Starting phenix.real_space_refine on Wed Jan 22 15:19:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xn4_38497/01_2025/8xn4_38497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xn4_38497/01_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_38497/01_2025/8xn4_38497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xn4_38497/01_2025/8xn4_38497.map" model { file = "/net/cci-nas-00/data/ceres_data/8xn4_38497/01_2025/8xn4_38497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xn4_38497/01_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 10.95, per 1000 atoms: 0.57 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: 4.97 Conformation dependent library (CDL) restraints added in 2.9 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: 2.78 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: 7.24 Time building geometry restraints manager: 5.77 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 44.570 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.460 ------------------------------------------------------------------------------- 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= 0.316 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 *********************** 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 : 2.234 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: 1.3663 time to fit residues: 1213.3267 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 : 2.044 ------------------------------------------------------------------------------- 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 = 28054.383| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.80 r_work: 0.3500 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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= 0.185 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 *********************** 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 : 2.127 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: 0.7799 (OUTLIER) cc_final: 0.7567 (tpt-90) REVERT: A 167 GLU cc_start: 0.8327 (tp30) cc_final: 0.8106 (tp30) REVERT: B 97 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8386 (mp10) REVERT: F 134 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8319 (tm-30) REVERT: H 59 GLU cc_start: 0.8214 (mp0) cc_final: 0.7973 (mp0) REVERT: J 152 ARG cc_start: 0.6556 (ptm160) cc_final: 0.5850 (ptm160) REVERT: J 204 GLU cc_start: 0.8158 (tp30) cc_final: 0.7957 (tp30) REVERT: K 104 PHE cc_start: 0.4155 (OUTLIER) cc_final: 0.3327 (m-80) REVERT: K 180 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7805 (mtp) REVERT: L 59 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8245 (mm-30) REVERT: L 60 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: L 122 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: M 60 GLU cc_start: 0.7798 (mp0) cc_final: 0.7542 (mp0) REVERT: M 146 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7969 (mpt) REVERT: M 152 ARG cc_start: 0.6405 (ptm160) cc_final: 0.5133 (ptm160) outliers start: 111 outliers final: 43 residues processed: 801 average time/residue: 1.3115 time to fit residues: 1180.7887 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 : 2.052 ------------------------------------------------------------------------------- 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: 0.0070 chunk 90 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 179 GLN C 58 ASN C 63 GLN C 138 HIS C 139 GLN C 179 GLN D 58 ASN D 138 HIS D 139 GLN D 179 GLN E 58 ASN E 63 GLN E 132 ASN E 138 HIS F 35 GLN 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 L 175 ASN M 75 ASN M 98 ASN N 75 ASN N 115 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.115682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.106410 restraints weight = 27863.745| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.82 r_work: 0.3524 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19460 Z= 0.158 Angle : 0.549 8.960 26369 Z= 0.280 Chirality : 0.041 0.152 3073 Planarity : 0.005 0.046 3451 Dihedral : 5.152 56.397 2728 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.31 % Allowed : 26.57 % 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: 2.02 (0.18), residues: 2478 helix: 2.40 (0.15), residues: 1358 sheet: 1.74 (0.34), residues: 217 loop : -0.44 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 189 HIS 0.004 0.001 HIS E 138 PHE 0.008 0.001 PHE I 58 TYR 0.010 0.001 TYR G 98 ARG 0.005 0.000 ARG H 152 *********************** 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 829 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 741 time to evaluate : 2.095 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: 0.7768 (OUTLIER) cc_final: 0.7450 (tpt-90) REVERT: A 134 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7190 (pp20) REVERT: A 167 GLU cc_start: 0.8369 (tp30) cc_final: 0.8135 (tp30) REVERT: A 189 TRP cc_start: 0.8173 (m100) cc_final: 0.7868 (m100) REVERT: C 97 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8634 (mp10) REVERT: D 179 GLN cc_start: 0.8996 (tp40) cc_final: 0.8749 (mm-40) REVERT: E 189 TRP cc_start: 0.8359 (m100) cc_final: 0.8077 (m100) REVERT: H 59 GLU cc_start: 0.8204 (mp0) cc_final: 0.7944 (mp0) REVERT: H 124 VAL cc_start: 0.8478 (m) cc_final: 0.8176 (t) REVERT: H 152 ARG cc_start: 0.6721 (mtp85) cc_final: 0.6489 (mtp85) REVERT: I 181 ARG cc_start: 0.8445 (ttt90) cc_final: 0.8024 (ttt180) REVERT: J 157 GLN cc_start: 0.8630 (pt0) cc_final: 0.8388 (pt0) REVERT: J 200 ARG cc_start: 0.7918 (mtm180) cc_final: 0.7680 (mtm180) REVERT: K 104 PHE cc_start: 0.4128 (OUTLIER) cc_final: 0.3251 (m-80) REVERT: K 200 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7443 (ttp-110) REVERT: L 59 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8281 (mm-30) REVERT: L 135 VAL cc_start: 0.6728 (t) cc_final: 0.6491 (p) REVERT: L 223 VAL cc_start: 0.8779 (t) cc_final: 0.8573 (p) REVERT: M 60 GLU cc_start: 0.7841 (mp0) cc_final: 0.7552 (mp0) REVERT: M 152 ARG cc_start: 0.6410 (ptm160) cc_final: 0.5205 (ptm160) REVERT: N 59 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: N 181 ARG cc_start: 0.8672 (tmm-80) cc_final: 0.8410 (ttt180) outliers start: 88 outliers final: 42 residues processed: 786 average time/residue: 1.2619 time to fit residues: 1114.8104 Evaluate side-chains 772 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 723 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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 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 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain F residue 191 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 78 MET 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 108 THR Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J 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 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 107 LEU 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 62 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain M residue 179 ARG 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 141 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 35 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 210 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 58 ASN C 138 HIS C 179 GLN D 58 ASN E 58 ASN E 132 ASN E 138 HIS F 35 GLN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 58 ASN G 132 ASN G 171 GLN H 157 GLN I 75 ASN K 75 ASN K 98 ASN K 222 GLN L 75 ASN L 98 ASN ** L 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN N 115 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.109512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100244 restraints weight = 28011.310| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.78 r_work: 0.3424 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19460 Z= 0.378 Angle : 0.661 11.641 26369 Z= 0.341 Chirality : 0.045 0.159 3073 Planarity : 0.005 0.042 3451 Dihedral : 5.158 50.721 2719 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.63 % Allowed : 25.83 % Favored : 68.54 % 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: 1.70 (0.17), residues: 2478 helix: 2.14 (0.14), residues: 1358 sheet: 1.58 (0.34), residues: 217 loop : -0.57 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 189 HIS 0.005 0.001 HIS A 138 PHE 0.019 0.002 PHE N 104 TYR 0.017 0.002 TYR I 54 ARG 0.008 0.001 ARG H 152 *********************** 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 870 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 755 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7278 (tpt-90) REVERT: A 74 ASP cc_start: 0.8307 (m-30) cc_final: 0.7947 (m-30) REVERT: A 97 GLN cc_start: 0.9075 (tp40) cc_final: 0.8811 (mm-40) REVERT: A 134 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: A 189 TRP cc_start: 0.8302 (m100) cc_final: 0.7928 (m100) REVERT: B 97 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8500 (mp10) REVERT: C 97 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8666 (mp10) REVERT: D 179 GLN cc_start: 0.9057 (tp40) cc_final: 0.8804 (mm-40) REVERT: H 59 GLU cc_start: 0.8373 (mp0) cc_final: 0.8099 (mp0) REVERT: H 104 PHE cc_start: 0.4348 (OUTLIER) cc_final: 0.3185 (m-80) REVERT: H 146 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.6366 (mpt) REVERT: H 152 ARG cc_start: 0.7402 (mtp85) cc_final: 0.7072 (mtp85) REVERT: H 208 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6701 (mt) REVERT: I 104 PHE cc_start: 0.4562 (OUTLIER) cc_final: 0.3653 (m-80) REVERT: J 61 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7941 (mtp-110) REVERT: J 104 PHE cc_start: 