Starting phenix.real_space_refine on Wed Nov 20 02:13:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/11_2024/8f6h_28883.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/11_2024/8f6h_28883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/11_2024/8f6h_28883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/11_2024/8f6h_28883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/11_2024/8f6h_28883.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6h_28883/11_2024/8f6h_28883.cif" } resolution = 3.9 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= 0.000 sd= 0.015 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 S 28 5.16 5 C 6652 2.51 5 N 1746 2.21 5 O 1989 1.98 5 H 10347 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20768 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4451 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 6, 'TRANS': 278} Chain: "B" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4213 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain breaks: 1 Chain: "C" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2915 Classifications: {'peptide': 192} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3134 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "E" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2915 Classifications: {'peptide': 192} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3134 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 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: 10.37, per 1000 atoms: 0.50 Number of scatterers: 20768 At special positions: 0 Unit cell: (78.767, 158.613, 145.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 28 16.00 O 1989 8.00 N 1746 7.00 C 6652 6.00 H 10347 1.00 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: 5.87 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 285 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 234 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 250 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 155 " 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=" ND1 HIS B 250 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 234 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 155 " 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 23 sheets defined 32.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 10 through 34 removed outlier: 3.566A pdb=" N ALA A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 62 Processing helix chain 'A' and resid 82 through 109 removed outlier: 4.004A pdb=" N ILE A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 4.389A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 176 removed outlier: 4.117A pdb=" N GLU A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 208 removed outlier: 3.612A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'A' and resid 258 through 277 removed outlier: 3.502A pdb=" N ALA A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 34 removed outlier: 3.942A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 64 removed outlier: 4.061A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 109 removed outlier: 3.581A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 141 removed outlier: 3.618A pdb=" N GLY B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 175 removed outlier: 3.938A pdb=" N LEU B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 206 removed outlier: 3.585A pdb=" N ASP B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 257 through 277 removed outlier: 4.125A pdb=" N GLU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.277A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 184 through 190 removed outlier: 4.001A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 64 through 68 removed outlier: 4.012A pdb=" N LYS F 68 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.239A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.239A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 8 removed outlier: 4.399A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 76 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.803A pdb=" N SER C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 35 " --> pdb=" O GLN C 90 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 99 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.634A pdb=" N ASN C 139 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 132 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AB1, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.522A pdb=" N VAL D 15 