERT: E 62 HIS cc_start: 0.6856 (p-80) cc_final: 0.6652 (p90) REVERT: E 113 GLU cc_start: 0.6224 (tt0) cc_final: 0.5896 (tt0) REVERT: E 204 SER cc_start: 0.8352 (t) cc_final: 0.8036 (t) REVERT: F 113 GLU cc_start: 0.6093 (tt0) cc_final: 0.5819 (tt0) REVERT: F 204 SER cc_start: 0.8275 (t) cc_final: 0.8047 (t) REVERT: G 113 GLU cc_start: 0.5980 (tt0) cc_final: 0.5744 (tt0) REVERT: G 122 ASP cc_start: 0.7105 (m-30) cc_final: 0.6886 (m-30) REVERT: G 126 PHE cc_start: 0.7891 (p90) cc_final: 0.7518 (p90) REVERT: G 204 SER cc_start: 0.8273 (t) cc_final: 0.7998 (t) REVERT: H 113 GLU cc_start: 0.6178 (tt0) cc_final: 0.5786 (tt0) REVERT: H 204 SER cc_start: 0.8376 (t) cc_final: 0.8107 (t) REVERT: I 113 GLU cc_start: 0.5865 (tt0) cc_final: 0.5590 (tt0) REVERT: I 204 SER cc_start: 0.8182 (t) cc_final: 0.7891 (t) REVERT: J 62 HIS cc_start: 0.6550 (p-80) cc_final: 0.5965 (p-80) REVERT: J 113 GLU cc_start: 0.6125 (tt0) cc_final: 0.5817 (tt0) REVERT: J 201 GLU cc_start: 0.7411 (tt0) cc_final: 0.7121 (tt0) REVERT: K 113 GLU cc_start: 0.6339 (tt0) cc_final: 0.5963 (tt0) REVERT: K 204 SER cc_start: 0.8376 (t) cc_final: 0.8107 (t) REVERT: L 113 GLU cc_start: 0.5964 (tt0) cc_final: 0.5716 (tt0) REVERT: L 204 SER cc_start: 0.8299 (t) cc_final: 0.8040 (t) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.5575 time to fit residues: 277.9404 Evaluate side-chains 358 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0270 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 121 GLN B 67 HIS B 175 GLN C 217 HIS D 67 HIS F 67 HIS F 217 HIS G 67 HIS H 67 HIS J 121 GLN J 157 GLN K 175 GLN L 175 GLN L 217 HIS L 219 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.215553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.172866 restraints weight = 27474.668| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.90 r_work: 0.4105 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22058 Z= 0.135 Angle : 0.653 13.810 30040 Z= 0.317 Chirality : 0.042 0.198 3480 Planarity : 0.004 0.038 3672 Dihedral : 4.643 18.757 2952 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.27 % Allowed : 9.69 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.76 (0.17), residues: 2592 helix: 1.02 (0.17), residues: 900 sheet: 0.47 (0.19), residues: 720 loop : -2.84 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 138 TYR 0.018 0.001 TYR J 102 PHE 0.023 0.001 PHE H 52 TRP 0.010 0.001 TRP G 43 HIS 0.009 0.002 HIS E 219 Details of bonding type rmsd covalent geometry : bond 0.00305 (22056) covalent geometry : angle 0.65351 (30036) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.49118 ( 4) hydrogen bonds : bond 0.03779 ( 806) hydrogen bonds : angle 5.07539 ( 2334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 376 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 VAL cc_start: 0.8198 (p) cc_final: 0.7920 (t) REVERT: A 126 PHE cc_start: 0.8314 (p90) cc_final: 0.8032 (p90) REVERT: B 57 MET cc_start: 0.6576 (ppp) cc_final: 0.6064 (ppp) REVERT: B 107 ARG cc_start: 0.7704 (ttt180) cc_final: 0.7486 (ttt-90) REVERT: C 57 MET cc_start: 0.7083 (ppp) cc_final: 0.6691 (ppp) REVERT: C 107 ARG cc_start: 0.7938 (ttt180) cc_final: 0.7703 (ttt-90) REVERT: D 113 GLU cc_start: 0.6654 (tt0) cc_final: 0.6422 (tt0) REVERT: D 126 PHE cc_start: 0.8314 (p90) cc_final: 0.8011 (p90) REVERT: E 185 SER cc_start: 0.8074 (p) cc_final: 0.7818 (t) REVERT: E 232 MET cc_start: 0.7324 (ptt) cc_final: 0.6917 (pmt) REVERT: G 126 PHE cc_start: 0.8228 (p90) cc_final: 0.7877 (p90) REVERT: I 86 VAL cc_start: 0.7911 (p) cc_final: 0.7661 (t) REVERT: I 113 GLU cc_start: 0.6353 (tt0) cc_final: 0.6135 (tt0) REVERT: J 62 HIS cc_start: 0.6417 (p-80) cc_final: 0.6022 (p-80) REVERT: J 162 LEU cc_start: 0.8170 (mt) cc_final: 0.7939 (mt) REVERT: K 113 GLU cc_start: 0.6808 (tt0) cc_final: 0.6551 (tt0) REVERT: K 232 MET cc_start: 0.6794 (ptt) cc_final: 0.6419 (pmt) REVERT: L 113 GLU cc_start: 0.6513 (tt0) cc_final: 0.6301 (tt0) outliers start: 31 outliers final: 22 residues processed: 