0.4774 (OUTLIER) cc_final: 0.4153 (m-80) REVERT: J 146 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7438 (mpt) REVERT: J 200 ARG cc_start: 0.7964 (mtm180) cc_final: 0.7727 (mtm180) REVERT: K 104 PHE cc_start: 0.4598 (OUTLIER) cc_final: 0.3905 (m-80) REVERT: K 122 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6741 (tp-100) REVERT: K 146 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.6899 (mpt) REVERT: K 185 GLU cc_start: 0.7755 (tt0) cc_final: 0.7279 (tt0) REVERT: L 59 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8262 (mm-30) REVERT: L 60 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: L 87 MET cc_start: 0.6197 (mpt) cc_final: 0.5812 (mpt) REVERT: L 135 VAL cc_start: 0.6827 (t) cc_final: 0.6556 (p) REVERT: N 59 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: N 75 ASN cc_start: 0.8628 (m-40) cc_final: 0.8381 (m110) REVERT: N 181 ARG cc_start: 0.8663 (tmm-80) cc_final: 0.8448 (ttt180) REVERT: N 200 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7777 (ttm110) outliers start: 115 outliers final: 48 residues processed: 809 average time/residue: 1.3236 time to fit residues: 1198.8639 Evaluate side-chains 813 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 748 time to evaluate : 2.467 ------------------------------------------------------------------------------- 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 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 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 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 104 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 122 GLN 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 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 194 THR 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 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 117 VAL 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 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 167 VAL 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: 0.8980 chunk 26 optimal weight: 4.9990 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: 1.9990 chunk 134 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 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 138 HIS G 179 GLN H 98 ASN H 157 GLN I 75 ASN K 75 ASN L 75 ASN ** L 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3724 r_free = 0.3724 target = 0.112229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.102991 restraints weight = 28321.546| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.79 r_work: 0.3478 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19460 Z= 0.211 Angle : 0.608 10.273 26369 Z= 0.308 Chirality : 0.042 0.156 3073 Planarity : 0.005 0.041 3451 Dihedral : 4.772 48.016 2717 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.60 % Allowed : 27.15 % Favored : 68.25 % 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 (0.18), residues: 2478 helix: 2.29 (0.15), residues: 1358 sheet: 1.48 (0.34), residues: 217 loop : -0.53 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 189 HIS 0.002 0.001 HIS D 138 PHE 0.012 0.001 PHE N 104 TYR 0.011 0.001 TYR B 98 ARG 0.008 0.001 ARG H 152 *********************** 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 826 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 732 time to evaluate : 2.402 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: 0.7814 (OUTLIER) cc_final: 0.7574 (tpt-90) REVERT: A 167 GLU cc_start: 0.8384 (tp30) cc_final: 0.8174 (tp30) REVERT: B 97 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8428 (mp10) REVERT: C 97 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8670 (mp10) REVERT: E 211 MET cc_start: 0.6893 (mtp) cc_final: 0.6686 (mtt) REVERT: G 189 TRP cc_start: 0.8487 (m100) cc_final: 0.7894 (m100) REVERT: H 59 GLU cc_start: 0.8244 (mp0) cc_final: 0.7985 (mp0) REVERT: H 104 PHE cc_start: 0.4510 (OUTLIER) cc_final: 0.3451 (m-80) REVERT: H 179 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7934 (tmm-80) REVERT: H 208 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6568 (mt) REVERT: I 104 PHE cc_start: 0.4621 (OUTLIER) cc_final: 0.3841 (m-80) REVERT: J 104 PHE cc_start: 0.4857 (OUTLIER) cc_final: 0.4462 (m-80) REVERT: K 104 PHE cc_start: 0.4508 (OUTLIER) cc_final: 0.3840 (m-80) REVERT: L 59 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: L 60 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: L 87 MET cc_start: 0.6072 (OUTLIER) cc_final: 0.5736 (mpt) REVERT: L 135 VAL cc_start: 0.6803 (t) cc_final: 0.6553 (p) REVERT: L 161 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: M 60 GLU cc_start: 0.7986 (mp0) cc_final: 0.7676 (mp0) REVERT: N 59 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: N 200 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7441 (ttm110) outliers start: 94 outliers final: 46 residues processed: 773 average time/residue: 1.3695 time to fit residues: 1180.9532 Evaluate side-chains 779 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 719 time to evaluate : 2.080 ------------------------------------------------------------------------------- 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 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 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 F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 206 THR 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 H residue 208 ILE 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 104 PHE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 128 GLN 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 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 161 GLU Chi-restraints excluded: chain L residue 185 GLU Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain M residue 128 GLN 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 141 THR 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: 3.9990 chunk 90 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 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 50 GLN G 58 ASN G 138 HIS G 179 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.112739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103511 restraints weight = 28369.141| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.80 r_work: 0.3485 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19460 Z= 0.201 Angle : 0.599 14.983 26369 Z= 0.302 Chirality : 0.042 0.153 3073 Planarity : 0.005 0.037 3451 Dihedral : 4.645 49.502 2716 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.06 % Allowed : 27.89 % Favored : 68.05 % 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: 1.95 (0.18), residues: 2478 helix: 2.36 (0.15), residues: 1358 sheet: 1.60 (0.34), residues: 210 loop : -0.45 (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 G 138 PHE 0.012 0.001 PHE N 104 TYR 0.015 0.001 TYR E 98 ARG 0.008 0.000 ARG B 182 *********************** 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 816 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 733 time to evaluate : 2.127 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: 0.7590 (tpt-90) REVERT: A 167 GLU cc_start: 0.8358 (tp30) cc_final: 0.8147 (tp30) REVERT: B 97 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8459 (mp10) REVERT: C 97 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8642 (mp10) REVERT: E 211 MET cc_start: 0.6917 (mtp) cc_final: 0.6709 (mtt) REVERT: G 189 TRP cc_start: 0.8402 (m100) cc_final: 0.7959 (m100) REVERT: H 59 GLU cc_start: 0.8203 (mp0) cc_final: 0.7952 (mp0) REVERT: H 179 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7913 (tmm-80) REVERT: I 104 PHE cc_start: 0.4625 (OUTLIER) cc_final: 0.3734 (m-80) REVERT: J 104 PHE cc_start: 0.4855 (OUTLIER) cc_final: 0.4475 (m-80) REVERT: J 202 ASP cc_start: 0.8782 (m-30) cc_final: 0.8521 (m-30) REVERT: K 104 PHE cc_start: 0.4502 (OUTLIER) cc_final: 0.3814 (m-80) REVERT: K 126 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8657 (pp-130) REVERT: K 204 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7946 (tm-30) REVERT: L 59 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: L 60 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: L 87 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5810 (mpt) REVERT: L 128 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: L 135 VAL cc_start: 0.6745 (t) cc_final: 0.6494 (p) REVERT: M 60 GLU cc_start: 0.8006 (mp0) cc_final: 0.7729 (mp0) REVERT: M 104 PHE cc_start: 0.4312 (OUTLIER) cc_final: 0.3083 (m-80) REVERT: M 181 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8458 (ttt180) REVERT: N 59 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7998 (mp0) outliers start: 83 outliers final: 45 residues processed: 765 average time/residue: 1.3625 time to fit residues: 1169.0149 Evaluate side-chains 781 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 722 time to evaluate : 2.255 ------------------------------------------------------------------------------- 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 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 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 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 117 VAL 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 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 104 PHE Chi-restraints excluded: chain J residue 128 GLN 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 126 MET 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 225 SER Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 128 GLN 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 141 