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.522A pdb=" N VAL D 15 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS D 99 " --> pdb=" O TRP D 121 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TRP D 121 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG D 101 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.755A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 197 " --> pdb=" O CYS D 157 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 198 " --> pdb=" O HIS D 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.755A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 194 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.585A pdb=" N ALA E 14 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR E 50 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.572A pdb=" N ASN E 139 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=AC1, first strand: chain 'F' and resid 6 through 10 removed outlier: 4.113A pdb=" N GLN F 6 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 21 " --> pdb=" O MET F 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 14 through 15 removed outlier: 6.776A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.575A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.575A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.571A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.41 Time building geometry restraints manager: 6.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10345 1.03 - 1.23: 12 1.23 - 1.42: 4504 1.42 - 1.62: 6091 1.62 - 1.81: 38 Bond restraints: 20990 Sorted by residual: bond pdb=" N GLU D 4 " pdb=" CA GLU D 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N TYR A 7 " pdb=" CA TYR A 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N GLU F 4 " pdb=" CA GLU F 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N GLU F 4 " pdb=" H GLU F 4 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" N GLU D 4 " pdb=" H GLU D 4 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 20985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 34886 0.91 - 1.82: 2777 1.82 - 2.73: 129 2.73 - 3.64: 57 3.64 - 4.55: 17 Bond angle restraints: 37866 Sorted by residual: angle pdb=" C SER D 220 " pdb=" N ASN D 221 " pdb=" CA ASN D 221 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.88e+00 angle pdb=" N PHE A 249 " pdb=" CA PHE A 249 " pdb=" C PHE A 249 " ideal model delta sigma weight residual 108.60 111.40 -2.80 1.46e+00 4.69e-01 3.67e+00 angle pdb=" CA LYS E 147 " pdb=" CB LYS E 147 " pdb=" CG LYS E 147 " ideal model delta sigma weight residual 114.10 117.91 -3.81 2.00e+00 2.50e-01 3.63e+00 angle pdb=" C GLN A 248 " pdb=" N PHE A 249 " pdb=" CA PHE A 249 " ideal model delta sigma weight residual 121.80 118.58 3.22 1.71e+00 3.42e-01 3.56e+00 angle pdb=" N VAL A 122 " pdb=" CA VAL A 122 " pdb=" C VAL A 122 " ideal model delta sigma weight residual 111.89 109.18 2.71 1.44e+00 4.82e-01 3.53e+00 ... (remaining 37861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9151 17.99 - 35.98: 596 35.98 - 53.98: 190 53.98 - 71.97: 37 71.97 - 89.96: 12 Dihedral angle restraints: 9986 sinusoidal: 5319 harmonic: 4667 Sorted by residual: 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 93.00 167.06 -74.06 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS F 157 " pdb=" SG CYS F 157 " pdb=" SG CYS F 213 " pdb=" CB CYS F 213 " ideal model delta sinusoidal sigma weight residual 93.00 165.83 -72.83 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CA ILE B 283 " pdb=" C ILE B 283 " pdb=" N ILE B 284 " pdb=" CA ILE B 284 " ideal model delta harmonic sigma weight residual 180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 9983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1066 0.028 - 0.057: 417 0.057 - 0.085: 96 0.085 - 0.113: 82 0.113 - 0.141: 23 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CA ILE E 22 " pdb=" N ILE E 22 " pdb=" C ILE E 22 " pdb=" CB ILE E 22 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE E 98 " pdb=" N ILE E 98 " pdb=" C ILE E 98 " pdb=" CB ILE E 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA LYS F 223 " pdb=" N LYS F 223 " pdb=" C LYS F 223 " pdb=" CB LYS F 223 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1681 not shown) Planarity restraints: 3110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 67 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 68 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 139 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO D 140 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 