Starting phenix.real_space_refine on Mon Jun 9 06:14:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6f_28882/06_2025/8f6f_28882.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6f_28882/06_2025/8f6f_28882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6f_28882/06_2025/8f6f_28882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6f_28882/06_2025/8f6f_28882.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6f_28882/06_2025/8f6f_28882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6f_28882/06_2025/8f6f_28882.cif" } resolution = 3.6 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= 0.001 sd= 0.061 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 28 5.16 5 C 6608 2.51 5 N 1736 2.21 5 O 1966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10344 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2150 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 1 Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1545 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 189} Chain breaks: 3 Chain: "B" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2150 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 1 Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1545 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 189} Chain breaks: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.33, per 1000 atoms: 0.71 Number of scatterers: 10344 At special positions: 0 Unit cell: (72.293, 156.455, 146.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 28 16.00 O 1966 8.00 N 1736 7.00 C 6608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 234 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 250 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 77 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 73 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 285 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 263 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 285 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 234 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 250 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 77 " pdb="ZN ZN B 303 " - pdb=" ND1 HIS B 73 " 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 22 sheets defined 30.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 10 through 36 removed outlier: 3.690A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 67 removed outlier: 3.799A pdb=" N SER A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 108 removed outlier: 3.898A pdb=" N ALA A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 3.541A pdb=" N THR A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.821A pdb=" N SER A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 174 removed outlier: 3.630A pdb=" N LEU A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 208 removed outlier: 4.235A pdb=" N ALA A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 195 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 258 through 277 removed outlier: 3.569A pdb=" N PHE A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 removed outlier: 3.668A pdb=" N LEU C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 removed outlier: 4.398A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 185 through 189' Processing helix chain 'B' and resid 11 through 36 Processing helix chain 'B' and resid 40 through 66 removed outlier: 4.141A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.679A pdb=" N ALA B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 118 through 140 removed outlier: 3.523A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 132 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.814A pdb=" N SER B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 174 removed outlier: 3.645A pdb=" N LEU B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 208 removed outlier: 3.930A pdb=" N ALA B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 258 through 277 removed outlier: 3.574A pdb=" N PHE B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 130 removed outlier: 3.669A pdb=" N LEU E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.586A pdb=" N HIS E 191 " --> pdb=" O TYR E 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.980A pdb=" N GLY A 232 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 252 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 241 removed outlier: 6.301A pdb=" N VAL A 245 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.613A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE C 72 " --> pdb=" O CYS C 