THR 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: 3.9990 chunk 166 optimal weight: 0.2980 chunk 231 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 50 GLN G 58 ASN G 138 HIS G 179 GLN H 75 ASN H 98 ASN 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: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105883 restraints weight = 28000.644| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.82 r_work: 0.3516 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2258 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= 0.171 Angle : 0.597 12.060 26369 Z= 0.298 Chirality : 0.041 0.148 3073 Planarity : 0.004 0.038 3451 Dihedral : 4.459 49.416 2713 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.11 % Allowed : 28.77 % Favored : 67.12 % 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: 2.05 (0.18), residues: 2478 helix: 2.45 (0.15), residues: 1358 sheet: 1.44 (0.34), residues: 217 loop : -0.39 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 189 HIS 0.004 0.001 HIS G 138 PHE 0.009 0.001 PHE N 104 TYR 0.010 0.001 TYR G 98 ARG 0.009 0.000 ARG B 182 *********************** 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 819 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 735 time to evaluate : 2.215 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: 0.7766 (OUTLIER) cc_final: 0.7474 (tpt-90) REVERT: A 167 GLU cc_start: 0.8390 (tp30) cc_final: 0.8163 (tp30) REVERT: C 97 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8659 (mp10) REVERT: D 211 MET cc_start: 0.7321 (ttp) cc_final: 0.6874 (ttm) REVERT: E 179 GLN cc_start: 0.8381 (tp40) cc_final: 0.8157 (tp-100) REVERT: E 211 MET cc_start: 0.6982 (mtp) cc_final: 0.6762 (mtt) REVERT: G 189 TRP cc_start: 0.8347 (m100) cc_final: 0.8131 (m100) REVERT: H 59 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: H 87 MET cc_start: 0.6556 (mpt) cc_final: 0.6316 (mpt) REVERT: I 104 PHE cc_start: 0.4616 (OUTLIER) cc_final: 0.3803 (m-80) REVERT: J 104 PHE cc_start: 0.4712 (OUTLIER) cc_final: 0.4378 (m-80) REVERT: K 104 PHE cc_start: 0.4541 (OUTLIER) cc_final: 0.3919 (m-80) REVERT: K 204 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7956 (tm-30) REVERT: L 59 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: L 60 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: L 87 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5803 (mpt) REVERT: L 135 VAL cc_start: 0.6773 (t) cc_final: 0.6488 (p) REVERT: M 60 GLU cc_start: 0.7978 (mp0) cc_final: 0.7698 (mp0) REVERT: M 78 MET cc_start: 0.7392 (ptm) cc_final: 0.7101 (ptm) REVERT: M 104 PHE cc_start: 0.4318 (OUTLIER) cc_final: 0.3606 (m-80) REVERT: M 181 ARG cc_start: 0.8710 (ttp80) cc_final: 0.8420 (ttt180) REVERT: M 204 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8051 (tm-30) REVERT: N 59 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: N 164 ARG cc_start: 0.5550 (OUTLIER) cc_final: 0.5216 (ttm110) outliers start: 84 outliers final: 50 residues processed: 771 average time/residue: 1.3195 time to fit residues: 1138.7513 Evaluate side-chains 793 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 731 time to evaluate : 2.241 ------------------------------------------------------------------------------- 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 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 170 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 134 GLU Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 203 ASP 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 78 MET Chi-restraints excluded: chain H residue 108 THR 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 185 GLU Chi-restraints excluded: chain H residue 227 ARG 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 104 PHE Chi-restraints excluded: chain J residue 126 MET 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 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 103 SER 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 225 SER 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 141 THR Chi-restraints excluded: chain N residue 160 SER 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: 0.9990 chunk 219 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 242 optimal weight: 0.5980 chunk 234 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 58 ASN B 171 GLN B 179 GLN C 58 ASN C 138 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 50 GLN G 58 ASN G 138 HIS G 171 GLN G 179 GLN H 98 ASN I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 98 ASN L 156 HIS L 175 ASN N 75 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.115687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.106255 restraints weight = 28164.845| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.84 r_work: 0.3523 