385 average time/residue: 0.6167 time to fit residues: 268.4192 Evaluate side-chains 380 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 358 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 230 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain K residue 101 MET Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain W residue 22 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 145 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 121 GLN B 121 GLN B 157 GLN C 121 GLN D 67 HIS D 121 GLN D 157 GLN F 67 HIS G 67 HIS H 67 HIS J 67 HIS L 219 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.213013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.169551 restraints weight = 27587.473| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.92 r_work: 0.4061 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22058 Z= 0.185 Angle : 0.679 15.230 30040 Z= 0.326 Chirality : 0.042 0.170 3480 Planarity : 0.004 0.036 3672 Dihedral : 4.809 20.831 2952 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.97 % Allowed : 12.77 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.91 (0.17), residues: 2592 helix: 0.96 (0.17), residues: 900 sheet: 0.31 (0.19), residues: 720 loop : -2.94 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 138 TYR 0.017 0.002 TYR G 213 PHE 0.015 0.001 PHE E 126 TRP 0.009 0.001 TRP B 43 HIS 0.009 0.002 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00425 (22056) covalent geometry : angle 0.67928 (30036) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.40664 ( 4) hydrogen bonds : bond 0.03561 ( 806) hydrogen bonds : angle 5.10003 ( 2334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 354 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 HIS cc_start: 0.7118 (m-70) cc_final: 0.6885 (m-70) REVERT: C 107 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7646 (ttt-90) REVERT: D 113 GLU cc_start: 0.6564 (tt0) cc_final: 0.6271 (tt0) REVERT: D 126 PHE cc_start: 0.8323 (p90) cc_final: 0.8087 (p90) REVERT: E 126 PHE cc_start: 0.8143 (p90) cc_final: 0.7604 (p90) REVERT: F 164 PHE cc_start: 0.7304 (m-10) cc_final: 0.6977 (m-10) REVERT: G 70 TYR cc_start: 0.7416 (m-10) cc_final: 0.6797 (m-10) REVERT: G 126 PHE cc_start: 0.8251 (p90) cc_final: 0.7877 (p90) REVERT: H 70 TYR cc_start: 0.7484 (m-10) cc_final: 0.6873 (m-10) REVERT: H 126 PHE cc_start: 0.8131 (p90) cc_final: 0.7775 (p90) REVERT: I 113 GLU cc_start: 0.6271 (tt0) cc_final: 0.6058 (tt0) REVERT: I 232 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.6195 (pmm) REVERT: J 62 HIS cc_start: 0.6563 (p-80) cc_final: 0.6121 (p90) REVERT: J 117 SER cc_start: 0.8372 (t) cc_final: 0.7901 (m) REVERT: J 162 LEU cc_start: 0.8167 (mt) cc_final: 0.7926 (mt) REVERT: K 113 GLU cc_start: 0.6823 (tt0) cc_final: 0.6599 (tt0) REVERT: K 232 MET cc_start: 0.6779 (ptt) cc_final: 0.6296 (pmt) REVERT: L 113 GLU cc_start: 0.6434 (tt0) cc_final: 0.6188 (tt0) outliers start: 48 outliers final: 30 residues processed: 372 average time/residue: 0.6080 time to fit residues: 255.9764 Evaluate side-chains 379 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 348 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 230 PHE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain W residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 100 optimal weight: 20.0000 chunk 250 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 202 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 121 GLN B 175 GLN C 67 HIS C 121 GLN C 217 HIS ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 HIS F 217 HIS I 217 HIS L 217 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.211033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.167835 restraints weight = 27553.013| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.87 r_work: 0.4032 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22058 Z= 0.223 Angle : 0.723 16.316 30040 Z= 0.347 Chirality : 0.043 0.159 3480 Planarity : 0.005 0.041 3672 Dihedral : 5.026 22.094 2952 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.75 % Allowed : 14.49 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.07 (0.16), residues: 2592 helix: 0.93 (0.17), residues: 900 sheet: -0.04 (0.19), residues: 624 loop : -2.67 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 152 TYR 0.019 0.002 TYR I 102 PHE 0.026 0.001 PHE K 52 TRP 0.008 0.001 TRP B 43 HIS 0.010 0.002 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00511 (22056) covalent geometry : angle 0.72349 (30036) SS BOND : bond 0.00154 ( 2) SS BOND : angle 0.42473 ( 4) hydrogen bonds : bond 0.03421 ( 806) hydrogen bonds : angle 5.16491 ( 2334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 339 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 MET cc_start: 0.6733 (ppp) cc_final: 0.5869 (ppp) REVERT: B 67 HIS cc_start: 0.7188 (m-70) cc_final: 0.6952 (m-70) REVERT: B 70 TYR cc_start: 0.7467 (m-10) cc_final: 0.6842 (m-10) REVERT: C 57 MET cc_start: 0.7109 (ppp) cc_final: 0.6331 (ppp) REVERT: C 107 ARG cc_start: 0.7846 (ttt180) cc_final: 0.7620 (ttt-90) REVERT: C 168 LEU cc_start: 0.7570 (mt) cc_final: 0.7366 (mp) REVERT: D 113 GLU cc_start: 0.6525 (tt0) cc_final: 0.6168 (tt0) REVERT: D 122 ASP cc_start: 0.7717 (m-30) cc_final: 0.7478 (m-30) REVERT: E 70 TYR cc_start: 0.7685 (m-10) cc_final: 0.7099 (m-10) REVERT: H 126 PHE cc_start: 0.8168 (p90) cc_final: 0.7789 (p90) REVERT: I 70 TYR cc_start: 0.7477 (m-10) cc_final: 0.7009 (m-10) REVERT: J 126 PHE cc_start: 0.8232 (p90) cc_final: 0.7861 (p90) REVERT: J 162 LEU cc_start: 0.8166 (mt) cc_final: 0.7940 (mt) REVERT: L 107 ARG cc_start: 0.7910 (ttt-90) cc_final: 0.7705 (tpt-90) REVERT: L 113 GLU cc_start: 0.6513 (tt0) cc_final: 0.6241 (tt0) outliers start: 67 outliers final: 40 residues processed: 374 average time/residue: 0.6034 time to fit residues: 256.2103 Evaluate side-chains 374 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 334 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 138 ARG Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain W residue 22 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 23 optimal weight: 0.0050 chunk 16 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 250 optimal weight: 0.0470 chunk 53 optimal weight: 0.9990 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS B 175 GLN C 121 GLN C 217 HIS D 67 HIS F 67 HIS ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 HIS G 67 HIS G 121 GLN H 67 HIS J 67 HIS L 67 HIS L 121 GLN L 217 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.210666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.168504 restraints weight = 27497.501| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.78 r_work: 0.4101 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22058 Z= 0.117 Angle : 0.656 16.891 30040 Z= 0.308 Chirality : 0.041 0.138 3480 Planarity : 0.004 0.041 3672 Dihedral : 4.516 21.677 2952 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.34 % Allowed : 16.17 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.81 (0.16), residues: 2592 helix: 1.21 (0.17), residues: 900 sheet: 0.17 (0.19), residues: 648 loop : -2.70 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 152 TYR 0.020 0.001 TYR K 56 PHE 0.012 0.001 PHE C 52 TRP 0.006 0.001 TRP G 43 HIS 0.013 0.002 HIS F 217 Details of bonding type rmsd covalent geometry : bond 0.00269 (22056) covalent geometry : angle 0.65558 (30036) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.31035 ( 4) hydrogen bonds : bond 0.02763 ( 806) hydrogen bonds : angle 4.81658 ( 2334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 363 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 HIS cc_start: 0.7143 (m-70) cc_final: 0.6908 (m-70) REVERT: B 232 MET cc_start: 0.7215 (ptt) cc_final: 0.6743 (pmt) REVERT: C 219 HIS cc_start: 0.6326 (t70) cc_final: 0.6018 (t-170) REVERT: D 113 GLU cc_start: 0.6399 (tt0) cc_final: 0.6082 (tt0) REVERT: D 126 PHE cc_start: 0.8317 (p90) cc_final: 0.8029 (p90) REVERT: H 224 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6264 (mtt90) REVERT: I 70 TYR cc_start: 0.7171 (m-10) cc_final: 0.6519 (m-10) REVERT: I 232 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.5994 (pmm) REVERT: J 62 HIS cc_start: 0.6654 (p90) cc_final: 0.6126 (p90) REVERT: J 126 PHE cc_start: 0.8256 (p90) cc_final: 0.7904 (p90) REVERT: L 113 GLU cc_start: 0.6419 (tt0) cc_final: 0.6137 (tt0) outliers start: 57 outliers final: 33 residues processed: 383 average time/residue: 0.5953 time to fit residues: 258.2270 Evaluate side-chains 396 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 361 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 230 PHE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 138 ARG Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain W residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 96 optimal weight: 0.1980 chunk 26 optimal weight: 0.1980 chunk 254 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 233 optimal weight: 2.9990 chunk 229 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS B 175 GLN C 217 HIS D 67 HIS ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 HIS ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 HIS G 67 HIS H 67 HIS J 67 HIS L 67 HIS L 217 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.210318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.168436 restraints weight = 27399.106| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.74 r_work: 0.4114 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22058 Z= 0.111 Angle : 0.667 17.051 30040 Z= 0.309 Chirality : 0.041 0.171 3480 Planarity : 0.004 0.053 3672 Dihedral : 4.328 18.938 2952 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.46 % Allowed : 17.24 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2592 helix: 1.36 (0.17), residues: 900 sheet: 0.39 (0.20), residues: 648 loop : -2.64 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 188 TYR 0.026 0.001 TYR L 102 PHE 0.029 0.001 PHE J 52 TRP 0.006 0.001 TRP B 43 HIS 0.014 0.001 HIS F 217 Details of bonding type rmsd covalent geometry : bond 0.00257 (22056) covalent geometry : angle 0.66730 (30036) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.29930 ( 4) hydrogen bonds : bond 0.02570 ( 806) hydrogen bonds : angle 4.68600 ( 2334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 348 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 HIS cc_start: 0.7138 (m-70) cc_final: 0.6902 (m-70) REVERT: C 219 HIS cc_start: 0.6325 (t70) cc_final: 0.6023 (t-170) REVERT: D 113 GLU cc_start: 0.6442 (tt0) cc_final: 0.6129 (tt0) REVERT: D 126 PHE cc_start: 0.8305 (p90) cc_final: 0.8003 (p90) REVERT: H 224 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6237 (mtt90) REVERT: I 232 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.6034 (pmm) REVERT: J 62 HIS cc_start: 0.6681 (p90) cc_final: 0.6068 (p-80) REVERT: J 126 PHE cc_start: 0.8253 (p90) cc_final: 0.7873 (p90) REVERT: L 113 GLU cc_start: 0.6391 (tt0) cc_final: 0.6120 (tt0) outliers start: 60 outliers final: 40 residues processed: 366 average time/residue: 0.6321 time to fit residues: 261.3864 Evaluate side-chains 390 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 348 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 230 PHE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 226 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 262 optimal weight: 0.2980 chunk 138 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 37 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 156 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 121 GLN B 175 GLN C 67 HIS C 217 HIS D 67 HIS ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 HIS F 217 HIS I 150 HIS J 67 HIS L 67 HIS L 217 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.213525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.169940 restraints weight = 27251.305| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.96 r_work: 0.4068 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22058 Z= 0.146 Angle : 0.691 18.177 30040 Z= 0.319 Chirality : 0.041 0.170 3480 Planarity : 0.004 0.062 3672 Dihedral : 4.465 19.888 2952 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 2.30 % Allowed : 17.73 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.50 (0.17), residues: 2592 helix: 1.37 (0.17), residues: 900 sheet: 0.54 (0.20), residues: 624 loop : -2.49 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 188 TYR 0.020 0.001 TYR I 151 PHE 0.027 0.001 PHE J 52 TRP 0.008 0.001 TRP N 20 HIS 0.013 0.002 HIS F 217 Details of bonding type rmsd covalent geometry : bond 0.00338 (22056) covalent geometry : angle 0.69092 (30036) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.28392 ( 4) hydrogen bonds : bond 0.02684 ( 806) hydrogen bonds : angle 4.72234 ( 2334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 337 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 MET cc_start: 0.6823 (ppp) cc_final: 0.6321 (ppp) REVERT: B 67 HIS cc_start: 0.7186 (m-70) cc_final: 0.6949 (m-70) REVERT: B 70 TYR cc_start: 0.7358 (m-10) cc_final: 0.6800 (m-10) REVERT: C 57 MET cc_start: 0.7175 (ppp) cc_final: 0.6567 (ppp) REVERT: C 168 LEU cc_start: 0.7532 (mt) cc_final: 0.7313 (mp) REVERT: D 113 GLU cc_start: 0.6467 (tt0) cc_final: 0.6148 (tt0) REVERT: D 126 PHE cc_start: 0.8318 (p90) cc_final: 0.8019 (p90) REVERT: E 70 TYR cc_start: 0.7451 (m-10) cc_final: 0.6832 (m-10) REVERT: G 70 TYR cc_start: 0.7215 (m-10) cc_final: 0.6530 (m-10) REVERT: G 204 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8182 (p) REVERT: H 70 TYR cc_start: 0.7441 (m-10) cc_final: 0.6858 (m-10) REVERT: H 224 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6270 (mtt90) REVERT: I 70 TYR cc_start: 0.7229 (m-10) cc_final: 0.6714 (m-10) REVERT: J 62 HIS cc_start: 0.6660 (p90) cc_final: 0.6088 (p-80) REVERT: J 126 PHE cc_start: 0.8244 (p90) cc_final: 0.7868 (p90) REVERT: L 113 GLU cc_start: 0.6428 (tt0) cc_final: 0.6160 (tt0) REVERT: M 19 PHE cc_start: 0.6143 (OUTLIER) cc_final: 0.5868 (t80) REVERT: P 19 PHE cc_start: 0.6464 (OUTLIER) cc_final: 0.6257 (t80) outliers start: 56 outliers final: 41 residues processed: 351 average time/residue: 0.6435 time to fit residues: 254.5241 Evaluate side-chains 378 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 230 PHE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain P residue 19 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 144 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 246 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 121 GLN B 175 GLN C 67 HIS C 217 HIS ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 HIS F 217 HIS ** H 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 HIS L 217 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.209556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.165777 restraints weight = 27650.416| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.94 r_work: 0.4033 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22058 Z= 0.201 Angle : 0.744 19.587 30040 Z= 0.347 Chirality : 0.042 0.181 3480 Planarity : 0.004 0.042 3672 Dihedral : 4.753 21.648 2952 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.67 % Allowed : 18.14 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2592 helix: 1.32 (0.17), residues: 900 sheet: 0.31 (0.20), residues: 624 loop : -2.53 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 188 TYR 0.034 0.002 TYR G 102 PHE 0.025 0.001 PHE J 52 TRP 0.007 0.001 TRP A 43 HIS 0.021 0.002 HIS F 217 Details of bonding type rmsd covalent geometry : bond 0.00462 (22056) covalent geometry : angle 0.74392 (30036) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.40094 ( 4) hydrogen bonds : bond 0.02957 ( 806) hydrogen bonds : angle 4.86487 ( 2334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 339 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 HIS cc_start: 0.7199 (m-70) cc_final: 0.6962 (m-70) REVERT: B 70 TYR cc_start: 0.7484 (m-10) cc_final: 0.6924 (m-10) REVERT: C 168 LEU cc_start: 