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.534A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.827A pdb=" N VAL C 135 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 134 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.515A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 23 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63 removed outlier: 3.588A pdb=" N SER D 60 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AA9, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.672A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.672A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 168 through 170 removed outlier: 3.803A pdb=" N CYS D 213 " --> pdb=" O LYS D 226 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS D 226 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL D 224 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS D 217 " --> pdb=" O THR D 222 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 222 " --> pdb=" O HIS D 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.963A pdb=" N GLY B 232 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 252 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 238 through 241 removed outlier: 6.369A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.622A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.501A pdb=" N TYR E 50 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.851A pdb=" N THR E 99 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 118 through 120 removed outlier: 3.875A pdb=" N VAL E 135 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL E 134 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.595A pdb=" N LEU F 23 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 60 through 63 removed outlier: 7.065A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER F 53 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE F 37 " --> pdb=" O SER F 53 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AC3, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.563A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 168 through 170 removed outlier: 3.767A pdb=" N CYS F 213 " --> pdb=" O LYS F 226 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS F 226 " --> pdb=" O CYS F 213 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL F 224 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HIS F 217 " --> pdb=" O THR F 222 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR F 222 " --> pdb=" O HIS F 217 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3288 1.34 - 1.46: 2546 1.46 - 1.58: 4694 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 10566 Sorted by residual: bond pdb=" C LYS E 40 " pdb=" N PRO E 41 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.38e-02 5.25e+03 3.14e+00 bond pdb=" C LYS C 40 " pdb=" N PRO C 41 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.13e+00 bond pdb=" CA ASP B 227 " pdb=" CB ASP B 227 " ideal model delta sigma weight residual 1.524 1.539 -0.014 1.55e-02 4.16e+03 8.32e-01 bond pdb=" N VAL E 59 " pdb=" CA VAL E 59 " ideal model delta sigma weight residual 1.468 1.460 0.008 1.05e-02 9.07e+03 6.44e-01 bond pdb=" C PHE D 139 " pdb=" O PHE D 139 " ideal model delta sigma weight residual 1.240 1.248 -0.009 1.16e-02 7.43e+03 5.72e-01 ... (remaining 10561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 13828 1.16 - 2.31: 425 2.31 - 3.47: 93 3.47 - 4.62: 26 4.62 - 5.78: 4 Bond angle restraints: 14376 Sorted by residual: angle pdb=" N ILE C 92 " pdb=" CA ILE C 92 " pdb=" C ILE C 92 " ideal model delta sigma weight residual 111.88 109.07 2.81 1.06e+00 8.90e-01 7.02e+00 angle pdb=" C GLY B 242 " pdb=" N LYS B 243 " pdb=" CA LYS B 243 " ideal model delta sigma weight residual 121.54 125.80 -4.26 1.91e+00 2.74e-01 4.96e+00 angle pdb=" N ILE E 92 " pdb=" CA ILE E 92 " pdb=" C ILE E 92 " ideal model delta sigma weight residual 111.88 109.60 2.28 1.06e+00 8.90e-01 4.64e+00 angle pdb=" N GLU E 145 " pdb=" CA GLU E 145 " pdb=" C GLU E 145 " ideal model delta sigma weight residual 108.58 112.12 -3.54 1.82e+00 3.02e-01 3.78e+00 angle pdb=" CA GLU B 226 " pdb=" CB GLU B 226 " pdb=" CG GLU B 226 " ideal model delta sigma weight residual 114.10 117.97 -3.87 2.00e+00 2.50e-01 3.74e+00 ... (remaining 14371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 5682 17.51 - 35.03: 492 35.03 - 52.54: 73 52.54 - 70.05: 11 70.05 - 87.57: 10 Dihedral angle restraints: 6268 sinusoidal: 2360 harmonic: 3908 Sorted by residual: dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 167.40 -74.40 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS F 25 " pdb=" SG CYS F 25 " pdb=" SG CYS