Starting phenix.real_space_refine on Mon Jun 16 14:24:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xn4_38497/06_2025/8xn4_38497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xn4_38497/06_2025/8xn4_38497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xn4_38497/06_2025/8xn4_38497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xn4_38497/06_2025/8xn4_38497.map" model { file = "/net/cci-nas-00/data/ceres_data/8xn4_38497/06_2025/8xn4_38497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xn4_38497/06_2025/8xn4_38497.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.009 sd= 0.080 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 112 5.16 5 C 12026 2.51 5 N 3269 2.21 5 O 3766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19173 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "E" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "F" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "G" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "H" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "I" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "K" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "L" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "M" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "N" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Time building chain proxies: 10.77, per 1000 atoms: 0.56 Number of scatterers: 19173 At special positions: 0 Unit cell: (115.92, 115.92, 108.36, 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 112 16.00 O 3766 8.00 N 3269 7.00 C 12026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 2.3 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 41 sheets defined 53.3% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.719A pdb=" N PHE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.637A pdb=" N LYS A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 85 through 99 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 148 through 174 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 85 through 99 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 149 through 174 removed outlier: 3.572A pdb=" N ILE C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 85 through 99 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 148 through 174 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 191 through 199 Processing helix chain 'D' and resid 207 through 211 removed outlier: 3.515A pdb=" N MET D 211 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 85 through 99 removed outlier: 3.678A pdb=" N GLY E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 removed outlier: 3.738A pdb=" N PHE E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 174 Processing helix chain 'E' and resid 176 through 185 removed outlier: 3.528A pdb=" N ILE E 180 " --> pdb=" O THR E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 199 Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 85 through 99 Processing helix chain 'F' and resid 113 through 121 removed outlier: 3.652A pdb=" N PHE F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 174 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 191 through 199 Processing helix chain 'F' and resid 207 through 211 removed outlier: 3.595A pdb=" N MET F 211 " --> pdb=" O ALA F 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 42 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.606A pdb=" N GLY G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 removed outlier: 3.709A pdb=" N PHE G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 174 Processing helix chain 'G' and resid 176 through 184 Processing helix chain 'G' and resid 191 through 199 Processing helix chain 'H' and resid 53 through 60 Processing helix chain 'H' and resid 70 through 87 removed outlier: 3.557A pdb=" N MET H 87 " --> pdb=" O CYS H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 removed outlier: 3.503A pdb=" N LEU H 107 " --> pdb=" O SER H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 167 through 191 Processing helix chain 'H' and resid 195 through 203 Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'I' and resid 53 through 60 Processing helix chain 'I' and resid 70 through 87 Processing helix chain 'I' and resid 103 through 117 Processing helix chain 'I' and resid 131 through 138 Processing helix chain 'I' and resid 167 through 192 Processing helix chain 'I' and resid 195 through 203 Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 70 through 87 removed outlier: 3.546A pdb=" N MET J 87 " --> pdb=" O CYS J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 117 Processing helix chain 'J' and resid 130 through 138 Processing helix chain 'J' and resid 167 through 193 Processing helix chain 'J' and resid 195 through 202 Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'K' and resid 53 through 60 Processing helix chain 'K' and resid 70 through 88 removed outlier: 3.819A pdb=" N MET K 87 " --> pdb=" O CYS K 83 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 117 Processing helix chain 'K' and resid 131 through 138 Processing helix chain 'K' and resid 167 through 191 Processing helix chain 'K' and resid 195 through 204 Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'L' and resid 53 through 60 Processing helix chain 'L' and resid 70 through 87 Processing helix chain 'L' and resid 103 through 117 Processing helix chain 'L' and resid 130 through 138 Processing helix chain 'L' and resid 166 through 191 removed outlier: 3.642A pdb=" N LEU L 170 " --> pdb=" O GLN L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 203 Processing helix chain 'L' and resid 210 through 218 Processing helix chain 'M' and resid 53 through 60 removed outlier: 3.502A pdb=" N GLU M 60 " --> pdb=" O LYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 87 Processing helix chain 'M' and resid 103 through 117 removed outlier: 3.540A pdb=" N LEU M 107 " --> pdb=" O SER M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 138 Processing helix chain 'M' and resid 167 through 192 Processing helix chain 'M' and resid 195 through 204 removed outlier: 3.535A pdb=" N GLU M 204 " --> pdb=" O ARG M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'N' and resid 53 through 60 Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.736A pdb=" N MET N 87 " --> pdb=" O CYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 117 Processing helix chain 'N' and resid 131 through 138 Processing helix chain 'N' and resid 167 through 192 Processing helix chain 'N' and resid 195 through 204 removed outlier: 3.601A pdb=" N GLU N 204 " --> pdb=" O ARG N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.031A pdb=" N ILE A 46 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN A 80 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 48 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 106 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 77 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET A 108 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 79 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU A 110 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU A 134 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY A 109 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU A 136 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA A 111 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 188 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.031A pdb=" N ILE A 46 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN A 80 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 