Starting phenix.real_space_refine on Sat Nov 16 04:30:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/11_2024/8f6f_28882.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/11_2024/8f6f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/11_2024/8f6f_28882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/11_2024/8f6f_28882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/11_2024/8f6f_28882.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/11_2024/8f6f_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.90, per 1000 atoms: 0.67 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 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: 1.18 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: 2.86 Time building geometry restraints manager: 2.80 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: 0.00 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: 2.190 Set stop_for_unknowns flag: 0.010 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.770 Find NCS groups from input model: 0.330 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.900 ------------------------------------------------------------------------------- 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 10566 Z= 0.172 Angle : 0.516 5.781 14376 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 *********************** 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 : 1.368 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: 0.2351 time to fit residues: 63.8950 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 : 1.180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 10566 Z= 0.364 Angle : 0.640 11.298 14376 Z= 0.340 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 *********************** 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 : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7794 (ppp) cc_final: 0.6890 (ppp) REVERT: D 118 MET cc_start: 0.8465 (mtt) cc_final: 0.8228 (mtt) REVERT: B 58 ASN cc_start: 0.8552 (t0) cc_final: 0.8351 (m-40) REVERT: B 201 TYR cc_start: 0.8086 (t80) cc_final: 0.7783 (t80) REVERT: E 189 GLU cc_start: 0.5670 (mp0) cc_final: 0.5418 (mp0) REVERT: F 118 MET cc_start: 0.8490 (mtt) cc_final: 0.8251 (mtt) outliers start: 14 outliers final: 8 residues processed: 179 average time/residue: 0.2351 time to fit residues: 58.3630 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 : 1.205 ------------------------------------------------------------------------------- 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 66 optimal weight: 30.0000 chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.0010 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 GLN C 140 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10566 Z= 0.201 Angle : 0.574 9.480 14376 Z= 0.296 Chirality : 0.042 0.165 1666 Planarity : 0.004 0.037 1804 Dihedral : 4.176 17.237 1440 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 1.33 % Allowed : 12.74 % Favored : 85.93 % 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: -0.29 (0.23), residues: 1312 helix: 1.63 (0.27), residues: 376 sheet: -0.49 (0.28), residues: 360 loop : -1.21 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 50 HIS 0.006 0.001 HIS A 155 PHE 0.022 0.001 PHE B 97 TYR 0.014 0.001 TYR A 156 ARG 0.006 0.000 ARG F 90 *********************** 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 180 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7698 (ppp) cc_final: 0.6848 (ppp) REVERT: A 170 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8091 (mp) REVERT: D 118 MET cc_start: 0.8391 (mtt) cc_final: 0.8153 (mtt) REVERT: B 58 ASN cc_start: 0.8625 (t0) cc_final: 0.8356 (t0) REVERT: B 179 TRP cc_start: 0.4741 (t-100) cc_final: 0.4517 (t-100) REVERT: B 201 TYR cc_start: 0.8036 (t80) cc_final: 0.7697 (t80) REVERT: F 118 MET cc_start: 0.8426 (mtt) cc_final: 0.8149 (mtt) REVERT: F 132 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6833 (pp30) outliers start: 15 outliers final: 7 residues processed: 175 average time/residue: 0.2531 time to fit residues: 62.7430 Evaluate side-chains 156 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 94 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10566 Z= 0.250 Angle : 0.579 8.750 14376 Z= 0.299 Chirality : 0.042 0.190 1666 Planarity : 0.004 0.037 1804 Dihedral : 4.239 17.542 1440 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.86 % Allowed : 15.13 % Favored : 83.01 % 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: -0.35 (0.23), residues: 1312 helix: 1.56 (0.27), residues: 384 sheet: -0.49 (0.27), residues: 360 loop : -1.29 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.004 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 *********************** 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 178 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7723 (ppp) cc_final: 0.6927 (ppp) REVERT: A 59 PHE cc_start: 0.8841 (t80) cc_final: 0.8635 (t80) REVERT: C 119 ILE cc_start: 0.7829 (mt) cc_final: 0.7467 (mm) REVERT: D 118 MET cc_start: 0.8416 (mtt) cc_final: 0.8188 (mtt) REVERT: B 58 ASN cc_start: 0.8699 (t0) cc_final: 0.8473 (t0) REVERT: B 201 TYR cc_start: 0.8045 (t80) cc_final: 0.7682 (t80) REVERT: E 119 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7204 (mm) REVERT: E 177 LEU cc_start: 0.9305 (tp) cc_final: 0.9100 (tp) REVERT: F 118 MET cc_start: 0.8458 (mtt) cc_final: 0.8210 (mtt) outliers start: 21 outliers final: 15 residues processed: 170 average time/residue: 0.2452 time to fit residues: 57.7592 Evaluate side-chains 160 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 0.0980 chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10566 Z= 0.212 Angle : 0.587 9.696 14376 Z= 0.294 Chirality : 0.042 0.287 1666 Planarity : 0.004 0.037 1804 Dihedral : 4.162 19.215 1440 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.48 % Allowed : 15.66 % Favored : 81.86 % 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: -0.19 (0.24), residues: 1312 helix: 1.75 (0.28), residues: 372 sheet: -0.39 (0.27), residues: 380 loop : -1.21 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.009 0.001 HIS A 155 PHE 0.020 0.001 PHE B 97 TYR 0.010 0.001 TYR B 156 ARG 0.007 0.000 ARG F 90 *********************** 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 180 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7695 (ppp) cc_final: 0.6756 (ppp) REVERT: C 82 GLU cc_start: 0.7403 (pm20) cc_final: 0.6956 (pm20) REVERT: C 119 ILE cc_start: 0.7831 (mt) cc_final: 0.7474 (mm) REVERT: D 118 MET cc_start: 0.8387 (mtt) cc_final: 0.8158 (mtt) REVERT: D 131 ASN cc_start: 0.8031 (p0) cc_final: 0.7814 (p0) REVERT: D 132 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7013 (pp30) REVERT: B 58 ASN cc_start: 0.8726 (t0) cc_final: 0.8495 (t0) REVERT: B 179 TRP cc_start: 0.4737 (t-100) cc_final: 0.4468 (t-100) REVERT: B 201 TYR cc_start: 0.8018 (t80) cc_final: 0.7689 (t80) REVERT: F 118 MET cc_start: 0.8425 (mtt) cc_final: 0.8177 (mtt) REVERT: F 132 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6680 (pp30) outliers start: 28 outliers final: 17 residues processed: 172 average time/residue: 0.2458 time to fit residues: 58.5461 Evaluate side-chains 160 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 101 PHE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10566 Z= 0.286 Angle : 0.614 9.731 14376 Z= 0.307 Chirality : 0.043 0.220 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.254 18.187 1440 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.39 % Allowed : 17.43 % Favored : 80.18 % 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: -0.28 (0.23), residues: 1312 helix: 1.70 (0.28), residues: 372 sheet: -0.44 (0.27), residues: 372 loop : -1.28 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 178 HIS 0.007 0.001 HIS A 234 PHE 0.016 0.001 PHE A 97 TYR 0.015 0.001 TYR B 191 ARG 0.006 0.000 ARG F 90 *********************** 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 176 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7670 (ppp) cc_final: 0.6739 (ppp) REVERT: A 133 LEU cc_start: 0.9292 (tp) cc_final: 0.9069 (pp) REVERT: C 119 ILE cc_start: 0.7973 (mt) cc_final: 0.7646 (mm) REVERT: D 131 ASN cc_start: 0.8101 (p0) cc_final: 0.7886 (p0) REVERT: D 132 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6988 (pp30) REVERT: B 58 ASN cc_start: 0.8715 (t0) cc_final: 0.8503 (t0) REVERT: B 201 TYR cc_start: 0.8051 (t80) cc_final: 0.7679 (t80) REVERT: F 118 MET cc_start: 0.8474 (mtt) cc_final: 0.8252 (mtt) outliers start: 27 outliers final: 21 residues processed: 166 average time/residue: 0.2422 time to fit residues: 56.1390 Evaluate side-chains 163 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 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 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 123 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 14 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10566 Z= 0.209 Angle : 0.604 11.146 14376 Z= 0.295 Chirality : 0.042 0.196 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.157 18.486 1440 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.12 % Allowed : 19.03 % Favored : 78.85 % 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: -0.20 (0.24), residues: 1312 helix: 1.81 (0.28), residues: 368 sheet: -0.39 (0.27), residues: 380 loop : -1.25 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.004 0.001 HIS A 155 PHE 0.021 0.001 PHE B 97 TYR 0.010 0.001 TYR B 156 ARG 0.005 0.000 ARG F 90 *********************** 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 174 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7614 (ppp) cc_final: 0.6702 (ppp) REVERT: A 133 LEU cc_start: 0.9306 (tp) cc_final: 0.9048 (pp) REVERT: C 82 GLU cc_start: 0.7500 (pm20) cc_final: 0.7007 (pm20) REVERT: C 119 ILE cc_start: 0.7980 (mt) cc_final: 0.7647 (mm) REVERT: D 132 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6905 (pp30) REVERT: B 58 ASN cc_start: 0.8716 (t0) cc_final: 0.8515 (t0) REVERT: B 201 TYR cc_start: 0.8047 (t80) cc_final: 0.7687 (t80) REVERT: F 118 MET cc_start: 0.8441 (mtt) cc_final: 0.8182 (mtt) outliers start: 24 outliers final: 22 residues processed: 168 average time/residue: 0.2569 time to fit residues: 59.5486 Evaluate side-chains 168 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 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 207 LEU Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 73 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** E 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10566 Z= 0.291 Angle : 0.643 9.549 14376 Z= 0.316 Chirality : 0.044 0.243 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.314 19.940 1440 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.39 % Allowed : 19.20 % Favored : 78.41 % 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: 1.74 (0.28), residues: 372 sheet: -0.43 (0.27), residues: 372 loop : -1.29 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 178 HIS 0.005 0.001 HIS B 234 PHE 0.016 0.001 PHE A 97 TYR 0.018 0.001 TYR B 191 ARG 0.006 0.000 ARG F 90 *********************** 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: 27 poor density : 150 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7564 (ppp) cc_final: 0.6679 (ppp) REVERT: A 133 LEU cc_start: 0.9320 (tp) cc_final: 0.9009 (pp) REVERT: C 82 GLU cc_start: 0.7494 (pm20) cc_final: 0.7016 (pm20) REVERT: C 119 ILE cc_start: 0.8013 (mt) cc_final: 0.7683 (mm) REVERT: D 131 ASN cc_start: 0.8189 (p0) cc_final: 0.7880 (p0) REVERT: D 132 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6843 (pp30) REVERT: B 201 TYR cc_start: 0.8071 (t80) cc_final: 0.7692 (t80) REVERT: E 82 GLU cc_start: 0.7329 (pm20) cc_final: 0.6979 (pm20) outliers start: 27 outliers final: 26 residues processed: 169 average time/residue: 0.2469 time to fit residues: 57.6614 Evaluate side-chains 170 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 187 LEU 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 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 282 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 73 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.0980 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 0.0060 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10566 Z= 0.182 Angle : 0.624 11.283 14376 Z= 0.302 Chirality : 0.042 0.246 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.111 19.796 1440 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 2.21 % Allowed : 19.91 % Favored : 77.88 % 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: -0.13 (0.24), residues: 1312 helix: 1.88 (0.28), residues: 368 sheet: -0.30 (0.27), residues: 378 loop : -1.25 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 178 HIS 0.004 0.001 HIS A 155 PHE 0.021 0.001 PHE B 97 TYR 0.011 0.001 TYR B 156 ARG 0.007 0.000 ARG F 90 *********************** 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 178 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7495 (ppp) cc_final: 0.6587 (ppp) REVERT: A 133 LEU cc_start: 0.9246 (tp) cc_final: 0.9026 (pp) REVERT: C 119 ILE cc_start: 0.8012 (mt) cc_final: 0.7678 (mm) REVERT: D 131 ASN cc_start: 0.8175 (p0) cc_final: 0.7855 (p0) REVERT: D 132 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6769 (pp30) REVERT: B 174 GLN cc_start: 0.4984 (tm-30) cc_final: 0.4734 (tm-30) REVERT: B 201 TYR cc_start: 0.8085 (t80) cc_final: 0.7734 (t80) REVERT: E 175 TYR cc_start: 0.7759 (m-10) cc_final: 0.7554 (m-10) REVERT: F 118 MET cc_start: 0.8381 (mtt) cc_final: 0.8150 (mtt) outliers start: 25 outliers final: 20 residues processed: 171 average time/residue: 0.2497 time to fit residues: 58.9357 Evaluate side-chains 163 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 132 GLN 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 E residue 73 THR 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 59 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 10 optimal weight: 0.0060 chunk 80 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10566 Z= 0.201 Angle : 0.628 11.603 14376 Z= 0.306 Chirality : 0.043 0.260 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.095 19.703 1440 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.59 % Rotamer: Outliers : 1.95 % Allowed : 20.44 % Favored : 77.61 % 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: -0.14 (0.24), residues: 1312 helix: 1.87 (0.28), residues: 368 sheet: -0.29 (0.27), residues: 378 loop : -1.26 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 178 HIS 0.004 0.001 HIS A 155 PHE 0.019 0.001 PHE A 184 TYR 0.020 0.001 TYR B 191 ARG 0.006 0.000 ARG F 90 ********************** 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 173 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7526 (ppp) cc_final: 0.6625 (ppp) REVERT: A 133 LEU cc_start: 0.9260 (tp) cc_final: 0.9053 (pp) REVERT: A 178 TRP cc_start: 0.7849 (t-100) cc_final: 0.7633 (t-100) REVERT: C 82 GLU cc_start: 0.7466 (pm20) cc_final: 0.7039 (pm20) REVERT: C 119 ILE cc_start: 0.8002 (mt) cc_final: 0.7642 (mm) REVERT: D 110 ARG cc_start: 0.7146 (mtt-85) cc_final: 0.6675 (mtp85) REVERT: D 132 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6758 (pp30) REVERT: B 174 GLN cc_start: 0.4992 (tm-30) cc_final: 0.4669 (tm-30) REVERT: B 201 TYR cc_start: 0.8092 (t80) cc_final: 0.7751 (t80) REVERT: E 82 GLU cc_start: 0.7130 (pm20) cc_final: 0.6839 (pm20) REVERT: E 177 LEU cc_start: 0.9307 (tp) cc_final: 0.9096 (tp) outliers start: 22 outliers final: 20 residues processed: 168 average time/residue: 0.2479 time to fit residues: 58.2932 Evaluate side-chains 165 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 132 GLN 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 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 96 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** B 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.163126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107743 restraints weight = 13941.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105404 restraints weight = 9442.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105956 restraints weight = 7408.776| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10566 Z= 0.285 Angle : 0.648 11.717 14376 Z= 0.320 Chirality : 0.043 0.253 1666 Planarity : 0.004 0.052 1804 Dihedral : 4.260 18.737 1440 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 2.30 % Allowed : 20.35 % Favored : 77.35 % 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: 1.84 (0.28), residues: 368 sheet: -0.35 (0.27), residues: 374 loop : -1.33 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 178 HIS 0.004 0.001 HIS B 285 PHE 0.022 0.001 PHE B 97 TYR 0.011 0.001 TYR E 175 ARG 0.006 0.000 ARG F 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2247.09 seconds wall clock time: 42 minutes 6.11 seconds (2526.11 seconds total)