F 99 " pdb=" CB CYS F 99 " ideal model delta sinusoidal sigma weight residual 93.00 165.09 -72.09 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CB CYS D 25 " pdb=" SG CYS D 25 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 164.82 -71.82 1 1.00e+01 1.00e-02 6.60e+01 ... (remaining 6265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 977 0.027 - 0.054: 450 0.054 - 0.080: 108 0.080 - 0.107: 107 0.107 - 0.134: 24 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CA ILE E 49 " pdb=" N ILE E 49 " pdb=" C ILE E 49 " pdb=" CB ILE E 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL A 67 " pdb=" N VAL A 67 " pdb=" C VAL A 67 " pdb=" CB VAL A 67 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL B 67 " pdb=" N VAL B 67 " pdb=" C VAL B 67 " pdb=" CB VAL B 67 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1663 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 40 " -0.032 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO E 41 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 41 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 41 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 40 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO C 41 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 184 " 0.009 2.00e-02 2.50e+03 1.14e-02 2.26e+00 pdb=" CG PHE B 184 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE B 184 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 184 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 184 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 184 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 184 " 0.001 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 87 2.59 - 3.17: 8525 3.17 - 3.74: 15219 3.74 - 4.32: 20115 4.32 - 4.90: 34061 Nonbonded interactions: 78007 Sorted by model distance: nonbonded pdb=" OD2 ASP B 287 " pdb="ZN ZN B 302 " model vdw 2.011 2.230 nonbonded pdb=" OD1 ASP B 287 " pdb="ZN ZN B 301 " model vdw 2.037 2.230 nonbonded pdb=" OD1 ASP A 287 " pdb="ZN ZN A 303 " model vdw 2.051 2.230 nonbonded pdb=" OD2 ASP A 287 " pdb="ZN ZN A 301 " model vdw 2.060 2.230 nonbonded pdb=" OD1 ASN D 216 " pdb=" NZ LYS D 223 " model vdw 2.241 3.120 ... (remaining 78002 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.020 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10586 Z= 0.117 Angle : 0.516 5.781 14392 Z= 0.269 Chirality : 0.039 0.134 1666 Planarity : 0.004 0.050 1804 Dihedral : 13.451 87.567 3724 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.27 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.37 (0.24), residues: 1312 helix: 0.98 (0.28), residues: 370 sheet: -0.20 (0.29), residues: 366 loop : -1.03 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 178 HIS 0.003 0.001 HIS A 234 PHE 0.026 0.001 PHE B 184 TYR 0.010 0.001 TYR B 156 ARG 0.007 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.28456 ( 427) hydrogen bonds : angle 8.91149 ( 1209) metal coordination : bond 0.00186 ( 12) SS BOND : bond 0.00117 ( 8) SS BOND : angle 0.88293 ( 16) covalent geometry : bond 0.00261 (10566) covalent geometry : angle 0.51576 (14376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.7970 (ppp) cc_final: 0.7154 (ppp) REVERT: B 195 GLN cc_start: 0.7625 (mt0) cc_final: 0.7148 (mt0) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.2285 time to fit residues: 62.0041 Evaluate side-chains 157 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 195 GLN E 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.171785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115152 restraints weight = 13846.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116610 restraints weight = 9983.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116995 restraints weight = 7412.780| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10586 Z= 0.238 Angle : 0.641 11.298 14392 Z= 0.341 Chirality : 0.045 0.186 1666 Planarity : 0.005 0.036 1804 Dihedral : 4.367 16.966 1440 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.34 % Favored : 94.44 % Rotamer: Outliers : 1.24 % Allowed : 9.91 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.38 (0.23), residues: 1312 helix: 1.49 (0.27), residues: 378 sheet: -0.53 (0.28), residues: 370 loop : -1.23 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 50 HIS 0.006 0.001 HIS A 234 PHE 0.013 0.002 PHE A 59 TYR 0.017 0.001 TYR A 191 ARG 0.005 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.06433 ( 427) hydrogen bonds : angle 5.85689 ( 1209) metal coordination : bond 0.00693 ( 12) SS BOND : bond 0.00470 ( 8) SS BOND : angle 1.29274 ( 16) covalent geometry : bond 0.00549 (10566) covalent geometry : angle 0.64037 (14376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7821 (ppp) cc_final: 0.6909 (ppp) REVERT: D 118 MET cc_start: 0.8495 (mtt) cc_final: 0.8256 (mtt) REVERT: B 201 TYR cc_start: 0.8200 (t80) cc_final: 0.7877 (t80) REVERT: E 189 GLU cc_start: 0.5680 (mp0) cc_final: 0.5426 (mp0) REVERT: F 118 MET cc_start: 0.8506 (mtt) cc_final: 0.8267 (mtt) outliers start: 14 outliers final: 8 residues processed: 179 average time/residue: 0.2353 time to fit residues: 58.8144 Evaluate side-chains 158 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 0.5980 chunk 116 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 101 optimal weight: 0.0060 chunk 36 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.175555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117451 restraints weight = 14127.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119368 restraints weight = 9641.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120680 restraints weight = 8420.902| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10586 Z= 0.119 Angle : 0.563 8.480 14392 Z= 0.289 Chirality : 0.041 0.155 1666 Planarity : 0.004 0.036 1804 Dihedral : 4.057 17.433 1440 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 1.06 % Allowed : 12.92 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.27 (0.23), residues: 1312 helix: 1.63 (0.27), residues: 376 sheet: -0.45 (0.28), residues: 360 loop : -1.19 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 178 HIS 0.004 0.001 HIS A 155 PHE 0.022 0.001 PHE B 97 TYR 0.014 0.001 TYR A 156 ARG 0.007 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 427) hydrogen bonds : angle 5.05710 ( 1209) metal coordination : bond 0.00190 ( 12) SS BOND : bond 0.00324 ( 8) SS BOND : angle 0.97344 ( 16) covalent geometry : bond 0.00253 (10566) covalent geometry : angle 0.56216 (14376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7773 (ppp) cc_final: 0.6960 (ppp) REVERT: A 59 PHE cc_start: 0.8797 (t80) cc_final: 0.8564 (t80) REVERT: D 118 MET cc_start: 0.8383 (mtt) cc_final: 0.8129 (mtt) REVERT: B 58 ASN cc_start: 0.8149 (m-40) cc_final: 0.7795 (m110) REVERT: B 201 TYR cc_start: 0.8148 (t80) cc_final: 0.7800 (t80) REVERT: F 118 MET cc_start: 0.8386 (mtt) cc_final: 0.8076 (mtt) outliers start: 12 outliers final: 4 residues processed: 177 average time/residue: 0.2424 time to fit residues: 59.4586 Evaluate side-chains 152 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain F residue 94 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 163 ASN C 140 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 195 GLN E 102 GLN E 140 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.162939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101144 restraints weight = 13955.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104518 restraints weight = 9052.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106706 restraints weight = 6964.747| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10586 Z= 0.183 Angle : 0.595 8.816 14392 Z= 0.307 Chirality : 0.043 0.204 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.277 16.891 1440 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.12 % Allowed : 15.13 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.37 (0.23), residues: 1312 helix: 1.51 (0.27), residues: 384 sheet: -0.49 (0.27), residues: 360 loop : -1.30 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 178 HIS 0.005 0.001 HIS A 234 PHE 0.014 0.001 PHE A 97 TYR 0.018 0.001 TYR B 191 ARG 0.005 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 427) hydrogen bonds : angle 4.91378 ( 1209) metal coordination : bond 0.00522 ( 12) SS BOND : bond 0.00319 ( 8) SS BOND : angle 0.93272 ( 16) covalent geometry : bond 0.00429 (10566) covalent geometry : angle 0.59497 (14376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7790 (ppp) cc_final: 0.6964 (ppp) REVERT: A 133 LEU cc_start: 0.9277 (mm) cc_final: 0.9029 (pp) REVERT: C 119 ILE cc_start: 0.7781 (mt) cc_final: 0.7418 (mm) REVERT: D 118 MET cc_start: 0.8601 (mtt) cc_final: 0.8371 (mtt) REVERT: B 201 TYR cc_start: 0.8244 (t80) cc_final: 0.7853 (t80) REVERT: E 119 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7151 (mm) REVERT: F 118 MET cc_start: 0.8628 (mtt) cc_final: 0.8374 (mtt) REVERT: F 132 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6495 (pp30) outliers start: 24 outliers final: 17 residues processed: 171 average time/residue: 0.2514 time to fit residues: 60.4819 Evaluate side-chains 162 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 118 optimal weight: 0.1980 chunk 74 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 234 HIS C 102 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.164335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110850 restraints weight = 13907.