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19460 Z= 0.179 Angle : 0.627 13.228 26369 Z= 0.307 Chirality : 0.042 0.150 3073 Planarity : 0.004 0.038 3451 Dihedral : 4.405 50.795 2713 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.31 % Allowed : 29.26 % Favored : 66.44 % 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: 2.14 (0.18), residues: 2478 helix: 2.49 (0.15), residues: 1358 sheet: 1.65 (0.34), residues: 210 loop : -0.30 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 189 HIS 0.011 0.001 HIS D 138 PHE 0.013 0.001 PHE B 190 TYR 0.015 0.001 TYR C 98 ARG 0.010 0.001 ARG B 182 *********************** 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 831 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 743 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7472 (tpt-90) REVERT: A 167 GLU cc_start: 0.8420 (tp30) cc_final: 0.8190 (tp30) REVERT: B 97 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8424 (mp10) REVERT: B 183 ASP cc_start: 0.8541 (m-30) cc_final: 0.8265 (OUTLIER) REVERT: B 211 MET cc_start: 0.6809 (mpp) cc_final: 0.6551 (mpt) REVERT: C 97 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8663 (mp10) REVERT: D 211 MET cc_start: 0.7275 (ttp) cc_final: 0.6838 (ttm) REVERT: H 59 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: H 87 MET cc_start: 0.6654 (mpt) cc_final: 0.6400 (mpt) REVERT: H 227 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5652 (tpt90) REVERT: I 59 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: I 104 PHE cc_start: 0.4576 (OUTLIER) cc_final: 0.3726 (m-80) REVERT: J 104 PHE cc_start: 0.4670 (OUTLIER) cc_final: 0.4296 (m-80) REVERT: J 181 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8235 (ttm-80) REVERT: K 104 PHE cc_start: 0.4503 (OUTLIER) cc_final: 0.3898 (m-80) REVERT: K 204 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7917 (tm-30) REVERT: L 59 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: L 60 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: L 87 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5840 (mpt) REVERT: L 135 VAL cc_start: 0.6788 (t) cc_final: 0.6508 (p) REVERT: M 60 GLU cc_start: 0.7991 (mp0) cc_final: 0.7691 (mp0) REVERT: M 104 PHE cc_start: 0.4299 (OUTLIER) cc_final: 0.3774 (m-80) REVERT: M 146 MET cc_start: 0.8686 (mpt) cc_final: 0.7880 (mpt) REVERT: M 181 ARG cc_start: 0.8722 (ttp80) cc_final: 0.8435 (ttt180) REVERT: M 204 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8083 (tm-30) REVERT: N 59 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: N 85 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.5266 (mp0) REVERT: N 122 GLN cc_start: 0.7868 (tp40) cc_final: 0.7548 (tp40) outliers start: 88 outliers final: 50 residues processed: 779 average time/residue: 1.2991 time to fit residues: 1133.7556 Evaluate side-chains 782 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 717 time to evaluate : 2.182 ------------------------------------------------------------------------------- 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 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 F residue 39 ARG 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 G residue 116 GLN Chi-restraints excluded: chain G residue 137 ILE 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 108 THR 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 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 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE 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 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 103 SER 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 208 ILE Chi-restraints excluded: chain L residue 223 VAL 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 85 GLU Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 167 VAL 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: 3.9990 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 13 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 58 ASN B 171 GLN B 179 GLN C 58 ASN C 138 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 132 ASN E 171 GLN E 179 GLN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 138 HIS G 171 GLN G 179 GLN H 98 ASN ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN I 157 GLN K 98 ASN L 75 ASN L 98 ASN L 156 HIS L 175 ASN N 75 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.116824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107505 restraints weight = 28116.401| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.83 r_work: 0.3543 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19460 Z= 0.175 Angle : 0.634 13.229 26369 Z= 0.310 Chirality : 0.042 0.156 3073 Planarity : 0.004 0.045 3451 Dihedral : 4.352 50.699 2711 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.82 % Allowed : 30.53 % Favored : 65.66 % 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: 2.22 (0.18), residues: 2478 helix: 2.53 (0.15), residues: 1358 sheet: 1.72 (0.34), residues: 210 loop : -0.24 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 189 HIS 0.015 0.001 HIS D 138 PHE 0.013 0.001 PHE B 190 TYR 0.017 0.001 TYR E 98 ARG 0.010 0.001 ARG B 182 *********************** 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: 78 poor density : 733 time to evaluate : 2.215 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: A 44 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7384 (tpt-90) REVERT: A 73 LYS cc_start: 0.8988 (mttm) cc_final: 0.8755 (mtpp) REVERT: A 98 TYR cc_start: 0.8451 (t80) cc_final: 0.8243 (t80) REVERT: A 167 GLU cc_start: 0.8369 (tp30) cc_final: 0.8148 (tp30) REVERT: D 211 MET cc_start: 0.7240 (ttp) cc_final: 0.6807 (ttm) REVERT: E 189 TRP cc_start: 0.8456 (m100) cc_final: 0.8161 (m100) REVERT: H 59 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: H 87 MET cc_start: 0.6609 (mpt) cc_final: 0.6372 (mpt) REVERT: H 227 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5626 (tpt90) REVERT: I 59 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: I 104 PHE cc_start: 0.4497 (OUTLIER) cc_final: 0.3720 (m-80) REVERT: J 104 PHE cc_start: 0.4708 (OUTLIER) cc_final: 0.4322 (m-80) REVERT: J 181 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8213 (ttm-80) REVERT: J 202 ASP cc_start: 0.8765 (m-30) cc_final: 0.8498 (m-30) REVERT: K 104 PHE cc_start: 0.4461 (OUTLIER) cc_final: 0.3915 (m-80) REVERT: K 204 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7931 (tm-30) REVERT: L 59 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: L 60 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: L 87 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5804 (mpt) REVERT: L 135 VAL cc_start: 0.6635 (t) cc_final: 0.6385 (p) REVERT: M 60 GLU cc_start: 0.7973 (mp0) cc_final: 0.7680 (mp0) REVERT: M 104 PHE cc_start: 0.4136 (OUTLIER) cc_final: 0.3681 (m-80) REVERT: M 146 MET cc_start: 0.8650 (mpt) cc_final: 0.7792 (mpt) REVERT: M 181 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8424 (ttt180) REVERT: M 204 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8084 (tm-30) REVERT: N 59 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: N 85 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.5155 (mp0) REVERT: N 122 GLN cc_start: 0.7874 (tp40) cc_final: 0.7543 (tp40) REVERT: N 164 ARG cc_start: 0.5436 (OUTLIER) cc_final: 0.5126 (ttm110) outliers start: 78 outliers final: 47 residues processed: 764 average time/residue: 1.3328 time to fit residues: 1141.2185 Evaluate side-chains 791 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 729 time to evaluate : 2.290 ------------------------------------------------------------------------------- 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 116 GLN Chi-restraints excluded: chain B residue 197 GLU 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 F residue 39 ARG 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 G residue 116 GLN Chi-restraints excluded: chain G residue 137 ILE 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 108 THR 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 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 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE 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 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 103 SER 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 223 VAL 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 85 GLU Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL 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: 0.3980 chunk 232 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 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 171 GLN A 179 GLN B 38 ASN B 58 ASN B 171 GLN C 58 ASN C 63 GLN C 138 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 132 ASN E 179 GLN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 138 HIS G 171 GLN G 179 GLN I 75 ASN J 222 GLN K 98 ASN L 75 ASN L 128 GLN 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 = 0.3766 r_free = 0.3766 target = 0.115014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105714 restraints weight = 28303.802| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.82 r_work: 0.3522 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19460 Z= 0.207 Angle : 0.679 13.651 26369 Z= 0.331 Chirality : 0.043 0.151 3073 Planarity : 0.004 0.039 3451 Dihedral : 4.487 52.126 2711 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.57 % Allowed : 31.41 % Favored : 65.02 % 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: 2.18 (0.18), residues: 2478 helix: 2.48 (0.14), residues: 1358 sheet: 1.76 (0.34), residues: 210 loop : -0.25 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP G 189 HIS 0.015 0.001 HIS D 138 PHE 0.016 0.001 PHE B 190 TYR 0.011 0.001 TYR D 98 ARG 0.007 0.001 ARG A 182 ********************** 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 795 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 722 time to evaluate : 2.192 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: A 44 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7447 (tpt-90) REVERT: A 73 LYS cc_start: 0.8991 (mttm) cc_final: 0.8759 (mtpp) REVERT: A 167 GLU cc_start: 0.8390 (tp30) cc_final: 0.8171 (tp30) REVERT: D 211 MET cc_start: 0.7246 (ttp) cc_final: 0.6809 (ttm) REVERT: G 53 ASP cc_start: 0.7960 (p0) cc_final: 0.7757 (p0) REVERT: H 59 GLU cc_start: 0.8182 (mp0) cc_final: 0.7939 (mp0) REVERT: H 87 MET cc_start: 0.6678 (mpt) cc_final: 0.6458 (mpt) REVERT: H 179 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8008 (tmm-80) REVERT: H 227 ARG cc_start: 0.6053 (OUTLIER) cc_final: 0.5692 (tpt90) REVERT: I 59 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: I 104 PHE cc_start: 0.4555 (OUTLIER) cc_final: 0.3772 (m-80) REVERT: I 135 VAL cc_start: 0.6446 (t) cc_final: 0.6154 (p) REVERT: J 104 PHE cc_start: 0.4873 (OUTLIER) cc_final: 0.4382 (m-80) REVERT: J 181 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8240 (ttm-80) REVERT: J 202 ASP cc_start: 0.8739 (m-30) cc_final: 0.8468 (m-30) REVERT: K 104 PHE cc_start: 0.4521 (OUTLIER) cc_final: 0.3899 (m-80) REVERT: K 204 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7927 (tm-30) REVERT: L 59 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: L 60 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: L 87 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5893 (mpt) REVERT: L 135 VAL cc_start: 0.6702 (t) cc_final: 0.6430 (p) REVERT: M 60 GLU cc_start: 0.8000 (mp0) cc_final: 0.7713 (mp0) REVERT: M 104 PHE cc_start: 0.4389 (OUTLIER) cc_final: 0.3858 (m-80) REVERT: M 146 MET cc_start: 0.8663 (mpt) cc_final: 0.7886 (mpt) REVERT: M 181 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8423 (ttt180) REVERT: M 204 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8080 (tm-30) REVERT: N 59 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: N 85 GLU cc_start: 0.5706 (OUTLIER) cc_final: 0.5330 (mp0) REVERT: N 122 GLN cc_start: 0.7864 (tp40) cc_final: 0.7556 (tp40) REVERT: N 164 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.5224 (ttm110) outliers start: 73 outliers final: 47 residues processed: 749 average time/residue: 1.3321 time to fit residues: 1117.4768 Evaluate side-chains 788 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 726 time to evaluate : 2.158 ------------------------------------------------------------------------------- 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 116 GLN Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 197 GLU 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 F residue 39 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 137 ILE 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 122 GLN 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 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE 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 125 CYS 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 103 SER 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 223 VAL 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 85 GLU Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL 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: 3.9990 chunk 21 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 58 ASN C 63 GLN C 138 HIS C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 132 ASN E 171 GLN E 179 GLN F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 138 HIS G 171 GLN G 179 GLN ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 122 GLN L 128 GLN L 156 HIS L 175 ASN N 75 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.102424 restraints weight = 28044.951| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.80 r_work: 0.3461 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19460 Z= 0.292 Angle : 0.740 13.720 26369 Z= 0.364 Chirality : 0.045 0.162 3073 Planarity : 0.005 0.039 3451 Dihedral : 4.787 56.086 2711 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.62 % Allowed : 31.75 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.94 (0.17), residues: 2478 helix: 2.29 (0.14), residues: 1358 sheet: 1.63 (0.34), residues: 210 loop : -0.36 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP G 189 HIS 0.014 0.001 HIS D 138 PHE 0.022 0.002 PHE B 190 TYR 0.018 0.001 TYR E 98 ARG 0.008 0.001 ARG M 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21076.43 seconds wall clock time: 370 minutes 40.95 seconds (22240.95 seconds total)