48 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 106 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 77 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET A 108 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 79 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU A 110 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N PHE A 128 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR A 105 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 5.476A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU B 134 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY B 109 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU B 136 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA B 111 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 188 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 48 removed outlier: 5.476A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE B 128 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR B 105 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.559A pdb=" N ALA B 142 " --> pdb=" O GLY J 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY J 165 " --> pdb=" O ALA B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.717A pdb=" N ILE C 46 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN C 80 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 48 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE C 106 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 77 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 108 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE C 79 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU C 110 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.717A pdb=" N ILE C 46 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN C 80 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 48 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE C 106 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 77 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 108 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE C 79 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU C 110 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE C 128 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR C 105 " --> pdb=" O PHE C 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.525A pdb=" N GLY K 165 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.713A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE D 75 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 106 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 77 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET D 108 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE D 79 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU D 110 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU D 134 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY D 109 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU D 136 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA D 111 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.713A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE D 75 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 106 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 77 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET D 108 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE D 79 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU D 110 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE D 128 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR D 105 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.367A pdb=" N ILE E 75 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE E 106 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 77 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET E 108 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE E 79 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU E 110 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU E 134 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY E 109 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU E 136 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA E 111 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.367A pdb=" N ILE E 75 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE E 106 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 77 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET E 108 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE E 79 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU E 110 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N PHE E 128 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR E 105 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.507A pdb=" N ALA E 142 " --> pdb=" O GLY M 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY M 165 " --> pdb=" O ALA E 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC2, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.469A pdb=" N ILE F 75 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE F 106 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 77 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET F 108 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE F 79 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU F 110 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU F 134 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY F 109 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU F 136 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA F 111 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 188 " --> pdb=" O ILE F 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.469A pdb=" N ILE F 75 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE F 106 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 77 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET F 108 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE F 79 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU F 110 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE F 128 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR F 105 " --> pdb=" O PHE F 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AC5, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AC6, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.695A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.695A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE G 128 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR G 105 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AC9, first strand: chain 'G' and resid 146 through 147 Processing sheet with id=AD1, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.423A pdb=" N ILE H 93 " --> pdb=" O GLN H 122 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL H 124 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL H 95 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N MET H 126 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE H 97 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN H 128 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 99 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG H 152 " --> pdb=" O CYS H 125 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY H 127 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LEU H 154 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA H 129 " --> pdb=" O LEU H 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.423A pdb=" N ILE H 93 " --> pdb=" O GLN H 122 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL H 124 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL H 95 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N MET H 126 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE H 97 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN H 128 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 99 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N MET H 146 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR H 123 " --> pdb=" O MET H 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 62 through 65 removed outlier: 5.465A pdb=" N SER I 99 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN I 128 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG I 152 " --> pdb=" O GLY I 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 62 through 65 removed outlier: 5.465A pdb=" N SER I 99 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN I 128 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N MET I 146 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR I 123 " --> pdb=" O MET I 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.332A pdb=" N ILE J 93 " --> pdb=" O GLN J 122 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL J 124 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL J 95 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET J 126 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE J 97 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN J 128 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG J 152 " --> pdb=" O CYS J 125 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY J 127 " --> pdb=" O ARG J 152 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LEU J 154 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA J 129 " --> pdb=" O LEU J 154 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.332A pdb=" N ILE J 93 " --> pdb=" O GLN J 122 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL J 124 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL J 95 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET J 126 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE J 97 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN J 128 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN J 222 " --> pdb=" O ARG J 145 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.579A pdb=" N SER K 99 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN K 128 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG K 152 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.579A pdb=" N SER K 99 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN K 128 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N MET K 146 " --> pdb=" O VAL K 121 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR K 123 " --> pdb=" O MET K 146 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 62 through 65 removed outlier: 6.187A pdb=" N ILE L 93 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET L 126 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE L 97 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN L 128 " --> pdb=" O ILE L 97 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG L 152 " --> pdb=" O CYS L 125 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY L 127 " --> pdb=" O ARG L 152 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N LEU L 154 " --> pdb=" O GLY L 127 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA L 129 " --> pdb=" O LEU L 154 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 62 through 65 removed outlier: 6.187A pdb=" N ILE L 93 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET L 126 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE L 97 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN L 128 " --> pdb=" O ILE L 97 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG L 145 " --> pdb=" O GLN L 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.781A pdb=" N ILE M 63 " --> pdb=" O TYR M 96 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASN M 98 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU M 65 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE M 93 " --> pdb=" O GLN M 122 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL M 124 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL M 95 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N MET M 126 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE M 97 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN M 128 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS M 207 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.781A pdb=" N ILE M 63 " --> pdb=" O TYR M 96 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASN M 98 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU M 65 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE M 93 " --> pdb=" O GLN M 122 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL M 124 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL M 95 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N MET M 126 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE M 97 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN M 128 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET M 146 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR M 123 " --> pdb=" O MET M 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.846A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN N 98 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU N 65 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE N 93 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL N 124 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL N 95 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET N 126 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE N 97 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN N 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.846A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN N 98 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU N 65 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE N 93 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL N 124 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL N 95 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET N 126 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE N 97 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN N 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3399 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: 6.38 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3387 1.30 - 1.43: 4415 1.43 - 1.56: 11448 1.56 - 1.69: 0 1.69 - 1.82: 210 Bond restraints: 19460 Sorted by residual: bond pdb=" CA SER L 160 " pdb=" CB SER L 160 " ideal model delta sigma weight residual 1.530 1.451 0.079 1.36e-02 5.41e+03 3.41e+01 bond pdb=" C ASP E 185 " pdb=" O ASP E 185 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.26e-02 6.30e+03 3.13e+01 bond pdb=" C GLU E 178 " pdb=" O GLU E 178 " ideal model delta sigma weight residual 1.237 1.297 -0.061 1.16e-02 7.43e+03 2.75e+01 bond pdb=" C THR E 181 " pdb=" O THR E 181 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.16e-02 7.43e+03 2.06e+01 bond pdb=" C PRO J 119 " pdb=" O PRO J 119 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.19e-02 7.06e+03 1.84e+01 ... (remaining 19455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 25890 2.72 - 5.44: 427 5.44 - 8.16: 34 8.16 - 10.88: 10 10.88 - 13.60: 8 Bond angle restraints: 26369 Sorted by residual: angle pdb=" C THR K 108 " pdb=" CA THR K 108 " pdb=" CB THR K 108 " ideal model delta sigma weight residual 109.95 