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106764 restraints weight = 9365.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107999 restraints weight = 7641.418| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.306 10586 Z= 0.164 Angle : 0.588 14.491 14392 Z= 0.292 Chirality : 0.042 0.247 1666 Planarity : 0.004 0.037 1804 Dihedral : 4.134 19.253 1440 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.48 % Allowed : 15.93 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.18 (0.24), residues: 1312 helix: 1.73 (0.28), residues: 372 sheet: -0.32 (0.27), residues: 376 loop : -1.21 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.003 0.001 HIS A 234 PHE 0.019 0.001 PHE B 97 TYR 0.010 0.001 TYR B 156 ARG 0.005 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 427) hydrogen bonds : angle 4.65533 ( 1209) metal coordination : bond 0.08830 ( 12) SS BOND : bond 0.00256 ( 8) SS BOND : angle 0.81614 ( 16) covalent geometry : bond 0.00301 (10566) covalent geometry : angle 0.58743 (14376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7721 (ppp) cc_final: 0.6787 (ppp) REVERT: C 82 GLU cc_start: 0.7794 (pm20) cc_final: 0.7345 (pm20) REVERT: C 119 ILE cc_start: 0.7776 (mt) cc_final: 0.7408 (mm) REVERT: D 118 MET cc_start: 0.8511 (mtt) cc_final: 0.8237 (mtt) REVERT: D 132 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7025 (pp30) REVERT: B 58 ASN cc_start: 0.8060 (m-40) cc_final: 0.7748 (m110) REVERT: B 201 TYR cc_start: 0.8217 (t80) cc_final: 0.7839 (t80) REVERT: E 119 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7252 (mm) REVERT: F 118 MET cc_start: 0.8552 (mtt) cc_final: 0.8255 (mtt) REVERT: F 132 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6592 (pp30) outliers start: 28 outliers final: 17 residues processed: 176 average time/residue: 0.2446 time to fit residues: 58.8979 Evaluate side-chains 167 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 69 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN F 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.163190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102057 restraints weight = 14022.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105709 restraints weight = 10101.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106447 restraints weight = 7015.381| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10586 Z= 0.172 Angle : 0.625 11.142 14392 Z= 0.307 Chirality : 0.043 0.223 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.248 18.522 1440 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.39 % Allowed : 17.79 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.26 (0.23), residues: 1312 helix: 1.65 (0.28), residues: 372 sheet: -0.37 (0.27), residues: 376 loop : -1.25 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 178 HIS 0.009 0.001 HIS A 155 PHE 0.015 0.001 PHE A 97 TYR 0.014 0.001 TYR B 191 ARG 0.007 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 427) hydrogen bonds : angle 4.63565 ( 1209) metal coordination : bond 0.00749 ( 12) SS BOND : bond 0.00284 ( 8) SS BOND : angle 0.78157 ( 16) covalent geometry : bond 0.00404 (10566) covalent geometry : angle 0.62455 (14376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7750 (ppp) cc_final: 0.6802 (ppp) REVERT: C 119 ILE cc_start: 0.7861 (mt) cc_final: 0.7520 (mm) REVERT: D 132 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6948 (pp30) REVERT: B 201 TYR cc_start: 0.8284 (t80) cc_final: 0.7891 (t80) REVERT: E 119 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7245 (mm) REVERT: F 118 MET cc_start: 0.8592 (mtt) cc_final: 0.8335 (mtt) REVERT: F 132 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6457 (pp30) outliers start: 27 outliers final: 21 residues processed: 170 average time/residue: 0.3138 time to fit residues: 73.9521 Evaluate side-chains 171 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 123 GLN Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 30.0000 chunk 81 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN C 102 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.163345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103448 restraints weight = 14037.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107097 restraints weight = 10075.