140 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 140 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 95 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO C 96 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 96 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 96 " 0.017 5.00e-02 4.00e+02 ... (remaining 3107 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 905 2.18 - 2.78: 41306 2.78 - 3.39: 54962 3.39 - 3.99: 69373 3.99 - 4.60: 107862 Nonbonded interactions: 274408 Sorted by model distance: nonbonded pdb=" OD1 ASP D 119 " pdb=" H TYR D 120 " model vdw 1.570 2.450 nonbonded pdb=" OE1 GLN B 290 " pdb=" H GLN B 290 " model vdw 1.618 2.450 nonbonded pdb=" OD1 ASP F 119 " pdb=" H TYR F 120 " model vdw 1.618 2.450 nonbonded pdb=" OD1 ASP B 51 " pdb=" HE2 HIS B 155 " model vdw 1.653 2.450 nonbonded pdb=" O GLY A 37 " pdb="HH12 ARG A 106 " model vdw 1.654 2.450 ... (remaining 274403 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' and ((resid 11 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA )) or resid 12 through 64 or resid 75 through \ 80 or (resid 81 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name OE2 or name H or name HA )) or resid 82 through \ 291 or resid 301 through 303)) 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: 2.610 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: 0.360 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 52.840 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.002 0.035 10643 Z= 0.162 Angle : 0.468 4.313 14486 Z= 0.250 Chirality : 0.038 0.141 1684 Planarity : 0.003 0.052 1820 Dihedral : 13.598 89.961 3747 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -0.05 (0.24), residues: 1332 helix: 1.88 (0.27), residues: 386 sheet: 0.18 (0.29), residues: 360 loop : -1.52 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 50 HIS 0.004 0.001 HIS D 38 PHE 0.015 0.001 PHE B 101 TYR 0.007 0.001 TYR D 98 ARG 0.001 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8606 (mmp) cc_final: 0.8386 (tpp) REVERT: A 109 ASN cc_start: 0.7929 (m-40) cc_final: 0.7620 (m-40) REVERT: A 279 ASP cc_start: 0.7411 (t70) cc_final: 0.7211 (t70) REVERT: B 163 ASN cc_start: 0.8609 (m110) cc_final: 0.8371 (m110) REVERT: B 183 LEU cc_start: 0.8953 (tp) cc_final: 0.8685 (tp) REVERT: D 165 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7231 (mm-30) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.5319 time to fit residues: 131.9039 Evaluate side-chains 145 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10643 Z= 0.217 Angle : 0.524 5.314 14486 Z= 0.281 Chirality : 0.040 0.145 1684 Planarity : 0.004 0.051 1820 Dihedral : 3.619 22.834 1457 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 0.44 % Allowed : 7.64 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.10 (0.24), residues: 1332 helix: 2.33 (0.26), residues: 390 sheet: 0.05 (0.28), residues: 380 loop : -1.62 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 95 HIS 0.006 0.001 HIS A 155 PHE 0.013 0.001 PHE C 118 TYR 0.016 0.001 TYR F 104 ARG 0.004 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.7385 (t70) cc_final: 0.7178 (t70) REVERT: B 163 ASN cc_start: 0.8680 (m110) cc_final: 0.8296 (m110) REVERT: D 165 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7363 (mm-30) outliers start: 5 outliers final: 3 residues processed: 158 average time/residue: 0.5144 time to fit residues: 114.0319 Evaluate side-chains 144 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 130 optimal weight: 0.0370 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10643 Z= 0.174 Angle : 0.493 5.284 14486 Z= 0.260 Chirality : 0.039 0.145 1684 Planarity : 0.003 0.051 1820 Dihedral : 3.564 22.466 1457 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 0.53 % Allowed : 9.66 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1332 helix: 2.57 (0.26), residues: 390 sheet: 0.01 (0.28), residues: 382 loop : -1.62 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 179 HIS 0.004 0.001 HIS A 155 PHE 0.012 0.001 PHE C 118 TYR 0.013 0.001 TYR F 104 ARG 0.003 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8905 (mm) cc_final: 0.8578 (mm) REVERT: B 63 ARG cc_start: 0.7591 (ttt-90) cc_final: 0.7099 (tmm160) REVERT: B 163 ASN cc_start: 0.8639 (m110) cc_final: 0.8335 (m110) REVERT: E 37 TYR cc_start: 0.8780 (m-80) cc_final: 0.8417 (m-80) outliers start: 6 outliers final: 6 residues processed: 162 average time/residue: 0.5468 time to fit residues: 122.9727 Evaluate side-chains 155 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 