122.12 -12.17 1.99e+00 2.53e-01 3.74e+01 angle pdb=" N THR K 108 " pdb=" CA THR K 108 " pdb=" C THR K 108 " ideal model delta sigma weight residual 113.18 106.02 7.16 1.21e+00 6.83e-01 3.50e+01 angle pdb=" C THR K 194 " pdb=" CA THR K 194 " pdb=" CB THR K 194 " ideal model delta sigma weight residual 108.86 117.06 -8.20 1.44e+00 4.82e-01 3.24e+01 angle pdb=" C THR J 194 " pdb=" CA THR J 194 " pdb=" CB THR J 194 " ideal model delta sigma weight residual 109.37 118.08 -8.71 1.59e+00 3.96e-01 3.00e+01 angle pdb=" C ALA C 113 " pdb=" CA ALA C 113 " pdb=" CB ALA C 113 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 ... (remaining 26364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10202 17.98 - 35.97: 1240 35.97 - 53.95: 384 53.95 - 71.93: 84 71.93 - 89.91: 39 Dihedral angle restraints: 11949 sinusoidal: 4697 harmonic: 7252 Sorted by residual: dihedral pdb=" CA GLU A 43 " pdb=" C GLU A 43 " pdb=" N ARG A 44 " pdb=" CA ARG A 44 " ideal model delta harmonic sigma weight residual 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" C THR K 108 " pdb=" N THR K 108 " pdb=" CA THR K 108 " pdb=" CB THR K 108 " ideal model delta harmonic sigma weight residual -122.00 -134.51 12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" CA MET J 87 " pdb=" C MET J 87 " pdb=" N ASP J 88 " pdb=" CA ASP J 88 " ideal model delta harmonic sigma weight residual -180.00 -158.31 -21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 11946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2592 0.063 - 0.127: 430 0.127 - 0.190: 44 0.190 - 0.253: 5 0.253 - 0.317: 2 Chirality restraints: 3073 Sorted by residual: chirality pdb=" CB VAL N 117 " pdb=" CA VAL N 117 " pdb=" CG1 VAL N 117 " pdb=" CG2 VAL N 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA THR K 108 " pdb=" N THR K 108 " pdb=" C THR K 108 " pdb=" CB THR K 108 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA VAL N 117 " pdb=" N VAL N 117 " pdb=" C VAL N 117 " pdb=" CB VAL N 117 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 3070 not shown) Planarity restraints: 3451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS K 191 " 0.022 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C HIS K 191 " -0.074 2.00e-02 2.50e+03 pdb=" O HIS K 191 " 0.026 2.00e-02 2.50e+03 pdb=" N SER K 192 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 70 " 0.061 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO F 71 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 71 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 71 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 70 " 0.061 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO D 71 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 71 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 71 " 0.050 5.00e-02 4.00e+02 ... (remaining 3448 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1829 2.74 - 3.28: 18769 3.28 - 3.82: 31384 3.82 - 4.36: 35858 4.36 - 4.90: 63556 Nonbonded interactions: 151396 Sorted by model distance: nonbonded pdb=" OE1 GLN L 222 " pdb=" N VAL L 223 " model vdw 2.200 3.120 nonbonded pdb=" OD2 ASP I 202 " pdb=" OH TYR I 217 " model vdw 2.205 3.040 nonbonded pdb=" O GLU L 171 " pdb=" ND2 ASN L 175 " model vdw 2.211 3.120 nonbonded pdb=" NH2 ARG A 186 " pdb=" OE2 GLU H 204 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR N 159 " pdb=" OE2 GLU N 161 " model vdw 2.216 3.040 ... (remaining 151391 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 41.820 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.005 0.079 19460 Z= 0.277 Angle : 0.808 13.603 26369 Z= 0.466 Chirality : 0.047 0.317 3073 Planarity : 0.007 0.128 3451 Dihedral : 18.213 89.913 7273 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.46 % Favored : 97.42 % Rotamer: Outliers : 3.23 % Allowed : 31.46 % Favored : 65.31 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.17), residues: 2478 helix: 1.73 (0.15), residues: 1337 sheet: 1.73 (0.34), residues: 217 loop : -0.57 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP A 189 HIS 0.006 0.001 HIS D 138 PHE 0.023 0.002 PHE A 128 TYR 0.021 0.001 TYR C 98 ARG 0.012 0.001 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.18790 ( 1103) hydrogen bonds : angle 5.82530 ( 3399) covalent geometry : bond 0.00476 (19460) covalent geometry : angle 0.80843 (26369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 762 time to evaluate : 2.405 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: C 179 GLN cc_start: 0.8976 (tp40) cc_final: 0.8357 (tp-100) REVERT: C 182 ARG cc_start: 0.8494 (ttp80) cc_final: 0.7887 (ttp80) REVERT: H 85 GLU cc_start: 0.7597 (tp30) cc_final: 0.7379 (tp30) REVERT: H 202 ASP cc_start: 0.8425 (m-30) cc_final: 0.8213 (m-30) REVERT: I 126 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8669 (ptp) REVERT: J 152 ARG cc_start: 0.6289 (ptm160) cc_final: 0.5551 (ptm160) REVERT: K 104 PHE cc_start: 0.4428 (OUTLIER) cc_final: 0.3445 (m-80) REVERT: L 78 MET cc_start: 0.7914 (ptt) cc_final: 0.7707 (ptt) REVERT: M 91 ARG cc_start: 0.8919 (mtp85) cc_final: 0.8678 (mtp180) REVERT: M 152 ARG cc_start: 0.6330 (ptm160) cc_final: 0.5035 (ptm160) REVERT: N 117 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8614 (m) outliers start: 66 outliers final: 35 residues processed: 795 average time/residue: 1.3084 time to fit residues: 1165.9566 Evaluate side-chains 791 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 753 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 168 SER Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 122 GLN Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 225 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 192 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 171 GLN A 179 GLN B 58 ASN B 80 ASN C 58 ASN D 58 ASN E 132 ASN E 138 HIS E 139 GLN F 35 GLN F 171 GLN F 179 GLN G 38 ASN G 58 ASN G 116 GLN H 75 ASN H 157 GLN I 75 ASN J 98 ASN K 75 ASN K 98 ASN K 122 GLN K 175 ASN L 75 ASN L 156 HIS M 75 ASN N 75 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.113939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104697 restraints weight = 28054.380| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.80 r_work: 0.3500 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19460 Z= 0.123 Angle : 0.583 9.306 26369 Z= 0.301 Chirality : 0.042 0.150 3073 Planarity : 0.005 0.065 3451 Dihedral : 6.164 77.319 2767 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.43 % Allowed : 25.44 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2478 helix: 2.19 (0.15), residues: 1358 sheet: 1.80 (0.33), residues: 217 loop : -0.54 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 189 HIS 0.005 0.001 HIS D 138 PHE 0.008 0.001 PHE I 58 TYR 0.012 0.001 TYR I 159 ARG 0.006 0.001 ARG N 91 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 1103) hydrogen bonds : angle 4.01060 ( 3399) covalent geometry : bond 0.00282 (19460) covalent geometry : angle 0.58347 (26369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 751 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7565 (tpt-90) REVERT: A 167 GLU cc_start: 0.8324 (tp30) cc_final: 0.8103 (tp30) REVERT: B 97 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8386 (mp10) REVERT: F 134 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8312 (tm-30) REVERT: H 59 GLU cc_start: 0.8214 (mp0) cc_final: 0.7973 (mp0) REVERT: J 152 ARG cc_start: 0.6551 (ptm160) cc_final: 0.5845 (ptm160) REVERT: K 104 PHE cc_start: 0.4152 (OUTLIER) cc_final: 0.3324 (m-80) REVERT: K 180 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7805 (mtp) REVERT: L 59 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: L 60 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: L 122 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: M 60 GLU cc_start: 0.7791 (mp0) cc_final: 0.7536 (mp0) REVERT: M 146 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7968 (mpt) REVERT: M 152 ARG cc_start: 0.6403 (ptm160) cc_final: 0.5129 (ptm160) outliers start: 111 outliers final: 43 residues processed: 801 average time/residue: 1.2646 time to fit residues: 1140.5888 Evaluate side-chains 789 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 738 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 128 GLN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 58 PHE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 185 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 80 ASN A 171 GLN A 179 GLN B 38 ASN B 58 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 179 GLN C 58 ASN C 63 GLN C 138 HIS C 139 GLN C 179 GLN D 58 ASN D 139 GLN D 179 GLN E 58 ASN E 63 GLN E 132 ASN E 138 HIS F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 58 ASN G 132 ASN I 75 ASN K 68 GLN K 75 ASN K 98 ASN K 115 GLN L 75 ASN ** L 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN M 75 ASN M 98 ASN N 75 ASN N 115 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.113320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.104125 restraints weight = 27752.218| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.79 r_work: 0.3501 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19460 Z= 0.134 Angle : 0.574 9.516 26369 Z= 0.294 Chirality : 0.042 0.153 3073 Planarity : 0.005 0.048 3451 Dihedral : 5.289 59.528 2728 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.60 % Allowed : 26.17 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.18), residues: 2478 helix: 2.32 (0.15), residues: 1358 sheet: 1.68 (0.33), residues: 217 loop : -0.50 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 189 HIS 0.003 0.001 HIS E 138 PHE 0.011 0.001 PHE I 104 TYR 0.011 0.001 TYR I 159 ARG 0.006 0.001 ARG H 152 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1103) hydrogen bonds : angle 3.77372 ( 3399) covalent geometry : bond 0.00318 (19460) covalent geometry : angle 0.57384 (26369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 744 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7531 (tpt-90) REVERT: A 134 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7228 (pp20) REVERT: A 167 GLU cc_start: 0.8374 (tp30) cc_final: 0.8162 (tp30) REVERT: A 189 TRP cc_start: 0.8220 (m100) cc_final: 0.7947 (m100) REVERT: B 97 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8420 (mp10) REVERT: C 97 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8631 (mp10) REVERT: D 179 GLN cc_start: 0.9007 (tp40) cc_final: 0.8765 (mm-40) REVERT: E 189 TRP cc_start: 0.8349 (m100) cc_final: 0.7801 (m100) REVERT: F 203 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8239 (t0) REVERT: H 59 GLU cc_start: 0.8256 (mp0) cc_final: 0.7994 (mp0) REVERT: H 87 MET cc_start: 0.6521 (mpt) cc_final: 0.6318 (mpt) REVERT: H 124 VAL cc_start: 0.8640 (m) cc_final: 0.8407 (t) REVERT: H 152 ARG cc_start: 0.6975 (mtp85) cc_final: 0.6744 (mtp85) REVERT: I 104 PHE cc_start: 0.4307 (OUTLIER) cc_final: 0.3878 (m-80) REVERT: I 181 ARG cc_start: 0.8475 (ttt90) cc_final: 0.8023 (ttt180) REVERT: J 146 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.6956 (mpt) REVERT: J 200 ARG cc_start: 0.7913 (mtm180) cc_final: 0.7674 (mtm180) REVERT: J 204 GLU cc_start: 0.8317 (tp30) cc_final: 0.8067 (tp30) REVERT: K 104 PHE cc_start: 0.4154 (OUTLIER) cc_final: 0.3661 (m-80) REVERT: K 185 GLU cc_start: 0.7708 (tt0) cc_final: 0.7088 (tt0) REVERT: L 59 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8299 (mm-30) REVERT: L 128 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: L 135 VAL cc_start: 0.6778 (t) cc_final: 0.6511 (p) REVERT: M 60 GLU cc_start: 0.7897 (mp0) cc_final: 0.7611 (mp0) REVERT: M 152 ARG cc_start: 0.6471 (ptm160) cc_final: 0.5099 (ptm160) REVERT: N 59 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: N 181 ARG cc_start: 0.8674 (tmm-80) cc_final: 0.8452 (ttt180) outliers start: 94 outliers final: 51 residues processed: 784 average time/residue: 1.2526 time to fit residues: 1102.3169 Evaluate side-chains 794 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 732 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 35 optimal weight: 8.9990 chunk 118 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 171 GLN A 179 GLN B 38 ASN B 58 ASN B 171 GLN B 179 GLN C 138 HIS C 179 GLN D 58 ASN E 58 ASN E 132 ASN E 138 HIS F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 58 ASN G 132 ASN G 171 GLN I 75 ASN ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 ASN K 222 GLN L 75 ASN L 98 ASN M 75 ASN N 75 ASN N 115 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.108711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099535 restraints weight = 28094.913| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.76 r_work: 0.3439 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19460 Z= 0.242 Angle : 0.672 12.815 26369 Z= 0.346 Chirality : 0.045 0.159 3073 Planarity : 0.005 0.044 3451 Dihedral : 5.326 58.844 2720 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.58 % Allowed : 25.59 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.17), residues: 2478 helix: 2.02 (0.14), residues: 1365 sheet: 1.48 (0.33), residues: 217 loop : -0.55 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 189 HIS 0.006 0.001 HIS A 138 PHE 0.020 0.002 PHE H 104 TYR 0.017 0.002 TYR I 54 ARG 0.008 0.001 ARG H 152 Details of bonding type rmsd hydrogen bonds : bond 0.05598 ( 1103) hydrogen bonds : angle 3.96708 ( 3399) covalent geometry : bond 0.00596 (19460) covalent geometry : angle 0.67158 (26369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 752 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7310 (tpt-90) REVERT: A 74 ASP cc_start: 0.8322 (m-30) cc_final: 0.7958 (m-30) REVERT: A 97 GLN cc_start: 0.9094 (tp40) cc_final: 0.8837 (mm-40) REVERT: A 134 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7072 (pp20) REVERT: A 189 TRP cc_start: 0.8302 (m100) cc_final: 0.7922 (m100) REVERT: B 97 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: C 97 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8660 (mp10) REVERT: D 179 GLN cc_start: 0.9063 (tp40) cc_final: 0.8802 (mm-40) REVERT: H 59 GLU cc_start: 0.8320 (mp0) cc_final: 0.8049 (mp0) REVERT: H 87 MET cc_start: 0.6779 (mpt) cc_final: 0.6356 (mpt) REVERT: H 146 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.6498 (mpt) REVERT: H 152 ARG cc_start: 0.7295 (mtp85) cc_final: 0.6900 (mtp85) REVERT: H 208 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6662 (mt) REVERT: I 104 PHE cc_start: 0.4552 (OUTLIER) cc_final: 0.3501 (m-80) REVERT: J 61 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7972 (mtp-110) REVERT: J 104 PHE cc_start: 0.4747 (OUTLIER) cc_final: 0.3976 (m-80) REVERT: J 146 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7513 (mpt) REVERT: J 200 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7689 (mtm180) REVERT: J 204 GLU cc_start: 0.8407 (tp30) cc_final: 0.8095 (tp30) REVERT: K 104 PHE cc_start: 0.4526 (OUTLIER) cc_final: 0.3756 (m-80) REVERT: K 122 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6725 (tp-100) REVERT: K 146 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.6984 (mpt) REVERT: L 59 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8261 (mm-30) REVERT: L 60 