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107777 restraints weight = 6732.025| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 0.028 10586 Z= 0.145 Angle : 0.612 10.623 14392 Z= 0.298 Chirality : 0.042 0.269 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.184 18.101 1440 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.65 % Allowed : 18.41 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.20 (0.24), residues: 1312 helix: 1.81 (0.28), residues: 368 sheet: -0.38 (0.27), residues: 380 loop : -1.24 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.003 0.001 HIS B 234 PHE 0.021 0.001 PHE B 97 TYR 0.010 0.001 TYR B 156 ARG 0.005 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 427) hydrogen bonds : angle 4.51684 ( 1209) metal coordination : bond 0.00352 ( 12) SS BOND : bond 0.00264 ( 8) SS BOND : angle 0.72278 ( 16) covalent geometry : bond 0.00341 (10566) covalent geometry : angle 0.61193 (14376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7665 (ppp) cc_final: 0.6762 (ppp) REVERT: A 133 LEU cc_start: 0.9366 (tp) cc_final: 0.9090 (pp) REVERT: C 82 GLU cc_start: 0.7843 (pm20) cc_final: 0.7267 (pm20) REVERT: C 119 ILE cc_start: 0.7896 (mt) cc_final: 0.7558 (mm) REVERT: D 132 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6984 (pp30) REVERT: B 58 ASN cc_start: 0.8112 (m-40) cc_final: 0.7874 (m110) REVERT: B 174 GLN cc_start: 0.5300 (tt0) cc_final: 0.5081 (tm-30) REVERT: B 201 TYR cc_start: 0.8243 (t80) cc_final: 0.7847 (t80) REVERT: F 118 MET cc_start: 0.8577 (mtt) cc_final: 0.8308 (mtt) REVERT: F 132 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6385 (pp30) outliers start: 30 outliers final: 24 residues processed: 172 average time/residue: 0.3689 time to fit residues: 89.3479 Evaluate side-chains 171 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 215 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 99 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.164167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108215 restraints weight = 13903.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107479 restraints weight = 9044.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108359 restraints weight = 6984.724| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10586 Z= 0.130 Angle : 0.618 10.378 14392 Z= 0.300 Chirality : 0.043 0.261 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.132 18.675 1440 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.48 % Allowed : 18.94 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.15 (0.24), residues: 1312 helix: 1.82 (0.28), residues: 368 sheet: -0.30 (0.27), residues: 378 loop : -1.24 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 178 HIS 0.004 0.001 HIS A 155 PHE 0.017 0.001 PHE A 184 TYR 0.018 0.001 TYR B 191 ARG 0.006 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 427) hydrogen bonds : angle 4.44974 ( 1209) metal coordination : bond 0.00250 ( 12) SS BOND : bond 0.00230 ( 8) SS BOND : angle 0.72463 ( 16) covalent geometry : bond 0.00303 (10566) covalent geometry : angle 0.61831 (14376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7576 (ppp) cc_final: 0.6689 (ppp) REVERT: A 133 LEU cc_start: 0.9261 (tp) cc_final: 0.9054 (pp) REVERT: C 119 ILE cc_start: 0.7930 (mt) cc_final: 0.7582 (mm) REVERT: B 174 GLN cc_start: 0.5297 (tt0) cc_final: 0.5032 (tm-30) REVERT: B 201 TYR cc_start: 0.8243 (t80) cc_final: 0.7866 (t80) REVERT: E 82 GLU cc_start: 0.7649 (pm20) cc_final: 0.7236 (pm20) REVERT: F 118 MET cc_start: 0.8554 (mtt) cc_final: 0.8237 (mtt) REVERT: F 132 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6365 (pp30) outliers start: 28 outliers final: 23 residues processed: 169 average time/residue: 0.2574 time to fit residues: 60.0301 Evaluate side-chains 165 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 123 GLN Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 215 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 81 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 40 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.164373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108404 restraints weight = 14080.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106305 restraints weight = 9107.