81 optimal weight: 0.0870 chunk 121 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10643 Z= 0.224 Angle : 0.511 6.646 14486 Z= 0.270 Chirality : 0.039 0.145 1684 Planarity : 0.004 0.050 1820 Dihedral : 3.662 22.726 1457 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.23 % Favored : 93.62 % Rotamer: Outliers : 0.79 % Allowed : 10.27 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.12 (0.24), residues: 1332 helix: 2.59 (0.25), residues: 390 sheet: 0.04 (0.29), residues: 352 loop : -1.71 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 36 HIS 0.004 0.001 HIS A 155 PHE 0.013 0.001 PHE A 249 TYR 0.011 0.001 TYR F 104 ARG 0.003 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8935 (mm) cc_final: 0.8605 (mm) REVERT: B 63 ARG cc_start: 0.7621 (ttt-90) cc_final: 0.7117 (tmm160) REVERT: B 163 ASN cc_start: 0.8684 (m110) cc_final: 0.8392 (m110) REVERT: B 220 ILE cc_start: 0.9104 (mt) cc_final: 0.8700 (tt) REVERT: E 37 TYR cc_start: 0.8780 (m-80) cc_final: 0.8374 (m-80) outliers start: 9 outliers final: 7 residues processed: 159 average time/residue: 0.4985 time to fit residues: 113.7486 Evaluate side-chains 152 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10643 Z= 0.226 Angle : 0.510 5.277 14486 Z= 0.269 Chirality : 0.040 0.156 1684 Planarity : 0.004 0.051 1820 Dihedral : 3.724 22.903 1457 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 0.79 % Allowed : 11.94 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.12 (0.24), residues: 1332 helix: 2.60 (0.25), residues: 389 sheet: 0.02 (0.29), residues: 352 loop : -1.71 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 95 HIS 0.003 0.001 HIS A 285 PHE 0.019 0.001 PHE F 163 TYR 0.010 0.001 TYR D 98 ARG 0.002 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8917 (mm) cc_final: 0.8539 (mm) REVERT: B 63 ARG cc_start: 0.7643 (ttt-90) cc_final: 0.7139 (tmm160) REVERT: B 163 ASN cc_start: 0.8698 (m110) cc_final: 0.8415 (m110) REVERT: C 118 PHE cc_start: 0.7711 (m-80) cc_final: 0.7412 (m-80) REVERT: E 37 TYR cc_start: 0.8853 (m-80) cc_final: 0.8380 (m-80) REVERT: F 118 MET cc_start: 0.8871 (mtm) cc_final: 0.8600 (mtm) outliers start: 9 outliers final: 8 residues processed: 156 average time/residue: 0.5052 time to fit residues: 112.3805 Evaluate side-chains 151 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10643 Z= 0.187 Angle : 0.501 6.535 14486 Z= 0.263 Chirality : 0.040 0.146 1684 Planarity : 0.004 0.051 1820 Dihedral : 3.654 22.715 1457 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.16 % Favored : 93.69 % Rotamer: Outliers : 1.05 % Allowed : 12.20 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.16 (0.24), residues: 1332 helix: 2.63 (0.25), residues: 389 sheet: -0.01 (0.29), residues: 350 loop : -1.63 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 95 HIS 0.003 0.001 HIS A 155 PHE 0.010 0.001 PHE A 249 TYR 0.013 0.001 TYR C 56 ARG 0.005 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8926 (mm) cc_final: 0.8574 (mm) REVERT: B 63 ARG cc_start: 0.7656 (ttt-90) cc_final: 0.7150 (tmm160) REVERT: B 163 ASN cc_start: 0.8709 (m110) cc_final: 0.8409 (m110) REVERT: C 91 GLN cc_start: 0.8944 (tm-30) cc_final: 0.7872 (tm-30) REVERT: C 118 PHE cc_start: 0.7750 (m-80) cc_final: 0.7459 (m-80) REVERT: E 37 TYR cc_start: 0.8829 (m-80) cc_final: 0.8270 (m-80) REVERT: E 179 SER cc_start: 0.8505 (t) cc_final: 0.8293 (p) REVERT: F 118 MET cc_start: 0.8854 (mtm) cc_final: 0.8496 (mtm) outliers start: 12 outliers final: 9 residues processed: 157 average time/residue: 0.4914 time to fit residues: 109.6105 Evaluate side-chains 154 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain F residue 215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10643 Z= 0.270 Angle : 0.529 6.206 14486 Z= 0.282 Chirality : 0.040 0.141 1684 Planarity : 0.004 0.050 1820 Dihedral : 3.804 23.240 1457 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.36 % Favored : 92.49 % Rotamer: Outliers : 1.23 % Allowed : 12.38 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.07 (0.24), residues: 1332 helix: 2.58 (0.25), residues: 389 sheet: -0.05 (0.29), residues: 348 loop : -1.71 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 113 HIS 0.004 0.001 HIS A 73 PHE 0.014 0.001 PHE A 249 TYR 0.012 0.001 TYR D 98 ARG 0.002 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8907 (tt) REVERT: B 63 ARG cc_start: 0.7660 (ttt-90) cc_final: 0.7156 (tmm160) REVERT: C 118 PHE cc_start: 0.7927 (m-80) cc_final: 0.7628 (m-80) REVERT: E 37 TYR cc_start: 0.8884 (m-80) cc_final: 0.8322 (m-80) outliers start: 14 outliers final: 12 residues processed: 150 average time/residue: 0.5173 time to fit residues: 111.3736 Evaluate side-chains 153 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain E residue 95 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10643 Z= 0.175 Angle : 0.502 8.006 14486 Z= 0.262 Chirality : 0.040 0.141 1684 Planarity : 0.004 0.052 1820 Dihedral : 3.678 22.671 1457 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.78 % Favored : 93.99 % Rotamer: Outliers : 1.14 % Allowed : 12.99 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1332 helix: 2.68 (0.25), residues: 389 sheet: -0.04 (0.29), residues: 350 loop : -1.62 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 95 HIS 0.003 0.001 HIS A 155 PHE 0.019 0.001 PHE F 163 TYR 0.012 0.001 TYR C 56 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8929 (tt) REVERT: B 63 ARG cc_start: 0.7589 (ttt-90) cc_final: 0.7060 (tmm160) REVERT: C 91 GLN cc_start: 0.8935 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 118 PHE cc_start: 0.7956 (m-80) cc_final: 0.7696 (m-80) REVERT: E 37 TYR cc_start: 0.8782 (m-80) cc_final: 0.8261 (m-80) REVERT: F 223 LYS cc_start: 0.7782 (mmtm) cc_final: 0.6743 (tttp) outliers start: 13 outliers final: 11 residues processed: 156 average time/residue: 0.5283 time to fit residues: 118.4525 Evaluate side-chains 158 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain E residue 95 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 chunk 126 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10643 Z= 0.184 Angle : 0.506 8.751 14486 Z= 0.263 Chirality : 0.040 0.139 1684 Planarity : 0.004 0.051 1820 Dihedral : 3.650 22.324 1457 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.77 % Rotamer: Outliers : 1.14 % Allowed : 13.35 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1332 helix: 2.62 (0.25), residues: 401 sheet: -0.04 (0.29), residues: 350 loop : -1.64 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.004 0.001 HIS A 155 PHE 0.011 0.001 PHE A 249 TYR 0.011 0.001 TYR C 56 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8928 (tt) REVERT: B 63 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.6999 (tmm160) REVERT: B 163 ASN cc_start: 0.8688 (m110) cc_final: 0.8373 (m110) REVERT: C 118 PHE cc_start: 0.7909 (m-80) cc_final: 0.7655 (m-80) REVERT: D 197 SER cc_start: 0.8852 (m) cc_final: 0.8565 (p) REVERT: E 37 TYR cc_start: 0.8792 (m-80) cc_final: 0.8258 (m-80) REVERT: F 223 LYS cc_start: 0.7849 (mmtm) cc_final: 0.6778 (tttp) outliers start: 13 outliers final: 11 residues processed: 157 average time/residue: 0.5055 time to fit residues: 112.7747 Evaluate side-chains 159 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain E residue 95 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 87 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10643 Z= 0.174 Angle : 0.510 8.996 14486 Z= 0.264 Chirality : 0.040 0.179 1684 Planarity : 0.004 0.052 1820 Dihedral : 3.610 22.138 1457 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.78 % Favored : 93.99 % Rotamer: Outliers : 1.14 % Allowed : 13.78 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.24 (0.24), residues: 1332 helix: 2.64 (0.26), residues: 401 sheet: -0.01 (0.29), residues: 350 loop : -1.60 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 179 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE F 163 TYR 0.011 0.001 TYR C 56 ARG 0.002 0.000 ARG A 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8921 (tt) REVERT: B 63 ARG cc_start: 0.7522 (ttt-90) cc_final: 0.7003 (tmm160) REVERT: B 163 ASN cc_start: 0.8687 (m110) cc_final: 0.8368 (m110) REVERT: C 118 PHE cc_start: 0.7909 (m-80) cc_final: 0.7670 (m-80) REVERT: D 197 SER cc_start: 0.8846 (m) cc_final: 0.8562 (p) REVERT: E 37 TYR cc_start: 0.8781 (m-80) cc_final: 0.8247 (m-80) REVERT: F 223 LYS cc_start: 0.7900 (mmtm) cc_final: 0.6711 (ttmm) outliers start: 13 outliers final: 11 residues processed: 155 average time/residue: 0.5132 time to fit residues: 111.7037 Evaluate side-chains 159 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 226 LYS Chi-restraints excluded: chain E residue 95 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118033 restraints weight = 51871.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119980 restraints weight = 51535.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120543 restraints weight = 42390.975| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2430 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: