Starting phenix.real_space_refine on Wed Feb 14 21:42:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/02_2024/8f6f_28882.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/02_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_28882/02_2024/8f6f_28882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/02_2024/8f6f_28882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/02_2024/8f6f_28882.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6f_28882/02_2024/8f6f_28882.pdb" } 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 Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "C ASP 2": "OD1" <-> "OD2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.73, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 3.85 Conformation dependent library (CDL) restraints added in 1.8 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: 1.11 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: 2.80 Time building geometry restraints manager: 4.19 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: 100.21 - 106.99: 279 106.99 - 113.77: 6004 113.77 - 120.55: 3969 120.55 - 127.32: 4009 127.32 - 134.10: 115 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 2.520 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 7.910 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.930 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.226 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: 0.2261 time to fit residues: 61.2826 Evaluate side-chains 157 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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: 0.6980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 137 GLN B 195 GLN B 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10566 Z= 0.313 Angle : 0.612 10.408 14376 Z= 0.322 Chirality : 0.043 0.210 1666 Planarity : 0.004 0.035 1804 Dihedral : 4.323 17.293 1440 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.49 % Favored : 94.28 % Rotamer: Outliers : 1.33 % Allowed : 10.27 % Favored : 88.41 % 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: -0.34 (0.23), residues: 1312 helix: 1.52 (0.27), residues: 376 sheet: -0.50 (0.28), residues: 368 loop : -1.19 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 50 HIS 0.005 0.001 HIS A 234 PHE 0.014 0.002 PHE B 184 TYR 0.019 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 183 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8039 (ppp) cc_final: 0.7107 (ppp) REVERT: D 118 MET cc_start: 0.8459 (mtt) cc_final: 0.8234 (mtt) REVERT: B 201 TYR cc_start: 0.8073 (t80) cc_final: 0.7735 (t80) REVERT: F 118 MET cc_start: 0.8475 (mtt) cc_final: 0.8264 (mtt) outliers start: 15 outliers final: 10 residues processed: 178 average time/residue: 0.2384 time to fit residues: 59.1415 Evaluate side-chains 163 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 213 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 213 ASP 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: 0.8980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8015 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10566 Z= 0.283 Angle : 0.569 7.647 14376 Z= 0.296 Chirality : 0.042 0.186 1666 Planarity : 0.004 0.039 1804 Dihedral : 4.265 17.328 1440 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.41 % Favored : 94.36 % Rotamer: Outliers : 1.77 % Allowed : 13.19 % Favored : 85.04 % 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: -0.34 (0.23), residues: 1312 helix: 1.62 (0.27), residues: 388 sheet: -0.54 (0.28), residues: 366 loop : -1.31 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 50 HIS 0.005 0.001 HIS A 234 PHE 0.017 0.001 PHE B 97 TYR 0.019 0.001 TYR B 191 ARG 0.005 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 179 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8003 (ppp) cc_final: 0.7057 (ppp) REVERT: A 170 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8135 (mp) REVERT: C 119 ILE cc_start: 0.7747 (mt) cc_final: 0.7389 (mm) REVERT: C 189 GLU cc_start: 0.5843 (mp0) cc_final: 0.5606 (mp0) REVERT: B 201 TYR cc_start: 0.8065 (t80) cc_final: 0.7653 (t80) REVERT: E 119 ILE cc_start: 0.7414 (mt) cc_final: 0.7200 (mm) outliers start: 20 outliers final: 15 residues processed: 174 average time/residue: 0.2273 time to fit residues: 55.0858 Evaluate side-chains 160 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 ASP 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 170 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 60 SER 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 118 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 13 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN C 7 GLN C 140 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10566 Z= 0.211 Angle : 0.558 9.552 14376 Z= 0.283 Chirality : 0.041 0.198 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.150 17.126 1440 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.41 % Favored : 94.44 % Rotamer: Outliers : 2.48 % Allowed : 14.69 % Favored : 82.83 % 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 (0.24), residues: 1312 helix: 1.75 (0.28), residues: 384 sheet: -0.52 (0.28), residues: 360 loop : -1.28 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 178 HIS 0.004 0.001 HIS B 285 PHE 0.015 0.001 PHE B 249 TYR 0.012 0.001 TYR A 191 ARG 0.004 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 187 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7958 (ppp) cc_final: 0.7038 (ppp) REVERT: A 170 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8136 (mp) REVERT: C 119 ILE cc_start: 0.7841 (mt) cc_final: 0.7478 (mm) REVERT: D 134 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7863 (ttpt) REVERT: B 201 TYR cc_start: 0.8031 (t80) cc_final: 0.7657 (t80) REVERT: E 119 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7347 (mm) REVERT: E 177 LEU cc_start: 0.9281 (tp) cc_final: 0.9080 (tp) outliers start: 28 outliers final: 20 residues processed: 179 average time/residue: 0.2325 time to fit residues: 58.4304 Evaluate side-chains 164 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 ASP 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 94 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 119 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN A 234 HIS C 102 GLN C 168 GLN B 58 ASN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN F 87 ASN F 123 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10566 Z= 0.429 Angle : 0.660 13.358 14376 Z= 0.334 Chirality : 0.044 0.254 1666 Planarity : 0.004 0.039 1804 Dihedral : 4.575 17.293 1440 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 92.99 % Rotamer: Outliers : 3.63 % Allowed : 16.90 % Favored : 79.47 % 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: -0.44 (0.23), residues: 1312 helix: 1.67 (0.27), residues: 384 sheet: -0.63 (0.27), residues: 372 loop : -1.42 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 50 HIS 0.007 0.002 HIS A 234 PHE 0.021 0.001 PHE B 97 TYR 0.014 0.002 TYR B 191 ARG 0.004 0.000 ARG D 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 197 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7975 (ppp) cc_final: 0.7037 (ppp) REVERT: C 119 ILE cc_start: 0.7989 (mt) cc_final: 0.7690 (mm) REVERT: D 118 MET cc_start: 0.8564 (mtt) cc_final: 0.8276 (mtt) REVERT: D 134 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7911 (ttpt) REVERT: B 201 TYR cc_start: 0.8111 (t80) cc_final: 0.7638 (t80) REVERT: F 118 MET cc_start: 0.8576 (mtt) cc_final: 0.8276 (mtt) outliers start: 41 outliers final: 33 residues processed: 184 average time/residue: 0.2215 time to fit residues: 57.2906 Evaluate side-chains 174 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 ASP 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 36 SER 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 170 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 66 SER 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 36 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 123 optimal weight: 0.0670 overall best weight: 0.6722 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN B 58 ASN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2461 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= 0.218 Angle : 0.596 11.817 14376 Z= 0.293 Chirality : 0.042 0.235 1666 Planarity : 0.004 0.038 1804 Dihedral : 4.293 16.990 1440 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.11 % Favored : 94.74 % Rotamer: Outliers : 3.19 % Allowed : 18.41 % 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 (0.24), residues: 1312 helix: 1.79 (0.28), residues: 384 sheet: -0.49 (0.28), residues: 372 loop : -1.35 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.005 0.001 HIS A 234 PHE 0.015 0.001 PHE A 97 TYR 0.014 0.001 TYR A 191 ARG 0.004 0.000 ARG D 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 192 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7871 (ppp) cc_final: 0.6975 (ppp) REVERT: C 119 ILE cc_start: 0.7961 (mt) cc_final: 0.7635 (mm) REVERT: D 118 MET cc_start: 0.8456 (mtt) cc_final: 0.8122 (mtt) REVERT: B 201 TYR cc_start: 0.8085 (t80) cc_final: 0.7639 (t80) REVERT: E 82 GLU cc_start: 0.7340 (pm20) cc_final: 0.6814 (pm20) REVERT: F 118 MET cc_start: 0.8484 (mtt) cc_final: 0.8182 (mtt) outliers start: 36 outliers final: 30 residues processed: 180 average time/residue: 0.2433 time to fit residues: 60.7350 Evaluate side-chains 174 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 282 VAL 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 186 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 66 SER 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 36 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 0.0030 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 163 ASN ** 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: 0.2538 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= 0.187 Angle : 0.588 10.894 14376 Z= 0.285 Chirality : 0.041 0.174 1666 Planarity : 0.004 0.037 1804 Dihedral : 4.147 16.839 1440 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.28 % Rotamer: Outliers : 2.92 % Allowed : 18.76 % Favored : 78.32 % 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: 1.86 (0.28), residues: 384 sheet: -0.33 (0.28), residues: 374 loop : -1.34 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.004 0.001 HIS B 285 PHE 0.020 0.001 PHE B 97 TYR 0.014 0.001 TYR B 191 ARG 0.006 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 184 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7830 (ppp) cc_final: 0.6906 (ppp) REVERT: C 119 ILE cc_start: 0.7993 (mt) cc_final: 0.7660 (mm) REVERT: D 118 MET cc_start: 0.8443 (mtt) cc_final: 0.8108 (mtt) REVERT: B 201 TYR cc_start: 0.8103 (t80) cc_final: 0.7710 (t80) REVERT: F 118 MET cc_start: 0.8469 (mtt) cc_final: 0.8169 (mtt) outliers start: 33 outliers final: 28 residues processed: 175 average time/residue: 0.2256 time to fit residues: 55.0049 Evaluate side-chains 171 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 282 VAL 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 186 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 66 SER 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 60 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10566 Z= 0.332 Angle : 0.639 10.179 14376 Z= 0.317 Chirality : 0.044 0.314 1666 Planarity : 0.004 0.037 1804 Dihedral : 4.387 16.809 1440 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.71 % Favored : 93.14 % Rotamer: Outliers : 3.45 % Allowed : 19.29 % Favored : 77.26 % 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 (0.24), residues: 1312 helix: 1.83 (0.28), residues: 386 sheet: -0.51 (0.28), residues: 372 loop : -1.41 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 178 HIS 0.005 0.001 HIS B 234 PHE 0.017 0.001 PHE A 97 TYR 0.018 0.001 TYR A 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 188 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7842 (ppp) cc_final: 0.6806 (ppp) REVERT: A 59 PHE cc_start: 0.8734 (t80) cc_final: 0.8491 (t80) REVERT: A 178 TRP cc_start: 0.8036 (t-100) cc_final: 0.7770 (t-100) REVERT: C 119 ILE cc_start: 0.7996 (mt) cc_final: 0.7664 (mm) REVERT: D 118 MET cc_start: 0.8512 (mtt) cc_final: 0.8218 (mtt) REVERT: B 201 TYR cc_start: 0.8169 (t80) cc_final: 0.7773 (t80) REVERT: E 82 GLU cc_start: 0.7193 (pm20) cc_final: 0.6768 (pm20) REVERT: F 118 MET cc_start: 0.8534 (mtt) cc_final: 0.8275 (mtt) outliers start: 39 outliers final: 35 residues processed: 177 average time/residue: 0.2331 time to fit residues: 57.8217 Evaluate side-chains 174 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 282 VAL 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 36 SER 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 D residue 212 ILE Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 73 THR 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 31 THR 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 125 THR Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.3980 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10566 Z= 0.182 Angle : 0.609 10.219 14376 Z= 0.295 Chirality : 0.043 0.255 1666 Planarity : 0.004 0.050 1804 Dihedral : 4.169 17.058 1440 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.27 % Rotamer: Outliers : 3.10 % Allowed : 20.09 % Favored : 76.81 % 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: 2.00 (0.28), residues: 382 