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106740 restraints weight = 7698.541| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10586 Z= 0.140 Angle : 0.635 10.247 14392 Z= 0.307 Chirality : 0.043 0.255 1666 Planarity : 0.004 0.037 1804 Dihedral : 4.141 19.917 1440 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.44 % Rotamer: Outliers : 2.30 % Allowed : 19.65 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.17 (0.24), residues: 1312 helix: 1.80 (0.28), residues: 372 sheet: -0.33 (0.27), residues: 378 loop : -1.26 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 178 HIS 0.003 0.001 HIS B 234 PHE 0.022 0.001 PHE B 97 TYR 0.018 0.001 TYR A 191 ARG 0.005 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 427) hydrogen bonds : angle 4.41943 ( 1209) metal coordination : bond 0.00290 ( 12) SS BOND : bond 0.00220 ( 8) SS BOND : angle 0.72364 ( 16) covalent geometry : bond 0.00331 (10566) covalent geometry : angle 0.63465 (14376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7566 (ppp) cc_final: 0.6645 (ppp) REVERT: A 133 LEU cc_start: 0.9324 (tp) cc_final: 0.9107 (pp) REVERT: C 82 GLU cc_start: 0.7858 (pm20) cc_final: 0.7393 (pm20) REVERT: C 119 ILE cc_start: 0.7927 (mt) cc_final: 0.7579 (mm) REVERT: B 174 GLN cc_start: 0.5290 (tt0) cc_final: 0.5003 (tm-30) REVERT: B 201 TYR cc_start: 0.8291 (t80) cc_final: 0.7930 (t80) REVERT: E 82 GLU cc_start: 0.7723 (pm20) cc_final: 0.7320 (pm20) REVERT: F 118 MET cc_start: 0.8538 (mtt) cc_final: 0.8250 (mtt) REVERT: F 132 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6392 (pp30) outliers start: 26 outliers final: 23 residues processed: 171 average time/residue: 0.2783 time to fit residues: 65.7254 Evaluate side-chains 168 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 0.0670 chunk 85 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103518 restraints weight = 14107.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104075 restraints weight = 12185.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106041 restraints weight = 8022.288| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10586 Z= 0.163 Angle : 0.649 10.781 14392 Z= 0.318 Chirality : 0.044 0.275 1666 Planarity : 0.004 0.049 1804 Dihedral : 4.233 19.026 1440 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 2.12 % Allowed : 20.80 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.22 (0.24), residues: 1312 helix: 1.78 (0.28), residues: 372 sheet: -0.36 (0.27), residues: 370 loop : -1.29 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 178 HIS 0.004 0.001 HIS B 234 PHE 0.019 0.001 PHE A 184 TYR 0.023 0.001 TYR B 191 ARG 0.005 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 427) hydrogen bonds : angle 4.46961 ( 1209) metal coordination : bond 0.00371 ( 12) SS BOND : bond 0.00252 ( 8) SS BOND : angle 0.71163 ( 16) covalent geometry : bond 0.00386 (10566) covalent geometry : angle 0.64924 (14376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7613 (ppp) cc_final: 0.6691 (ppp) REVERT: A 133 LEU cc_start: 0.9299 (tp) cc_final: 0.9078 (pp) REVERT: A 178 TRP cc_start: 0.8146 (t-100) cc_final: 0.7749 (t-100) REVERT: C 82 GLU cc_start: 0.7887 (pm20) cc_final: 0.7427 (pm20) REVERT: C 119 ILE cc_start: 0.7962 (mt) cc_final: 0.7592 (mm) REVERT: B 174 GLN cc_start: 0.5253 (tt0) cc_final: 0.4895 (tm-30) REVERT: B 201 TYR cc_start: 0.8297 (t80) cc_final: 0.7926 (t80) REVERT: E 82 GLU cc_start: 0.7767 (pm20) cc_final: 0.7399 (pm20) outliers start: 24 outliers final: 23 residues processed: 167 average time/residue: 0.2397 time to fit residues: 55.7416 Evaluate side-chains 165 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 109 optimal weight: 0.9990 chunk 66 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 59 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110043 restraints weight = 13939.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107206 restraints weight = 8958.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107083 restraints weight = 7530.497| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10586 Z= 0.142 Angle : 0.646 11.154 14392 Z= 0.312 Chirality : 0.043 0.269 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.187 19.553 1440 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.59 % Rotamer: Outliers : 2.12 % Allowed : 20.97 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.20 (0.24), residues: 1312 helix: 1.79 (0.28), residues: 372 sheet: -0.34 (0.27), residues: 372 loop : -1.29 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 178 HIS 0.003 0.001 HIS B 234 PHE 0.023 0.001 PHE B 97 TYR 0.019 0.001 TYR A 191 ARG 0.005 0.000 ARG F 90 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 427) hydrogen bonds : angle 4.40276 ( 1209) metal coordination : bond 0.00274 ( 12) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.67155 ( 16) covalent geometry : bond 0.00335 (10566) covalent geometry : angle 0.64605 (14376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3791.49 seconds wall clock time: 68 minutes 13.56 seconds (4093.56 seconds total)