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: L 135 VAL cc_start: 0.6829 (t) cc_final: 0.6546 (p) REVERT: N 59 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: N 75 ASN cc_start: 0.8623 (m-40) cc_final: 0.8384 (m110) outliers start: 114 outliers final: 59 residues processed: 806 average time/residue: 1.2681 time to fit residues: 1144.9889 Evaluate side-chains 821 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 746 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 185 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 132 ASN A 139 GLN A 171 GLN A 179 GLN B 38 ASN B 58 ASN B 139 GLN B 179 GLN C 179 GLN D 58 ASN D 138 HIS E 58 ASN E 132 ASN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 58 ASN G 132 ASN G 179 GLN H 157 GLN I 75 ASN K 75 ASN L 75 ASN L 156 HIS M 75 ASN N 115 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.113747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104323 restraints weight = 28022.358| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.82 r_work: 0.3489 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19460 Z= 0.118 Angle : 0.596 10.325 26369 Z= 0.300 Chirality : 0.042 0.151 3073 Planarity : 0.005 0.049 3451 Dihedral : 4.780 48.234 2718 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.79 % Allowed : 26.42 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.18), residues: 2478 helix: 2.31 (0.15), residues: 1358 sheet: 1.45 (0.34), residues: 217 loop : -0.50 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 189 HIS 0.003 0.001 HIS L 156 PHE 0.011 0.001 PHE H 104 TYR 0.011 0.001 TYR B 98 ARG 0.009 0.000 ARG H 152 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 1103) hydrogen bonds : angle 3.65543 ( 3399) covalent geometry : bond 0.00275 (19460) covalent geometry : angle 0.59567 (26369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 736 time to evaluate : 2.143 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: A 44 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7526 (tpt-90) REVERT: A 167 GLU cc_start: 0.8407 (tp30) cc_final: 0.8192 (tp30) REVERT: C 97 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8654 (mp10) REVERT: E 211 MET cc_start: 0.6885 (mtp) cc_final: 0.6628 (mtt) REVERT: G 189 TRP cc_start: 0.8487 (m100) cc_final: 0.7972 (m100) REVERT: H 59 GLU cc_start: 0.8187 (mp0) cc_final: 0.7938 (mp0) REVERT: H 87 MET cc_start: 0.6627 (mpt) cc_final: 0.6213 (mpt) REVERT: H 104 PHE cc_start: 0.4280 (OUTLIER) cc_final: 0.3240 (m-80) REVERT: H 179 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7927 (tmm-80) REVERT: H 208 ILE cc_start: 0.6803 (mt) cc_final: 0.6567 (mt) REVERT: I 104 PHE cc_start: 0.4479 (OUTLIER) cc_final: 0.3624 (m-80) REVERT: K 104 PHE cc_start: 0.4402 (OUTLIER) cc_final: 0.3793 (m-80) REVERT: L 59 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: L 60 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: L 128 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: L 135 VAL cc_start: 0.6796 (t) cc_final: 0.6550 (p) REVERT: L 181 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8385 (ttt90) REVERT: M 60 GLU cc_start: 0.8016 (mp0) cc_final: 0.7728 (mp0) REVERT: N 59 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: N 164 ARG cc_start: 0.5558 (OUTLIER) cc_final: 0.5175 (ttm110) outliers start: 98 outliers final: 48 residues processed: 783 average time/residue: 1.3748 time to fit residues: 1206.4323 Evaluate side-chains 775 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 715 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 185 GLU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 186 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 132 ASN A 171 GLN A 179 GLN B 58 ASN B 171 GLN B 179 GLN C 58 ASN C 63 GLN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 132 ASN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 58 ASN G 179 GLN H 75 ASN H 157 GLN ** H 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 ASN L 75 ASN L 156 HIS M 75 ASN N 75 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104900 restraints weight = 28012.546| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.82 r_work: 0.3514 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19460 Z= 0.119 Angle : 0.595 14.146 26369 Z= 0.299 Chirality : 0.042 0.179 3073 Planarity : 0.004 0.038 3451 Dihedral : 4.553 47.841 2714 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.50 % Allowed : 27.50 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.18), residues: 2478 helix: 2.37 (0.15), residues: 1358 sheet: 1.63 (0.34), residues: 210 loop : -0.40 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 189 HIS 0.003 0.001 HIS L 156 PHE 0.011 0.001 PHE H 104 TYR 0.015 0.001 TYR E 98 ARG 0.008 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1103) hydrogen bonds : angle 3.62455 ( 3399) covalent geometry : bond 0.00280 (19460) covalent geometry : angle 0.59469 (26369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 734 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7538 (tpt-90) REVERT: A 167 GLU cc_start: 0.8393 (tp30) cc_final: 0.8178 (tp30) REVERT: B 97 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8414 (mp10) REVERT: C 97 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8650 (mp10) REVERT: G 134 GLU cc_start: 0.8327 (pt0) cc_final: 0.8023 (pt0) REVERT: G 189 TRP cc_start: 0.8420 (m100) cc_final: 0.8046 (m100) REVERT: H 59 GLU cc_start: 0.8196 (mp0) cc_final: 0.7939 (mp0) REVERT: H 87 MET cc_start: 0.6833 (mpt) cc_final: 0.6408 (mpt) REVERT: H 104 PHE cc_start: 0.4376 (OUTLIER) cc_final: 0.3954 (m-80) REVERT: H 179 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7941 (tmm-80) REVERT: H 208 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6384 (mt) REVERT: I 104 PHE cc_start: 0.4591 (OUTLIER) cc_final: 0.3664 (m-80) REVERT: K 104 PHE cc_start: 0.4487 (OUTLIER) cc_final: 0.3869 (m-80) REVERT: K 204 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7935 (tm-30) REVERT: L 59 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: L 60 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: L 128 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: L 135 VAL cc_start: 0.6819 (t) cc_final: 0.6550 (p) REVERT: M 60 GLU cc_start: 0.7992 (mp0) cc_final: 0.7709 (mp0) REVERT: M 104 PHE cc_start: 0.4294 (OUTLIER) cc_final: 0.3080 (m-80) REVERT: M 181 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8438 (ttt180) REVERT: N 59 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: N 164 ARG cc_start: 0.5424 (OUTLIER) cc_final: 0.5046 (ttm110) outliers start: 92 outliers final: 55 residues processed: 771 average time/residue: 1.2905 time to fit residues: 1115.1238 Evaluate side-chains 788 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 719 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 0.0040 chunk 166 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 132 ASN A 171 GLN A 179 GLN B 58 ASN B 171 GLN B 179 GLN C 63 GLN C 132 ASN C 138 HIS C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 132 ASN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 171 GLN G 179 GLN H 157 GLN H 222 GLN I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 156 HIS M 75 ASN N 75 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.112787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103553 restraints weight = 28103.513| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.78 r_work: 0.3498 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19460 Z= 0.141 Angle : 0.623 11.704 26369 Z= 0.312 Chirality : 0.043 0.159 3073 Planarity : 0.005 0.038 3451 Dihedral : 4.596 50.591 2713 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.60 % Allowed : 28.42 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.18), residues: 2478 helix: 2.29 (0.15), residues: 1365 sheet: 1.34 (0.34), residues: 217 loop : -0.38 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 189 HIS 0.004 0.001 HIS D 138 PHE 0.015 0.001 PHE N 104 TYR 0.016 0.001 TYR E 98 ARG 0.009 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 1103) hydrogen bonds : angle 3.66049 ( 3399) covalent geometry : bond 0.00341 (19460) covalent geometry : angle 0.62273 (26369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 731 time to evaluate : 1.992 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: A 44 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7601 (tpt-90) REVERT: A 167 GLU cc_start: 0.8395 (tp30) cc_final: 0.8186 (tp30) REVERT: B 97 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8435 (mp10) REVERT: C 97 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8644 (mp10) REVERT: D 205 MET cc_start: 0.8056 (pmm) cc_final: 0.7844 (pmm) REVERT: G 134 GLU cc_start: 0.8434 (pt0) cc_final: 0.7838 (pt0) REVERT: G 189 TRP cc_start: 0.8432 (m100) cc_final: 0.7950 (m100) REVERT: H 59 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: H 87 MET cc_start: 0.6892 (mpt) cc_final: 0.6617 (mpt) REVERT: H 104 PHE cc_start: 0.4452 (OUTLIER) cc_final: 0.3951 (m-80) REVERT: H 179 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7988 (tmm-80) REVERT: H 208 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6352 (mt) REVERT: I 59 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: I 104 PHE cc_start: 0.4664 (OUTLIER) cc_final: 0.3620 (m-80) REVERT: J 85 GLU cc_start: 0.6440 (tt0) cc_final: 0.6211 (tt0) REVERT: J 181 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8204 (ttm-80) REVERT: K 104 PHE cc_start: 0.4568 (OUTLIER) cc_final: 0.3826 (m-80) REVERT: K 204 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7958 (tm-30) REVERT: L 59 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: L 60 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: L 128 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: L 135 VAL cc_start: 0.6842 (t) cc_final: 0.6561 (p) REVERT: M 60 GLU cc_start: 0.8052 (mp0) cc_final: 0.7773 (mp0) REVERT: M 104 PHE cc_start: 0.4244 (OUTLIER) cc_final: 0.3466 (m-80) REVERT: N 59 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: N 122 GLN cc_start: 0.7856 (tp40) cc_final: 0.7593 (tp40) REVERT: N 164 ARG cc_start: 0.5567 (OUTLIER) cc_final: 0.5186 (ttm110) outliers start: 94 outliers final: 55 residues processed: 766 average time/residue: 1.2990 time to fit residues: 1112.8439 Evaluate side-chains 800 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 728 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 64 optimal weight: 0.6980 chunk 219 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 132 ASN A 171 GLN A 179 GLN B 58 ASN B 179 GLN C 58 ASN C 63 GLN C 80 ASN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 132 ASN F 35 GLN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 171 GLN G 179 GLN H 75 ASN H 98 ASN ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN K 75 ASN L 75 ASN L 156 HIS M 75 ASN N 75 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.113928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104799 restraints weight = 28273.052| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.80 r_work: 0.3504 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19460 Z= 0.127 Angle : 0.623 12.662 26369 Z= 0.311 Chirality : 0.042 0.154 3073 Planarity : 0.004 0.042 3451 Dihedral : 4.548 50.454 2713 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.60 % Allowed : 28.91 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.18), residues: 2478 helix: 2.39 (0.15), residues: 1358 sheet: 1.57 (0.34), residues: 210 loop : -0.36 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 189 HIS 0.004 0.001 HIS D 138 PHE 0.012 0.001 PHE H 104 TYR 0.013 0.001 TYR A 98 ARG 0.011 0.001 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 1103) hydrogen bonds : angle 3.61522 ( 3399) covalent geometry : bond 0.00304 (19460) covalent geometry : angle 0.62302 (26369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 734 time to evaluate : 2.028 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: A 44 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7532 (tpt-90) REVERT: A 98 TYR cc_start: 0.8452 (t80) cc_final: 0.8238 (t80) REVERT: A 167 GLU cc_start: 0.8316 (tp30) cc_final: 0.8116 (tp30) REVERT: B 97 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: B 211 MET cc_start: 0.6802 (mpp) cc_final: 0.6411 (mpt) REVERT: C 97 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8627 (mp10) REVERT: D 211 MET cc_start: 0.7126 (ttp) cc_final: 0.6566 (ttm) REVERT: E 179 GLN cc_start: 0.8400 (tp40) cc_final: 0.8184 (tp-100) REVERT: G 134 GLU cc_start: 0.8439 (pt0) cc_final: 0.7803 (pt0) REVERT: G 189 TRP cc_start: 0.8436 (m100) cc_final: 0.7962 (m100) REVERT: G 206 THR cc_start: 0.7997 (m) cc_final: 0.7762 (p) REVERT: H 59 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: H 87 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6515 (mpt) REVERT: H 104 PHE cc_start: 0.4382 (OUTLIER) cc_final: 0.4004 (m-80) REVERT: H 179 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8010 (tmm-80) REVERT: I 59 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: I 104 PHE cc_start: 0.4533 (OUTLIER) cc_final: 0.3643 (m-80) REVERT: J 181 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8105 (ttm-80) REVERT: K 104 PHE cc_start: 0.4535 (OUTLIER) cc_final: 0.3849 (m-80) REVERT: K 204 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7916 (tm-30) REVERT: L 59 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: L 60 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: L 135 VAL cc_start: 0.6845 (t) cc_final: 0.6506 (p) REVERT: M 60 GLU cc_start: 0.7948 (mp0) cc_final: 0.7676 (mp0) REVERT: M 104 PHE cc_start: 0.4322 (OUTLIER) cc_final: 0.3679 (m-80) REVERT: M 181 ARG cc_start: 0.8723 (ttp80) cc_final: 0.8439 (ttt180) REVERT: N 59 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: N 122 GLN cc_start: 0.7841 (tp40) cc_final: 0.7558 (tp40) REVERT: N 164 ARG cc_start: 0.5442 (OUTLIER) cc_final: 0.5076 (ttm110) REVERT: N 200 ARG cc_start: 0.7425 (ttm110) cc_final: 0.7213 (mtm110) outliers start: 94 outliers final: 59 residues processed: 774 average time/residue: 1.2542 time to fit residues: 1090.5709 Evaluate side-chains 791 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 716 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 58 ASN A 132 ASN A 171 GLN A 179 GLN B 58 ASN B 171 GLN B 179 GLN C 63 GLN C 80 ASN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 132 ASN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 171 GLN G 179 GLN H 98 ASN H 157 GLN I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 156 HIS L 175 ASN M 75 ASN N 75 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104528 restraints weight = 27906.733| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.82 r_work: 0.3496 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19460 Z= 0.140 Angle : 0.651 13.170 26369 Z= 0.323 Chirality : 0.043 0.160 3073 Planarity : 0.005 0.049 3451 Dihedral : 4.594 52.514 2711 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.16 % Allowed : 29.65 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.18), residues: 2478 helix: 2.29 (0.14), residues: 1365 sheet: 1.58 (0.34), residues: 210 loop : -0.30 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 189 HIS 0.012 0.001 HIS D 138 PHE 0.014 0.001 PHE H 104 TYR 0.017 0.001 TYR E 98 ARG 0.012 0.001 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 1103) hydrogen bonds : angle 3.64816 ( 3399) covalent geometry : bond 0.00340 (19460) covalent geometry : angle 0.65051 (26369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 726 time to evaluate : 2.047 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: A 44 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7579 (tpt-90) REVERT: B 97 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8460 (mp10) REVERT: B 211 MET cc_start: 0.6761 (mpp) cc_final: 0.6473 (mpt) REVERT: C 97 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8650 (mp10) REVERT: D 211 MET cc_start: 0.7099 (ttp) cc_final: 0.6555 (ttm) REVERT: E 179 GLN cc_start: 0.8375 (tp40) cc_final: 0.8131 (tp-100) REVERT: G 134 GLU cc_start: 0.8495 (pt0) cc_final: 0.7640 (pt0) REVERT: G 189 TRP cc_start: 0.8449 (m100) cc_final: 0.7842 (m100) REVERT: G 206 THR cc_start: 0.7972 (m) cc_final: 0.7746 (p) REVERT: H 59 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: H 87 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6575 (mpt) REVERT: H 104 PHE cc_start: 0.4376 (OUTLIER) cc_final: 0.3982 (m-80) REVERT: H 179 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7962 (tmm-80) REVERT: I 59 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: I 104 PHE cc_start: 0.4604 (OUTLIER) cc_final: 0.3741 (m-80) REVERT: J 181 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8232 (ttm-80) REVERT: K 104 PHE cc_start: 0.4440 (OUTLIER) cc_final: 0.3767 (m-80) REVERT: K 204 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7988 (tm-30) REVERT: L 59 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: L 60 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: L 135 VAL cc_start: 0.6834 (t) cc_final: 0.6534 (p) REVERT: L 181 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8440 (ttt90) REVERT: M 60 GLU cc_start: 0.8051 (mp0) cc_final: 0.7759 (mp0) REVERT: M 104 PHE cc_start: 0.4439 (OUTLIER) cc_final: 0.3815 (m-80) REVERT: N 59 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: N 122 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7674 (tp40) REVERT: N 164 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.5191 (ttm110) outliers start: 85 outliers final: 58 residues processed: 759 average time/residue: 1.3110 time to fit residues: 1113.4940 Evaluate side-chains 801 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 725 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 122 GLN Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 132 ASN A 171 GLN A 179 GLN B 58 ASN B 179 GLN C 58 ASN C 63 GLN C 80 ASN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 171 GLN G 179 GLN H 98 ASN ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 156 HIS L 175 ASN M 75 ASN N 75 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.113490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104049 restraints weight = 27922.781| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.82 r_work: 0.3502 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19460 Z= 0.143 Angle : 0.678 13.547 26369 Z= 0.335 Chirality : 0.043 0.190 3073 Planarity : 0.005 0.051 3451 Dihedral : 4.624 53.029 2711 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.40 % Allowed : 29.79 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.17), residues: 2478 helix: 2.23 (0.14), residues: 1365 sheet: 1.59 (0.34), residues: 210 loop : -0.30 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 189 HIS 0.015 0.001 HIS D 138 PHE 0.014 0.001 PHE H 104 TYR 0.012 0.001 TYR D 98 ARG 0.011 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 1103) hydrogen bonds : angle 3.71621 ( 3399) covalent geometry : bond 0.00345 (19460) covalent geometry : angle 0.67781 (26369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 727 time to evaluate : 2.253 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: A 44 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7579 (tpt-90) REVERT: B 211 MET cc_start: 0.6632 (mpp) cc_final: 0.6411 (mpt) REVERT: C 97 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8661 (mp10) REVERT: D 205 MET cc_start: 0.7926 (pmm) cc_final: 0.7705 (pmm) REVERT: D 211 MET cc_start: 0.7092 (ttp) cc_final: 0.6506 (ttm) REVERT: G 134 GLU cc_start: 0.8466 (pt0) cc_final: 0.7589 (pt0) REVERT: G 189 TRP cc_start: 0.8455 (m100) cc_final: 0.7830 (m100) REVERT: H 59 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: H 87 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6528 (mpt) REVERT: H 104 PHE cc_start: 0.4489 (OUTLIER) cc_final: 0.4121 (m-80) REVERT: H 126 MET cc_start: 0.6737 (tpt) cc_final: 0.6349 (tpt) REVERT: H 152 ARG cc_start: 0.7292 (mtp85) cc_final: 0.7037 (mtp85) REVERT: H 176 GLU cc_start: 0.8329 (tp30) cc_final: 0.8098 (tp30) REVERT: H 179 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7955 (tmm-80) REVERT: I 59 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: I 78 MET cc_start: 0.7522 (ptp) cc_final: 0.7235 (ptp) REVERT: I 104 PHE cc_start: 0.4587 (OUTLIER) cc_final: 0.3730 (m-80) REVERT: I 135 VAL cc_start: 0.6550 (t) cc_final: 0.6249 (p) REVERT: J 181 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8131 (ttm-80) REVERT: K 104 PHE cc_start: 0.4577 (OUTLIER) cc_final: 0.3891 (m-80) REVERT: L 59 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: L 60 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: L 135 VAL cc_start: 0.6817 (t) cc_final: 0.6518 (p) REVERT: L 181 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8446 (ttt90) REVERT: M 60 GLU cc_start: 0.8077 (mp0) cc_final: 0.7777 (mp0) REVERT: M 104 PHE cc_start: 0.4242 (OUTLIER) cc_final: 0.3608 (m-80) REVERT: N 59 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: N 164 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.5187 (ttm110) outliers start: 90 outliers final: 61 residues processed: 767 average time/residue: 1.5348 time to fit residues: 1321.2808 Evaluate side-chains 795 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 718 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 132 ASN A 171 GLN A 179 GLN B 58 ASN B 179 GLN C 63 GLN C 80 ASN C 179 GLN D 58 ASN D 179 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 179 GLN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 171 GLN G 179 GLN I 75 ASN K 75 ASN L 75 ASN L 156 HIS L 175 ASN M 75 ASN N 75 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.113025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103579 restraints weight = 28042.089| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.82 r_work: 0.3481 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19460 Z= 0.151 Angle : 0.690 13.433 26369 Z= 0.343 Chirality : 0.044 0.193 3073 Planarity : 0.005 0.045 3451 Dihedral : 4.672 54.089 2711 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.96 % Allowed : 30.68 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.17), residues: 2478 helix: 2.17 (0.14), residues: 1365 sheet: 1.59 (0.34), residues: 210 loop : -0.32 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 189 HIS 0.006 0.001 HIS D 138 PHE 0.015 0.002 PHE H 104 TYR 0.019 0.001 TYR E 98 ARG 0.007 0.001 ARG H 91 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 1103) hydrogen bonds : angle 3.74179 ( 3399) covalent geometry : bond 0.00365 (19460) covalent geometry : angle 0.68998 (26369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21978.58 seconds wall clock time: 378 minutes 13.86 seconds (22693.86 seconds total)