0.7535 (mt) cc_final: 0.7322 (mp) REVERT: D 70 TYR cc_start: 0.7509 (m-10) cc_final: 0.6505 (m-10) REVERT: D 113 GLU cc_start: 0.6517 (tt0) cc_final: 0.6195 (tt0) REVERT: E 70 TYR cc_start: 0.7512 (m-10) cc_final: 0.6991 (m-10) REVERT: G 70 TYR cc_start: 0.7481 (m-10) cc_final: 0.6938 (m-10) REVERT: G 204 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8214 (p) REVERT: H 224 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6271 (mtt90) REVERT: I 70 TYR cc_start: 0.7397 (m-10) cc_final: 0.7000 (m-10) REVERT: J 62 HIS cc_start: 0.6783 (p90) cc_final: 0.6130 (p-80) REVERT: J 126 PHE cc_start: 0.8233 (p90) cc_final: 0.7863 (p90) REVERT: L 70 TYR cc_start: 0.7484 (m-10) cc_final: 0.6749 (m-10) REVERT: L 113 GLU cc_start: 0.6438 (tt0) cc_final: 0.6165 (tt0) REVERT: M 19 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5918 (t80) REVERT: P 19 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.6332 (t80) outliers start: 65 outliers final: 49 residues processed: 364 average time/residue: 0.6201 time to fit residues: 255.0157 Evaluate side-chains 387 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 334 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 217 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain P residue 19 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 203 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS B 175 GLN C 67 HIS C 217 HIS F 67 HIS F 217 HIS G 190 ASN J 67 HIS L 67 HIS L 217 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.211353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.168381 restraints weight = 27462.418| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.86 r_work: 0.4070 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22058 Z= 0.152 Angle : 0.739 20.485 30040 Z= 0.340 Chirality : 0.041 0.163 3480 Planarity : 0.004 0.039 3672 Dihedral : 4.602 21.076 2952 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.34 % Allowed : 18.68 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.68 (0.17), residues: 2592 helix: 1.39 (0.17), residues: 900 sheet: 0.14 (0.20), residues: 648 loop : -2.62 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 188 TYR 0.028 0.001 TYR B 102 PHE 0.025 0.001 PHE J 52 TRP 0.006 0.001 TRP A 43 HIS 0.016 0.002 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00354 (22056) covalent geometry : angle 0.73887 (30036) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.34733 ( 4) hydrogen bonds : bond 0.02665 ( 806) hydrogen bonds : angle 4.74141 ( 2334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 341 time to evaluate : 0.716 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 67 HIS cc_start: 0.7163 (m-70) cc_final: 0.6927 (m-70) REVERT: B 70 TYR cc_start: 0.7420 (m-10) cc_final: 0.6904 (m-10) REVERT: C 57 MET cc_start: 0.7220 (ppp) cc_final: 0.6552 (ppp) REVERT: C 168 LEU cc_start: 0.7542 (mt) cc_final: 0.7334 (mp) REVERT: D 70 TYR cc_start: 0.7365 (m-10) cc_final: 0.6409 (m-10) REVERT: D 113 GLU cc_start: 0.6478 (tt0) cc_final: 0.6155 (tt0) REVERT: E 70 TYR cc_start: 0.7467 (m-10) cc_final: 0.6868 (m-10) REVERT: G 70 TYR cc_start: 0.7315 (m-10) cc_final: 0.6694 (m-10) REVERT: G 204 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8171 (p) REVERT: H 224 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6205 (mtt90) REVERT: I 70 TYR cc_start: 0.7281 (m-10) cc_final: 0.6793 (m-10) REVERT: J 62 HIS cc_start: 0.6708 (p90) cc_final: 0.6082 (p-80) REVERT: J 126 PHE cc_start: 0.8235 (p90) cc_final: 0.7880 (p90) REVERT: L 113 GLU cc_start: 0.6461 (tt0) cc_final: 0.6189 (tt0) outliers start: 57 outliers final: 46 residues processed: 358 average time/residue: 0.6400 time to fit residues: 258.6221 Evaluate side-chains 385 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 337 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 178 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS B 175 GLN C 67 HIS C 217 HIS F 67 HIS F 217 HIS ** H 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 HIS L 67 HIS L 217 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.216545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.172327 restraints weight = 27582.523| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.93 r_work: 0.4049 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22058 Z= 0.172 Angle : 0.767 22.470 30040 Z= 0.355 Chirality : 0.042 0.158 3480 Planarity : 0.004 0.050 3672 Dihedral : 4.716 25.741 2952 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.34 % Allowed : 19.46 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.66 (0.17), residues: 2592 helix: 1.35 (0.17), residues: 900 sheet: 0.26 (0.20), residues: 624 loop : -2.57 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 188 TYR 0.027 0.001 TYR C 102 PHE 0.024 0.001 PHE J 52 TRP 0.007 0.001 TRP P 20 HIS 0.017 0.002 HIS H 67 Details of bonding type rmsd covalent geometry : bond 0.00398 (22056) covalent geometry : angle 0.76717 (30036) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.28343 ( 4) hydrogen bonds : bond 0.02758 ( 806) hydrogen bonds : angle 4.78456 ( 2334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 343 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 HIS cc_start: 0.7185 (m-70) cc_final: 0.6935 (m-70) REVERT: B 70 TYR cc_start: 0.7473 (m-10) cc_final: 0.6960 (m-10) REVERT: C 57 MET cc_start: 0.7252 (ppp) cc_final: 0.6558 (ppp) REVERT: C 168 LEU cc_start: 0.7556 (mt) cc_final: 0.7339 (mp) REVERT: D 70 TYR cc_start: 0.7470 (m-10) cc_final: 0.6508 (m-10) REVERT: D 113 GLU cc_start: 0.6472 (tt0) cc_final: 0.6141 (tt0) REVERT: E 70 TYR cc_start: 0.7533 (m-10) cc_final: 0.7062 (m-10) REVERT: G 70 TYR cc_start: 0.7436 (m-10) cc_final: 0.6829 (m-10) REVERT: G 204 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8178 (p) REVERT: H 224 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6225 (mtt90) REVERT: I 70 TYR cc_start: 0.7450 (m-10) cc_final: 0.7073 (m-10) REVERT: J 62 HIS cc_start: 0.6732 (p90) cc_final: 0.6131 (p-80) REVERT: J 126 PHE cc_start: 0.8233 (p90) cc_final: 0.7870 (p90) REVERT: L 113 GLU cc_start: 0.6496 (tt0) cc_final: 0.6219 (tt0) outliers start: 57 outliers final: 48 residues processed: 360 average time/residue: 0.6039 time to fit residues: 246.2340 Evaluate side-chains 391 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 341 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain I residue 52 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 160 ASP Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 114 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 237 optimal weight: 0.0270 chunk 51 optimal weight: 0.9980 chunk 163 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 160 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS B 175 GLN C 67 HIS C 217 HIS F 67 HIS F 217 HIS G 67 HIS I 229 ASN L 67 HIS L 217 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.212121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.169572 restraints weight = 27739.068| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.86 r_work: 0.4088 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22058 Z= 0.123 Angle : 0.739 22.284 30040 Z= 0.339 Chirality : 0.041 0.151 3480 Planarity : 0.004 0.055 3672 Dihedral : 4.464 25.960 2952 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.30 % Allowed : 19.50 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2592 helix: 1.48 (0.17), residues: 900 sheet: 0.25 (0.20), residues: 648 loop : -2.65 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 188 TYR 0.019 0.001 TYR C 102 PHE 0.025 0.001 PHE L 126 TRP 0.007 0.001 TRP P 20 HIS 0.017 0.002 HIS F 217 Details of bonding type rmsd covalent geometry : bond 0.00286 (22056) covalent geometry : angle 0.73892 (30036) SS BOND : bond 0.00258 ( 2) SS BOND : angle 0.28321 ( 4) hydrogen bonds : bond 0.02455 ( 806) hydrogen bonds : angle 4.63195 ( 2334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6520.44 seconds wall clock time: 112 minutes 20.54 seconds (6740.54 seconds total)