sheet: -0.40 (0.28), residues: 370 loop : -1.35 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 178 HIS 0.003 0.001 HIS A 285 PHE 0.023 0.001 PHE B 97 TYR 0.017 0.001 TYR B 191 ARG 0.006 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 181 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7736 (ppp) cc_final: 0.6727 (ppp) REVERT: A 59 PHE cc_start: 0.8639 (t80) cc_final: 0.8422 (t80) REVERT: C 119 ILE cc_start: 0.8078 (mt) cc_final: 0.7735 (mm) REVERT: C 177 LEU cc_start: 0.9286 (tp) cc_final: 0.9070 (tp) REVERT: D 118 MET cc_start: 0.8428 (mtt) cc_final: 0.8141 (mtt) REVERT: B 174 GLN cc_start: 0.5210 (tm-30) cc_final: 0.4940 (tm-30) REVERT: B 201 TYR cc_start: 0.8161 (t80) cc_final: 0.7788 (t80) REVERT: E 82 GLU cc_start: 0.7185 (pm20) cc_final: 0.6772 (pm20) REVERT: E 177 LEU cc_start: 0.9275 (tp) cc_final: 0.9058 (tp) REVERT: F 118 MET cc_start: 0.8466 (mtt) cc_final: 0.8188 (mtt) REVERT: F 125 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8244 (p) outliers start: 35 outliers final: 29 residues processed: 171 average time/residue: 0.2336 time to fit residues: 55.7719 Evaluate side-chains 174 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 282 VAL 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 186 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 66 SER 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 125 THR Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 0.0060 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2742 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= 0.209 Angle : 0.611 10.026 14376 Z= 0.296 Chirality : 0.043 0.260 1666 Planarity : 0.004 0.037 1804 Dihedral : 4.199 24.982 1440 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.98 % Rotamer: Outliers : 2.83 % Allowed : 20.62 % Favored : 76.55 % 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: 0.01 (0.24), residues: 1312 helix: 2.21 (0.28), residues: 372 sheet: -0.39 (0.28), residues: 370 loop : -1.21 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 178 HIS 0.004 0.001 HIS B 285 PHE 0.017 0.001 PHE A 184 TYR 0.020 0.001 TYR A 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 183 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7766 (ppp) cc_final: 0.6711 (ppp) REVERT: C 82 GLU cc_start: 0.7482 (pm20) cc_final: 0.6935 (pm20) REVERT: C 119 ILE cc_start: 0.8071 (mt) cc_final: 0.7722 (mm) REVERT: D 118 MET cc_start: 0.8444 (mtt) cc_final: 0.8129 (mtt) REVERT: D 134 LYS cc_start: 0.7881 (ttpt) cc_final: 0.7495 (pttt) REVERT: B 174 GLN cc_start: 0.5184 (tm-30) cc_final: 0.4880 (tm-30) REVERT: B 201 TYR cc_start: 0.8163 (t80) cc_final: 0.7791 (t80) REVERT: F 118 MET cc_start: 0.8487 (mtt) cc_final: 0.8165 (mtt) outliers start: 32 outliers final: 30 residues processed: 173 average time/residue: 0.2265 time to fit residues: 54.9160 Evaluate side-chains 177 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 ASP 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 31 THR 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 D residue 212 ILE Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 31 THR 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 125 THR Chi-restraints excluded: chain F residue 212 ILE 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: 0.6980 chunk 29 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.163583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103334 restraints weight = 13925.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105942 restraints weight = 9908.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106236 restraints weight = 7327.920| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2778 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= 0.249 Angle : 0.642 16.299 14376 Z= 0.308 Chirality : 0.043 0.259 1666 Planarity : 0.004 0.037 1804 Dihedral : 4.252 27.247 1440 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.64 % Favored : 94.13 % Rotamer: Outliers : 3.01 % Allowed : 20.88 % Favored : 76.11 % 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: -0.00 (0.24), residues: 1312 helix: 2.19 (0.28), residues: 372 sheet: -0.41 (0.28), residues: 370 loop : -1.20 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 178 HIS 0.004 0.001 HIS B 285 PHE 0.023 0.001 PHE B 97 TYR 0.021 0.001 TYR B 191 ARG 0.005 0.000 ARG F 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2179.19 seconds wall clock time: 40 minutes 41.90 seconds (2441.90 seconds total)