Starting phenix.real_space_refine on Sat Jul 20 00:22:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/07_2024/7w40_32298.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/07_2024/7w40_32298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/07_2024/7w40_32298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/07_2024/7w40_32298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/07_2024/7w40_32298.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/07_2024/7w40_32298.cif" } resolution = 3.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5882 2.51 5 N 1573 2.21 5 O 1724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "H TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9236 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2280 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 14, 'TRANS': 286} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2330 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2409 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 5, 'TRANS': 309} Chain: "D" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 365 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "H" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 81 Unusual residues: {'BAL': 1} Classifications: {'peptide': 8, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'POST-BETA-TRANS': 1, 'PRE-BETA-TRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BAL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.43, per 1000 atoms: 0.59 Number of scatterers: 9236 At special positions: 0 Unit cell: (111.54, 112.554, 128.778, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1724 8.00 N 1573 7.00 C 5882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 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: 3.77 Conformation dependent library (CDL) restraints added in 1.7 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN E 1 " Input volumes are d-peptide like pdb=" CB BAL E 6 " Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 39.2% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 37 through 69 Proline residue: A 44 - end of helix removed outlier: 4.306A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 103 removed outlier: 3.600A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 108 through 144 removed outlier: 4.061A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Proline residue: A 117 - end of helix removed outlier: 3.523A pdb=" N THR A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 173 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.549A pdb=" N TYR A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 290 removed outlier: 3.717A pdb=" N LYS A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.743A pdb=" N LEU A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 326 removed outlier: 3.593A pdb=" N ASN A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Proline residue: A 319 - end of helix removed outlier: 3.847A pdb=" N LEU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'B' and resid 12 through 38 removed outlier: 3.822A pdb=" N ARG B 38 " --> pdb=" O GLU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 68 through 88 removed outlier: 4.687A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.750A pdb=" N GLU B 150 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 275 through 286 removed outlier: 4.434A pdb=" N MET B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 removed outlier: 4.171A pdb=" N TYR B 291 " --> pdb=" O HIS B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 315 Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.509A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 removed outlier: 8.867A pdb=" N VAL A 294 " --> pdb=" O PRO A 183 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS A 185 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 196 removed outlier: 6.347A pdb=" N LEU B 40 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL B 204 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 42 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 225 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 226 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE B 272 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE B 228 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASN B 274 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 230 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.739A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.697A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.072A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.660A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.895A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.286A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.595A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.730A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.327A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'H' and resid 147 through 148 removed outlier: 3.616A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1272 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: 2.58 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2015 1.33 - 1.45: 2197 1.45 - 1.57: 5142 1.57 - 1.69: 0 1.69 - 1.82: 86 Bond restraints: 9440 Sorted by residual: bond pdb=" CG TRP E 3 " pdb=" CD2 TRP E 3 " ideal model delta sigma weight residual 1.433 1.333 0.100 1.80e-02 3.09e+03 3.07e+01 bond pdb=" CB PHE E 8 " pdb=" CG PHE E 8 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.57e+01 bond pdb=" CG HIS E 7 " pdb=" ND1 HIS E 7 " ideal model delta sigma weight residual 1.378 1.324 0.054 1.10e-02 8.26e+03 2.37e+01 bond pdb=" CB DPN E 1 " pdb=" CG DPN E 1 " ideal model delta sigma weight residual 1.502 1.391 0.111 2.30e-02 1.89e+03 2.34e+01 bond pdb=" C VAL A 266 " pdb=" O VAL A 266 " ideal model delta sigma weight residual 1.237 1.292 -0.055 1.17e-02 7.31e+03 2.19e+01 ... (remaining 9435 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.44: 181 105.44 - 112.66: 4739 112.66 - 119.88: 3741 119.88 - 127.10: 4039 127.10 - 134.32: 99 Bond angle restraints: 12799 Sorted by residual: angle pdb=" N ASP C 247 " pdb=" CA ASP C 247 " pdb=" C ASP C 247 " ideal model delta sigma weight residual 110.35 102.15 8.20 1.36e+00 5.41e-01 3.64e+01 angle pdb=" N ALA A 176 " pdb=" CA ALA A 176 " pdb=" C ALA A 176 " ideal model delta sigma weight residual 113.97 106.80 7.17 1.28e+00 6.10e-01 3.14e+01 angle pdb=" CA GLY H 114 " pdb=" C GLY H 114 " pdb=" O GLY H 114 " ideal model delta sigma weight residual 121.88 117.85 4.03 7.80e-01 1.64e+00 2.67e+01 angle pdb=" N LEU A 205 " pdb=" CA LEU A 205 " pdb=" C LEU A 205 " ideal model delta sigma weight residual 113.55 107.06 6.49 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N ARG C 48 " pdb=" CA ARG C 48 " pdb=" C ARG C 48 " ideal model delta sigma weight residual 113.23 106.84 6.39 1.24e+00 6.50e-01 2.65e+01 ... (remaining 12794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 5102 16.73 - 33.46: 405 33.46 - 50.20: 78 50.20 - 66.93: 15 66.93 - 83.66: 2 Dihedral angle restraints: 5602 sinusoidal: 2154 harmonic: 3448 Sorted by residual: dihedral pdb=" C TYR H 235 " pdb=" N TYR H 235 " pdb=" CA TYR H 235 " pdb=" CB TYR H 235 " ideal model delta harmonic sigma weight residual -122.60 -140.20 17.60 0 2.50e+00 1.60e-01 4.96e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.36 56.64 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CA TYR H 235 " pdb=" CB TYR H 235 " ideal model delta harmonic sigma weight residual 122.80 139.06 -16.26 0 2.50e+00 1.60e-01 4.23e+01 ... (remaining 5599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 1285 0.135 - 0.270: 145 0.270 - 0.405: 8 0.405 - 0.540: 0 0.540 - 0.675: 1 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CA TYR H 235 " pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CB TYR H 235 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA LEU C 79 " pdb=" N LEU C 79 " pdb=" C LEU C 79 " pdb=" CB LEU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA LEU H 4 " pdb=" N LEU H 4 " pdb=" C LEU H 4 " pdb=" CB LEU H 4 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1436 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 175 " 0.016 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR H 175 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR H 175 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR H 175 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR H 175 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR H 175 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR H 175 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 175 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 127 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LYS C 127 " -0.055 2.00e-02 2.50e+03 pdb=" O LYS C 127 " 0.021 2.00e-02 2.50e+03 pdb=" N THR C 128 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 315 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C VAL C 315 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL C 315 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 316 " -0.017 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1996 2.79 - 3.32: 8658 3.32 - 3.85: 14852 3.85 - 4.37: 18476 4.37 - 4.90: 31094 Nonbonded interactions: 75076 Sorted by model distance: nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.266 2.440 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.290 2.440 nonbonded pdb=" NE ARG C 283 " pdb=" OD1 ASP C 298 " model vdw 2.309 2.520 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.322 2.440 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.341 2.440 ... (remaining 75071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.720 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 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 : 0.011 0.117 9440 Z= 0.709 Angle : 1.288 8.202 12799 Z= 0.929 Chirality : 0.085 0.675 1439 Planarity : 0.006 0.053 1630 Dihedral : 12.467 83.658 3371 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 3.84 % Favored : 94.24 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.42 (0.23), residues: 1162 helix: 0.42 (0.25), residues: 411 sheet: 0.10 (0.31), residues: 286 loop : -1.08 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 82 HIS 0.009 0.002 HIS C 311 PHE 0.030 0.003 PHE C 199 TYR 0.056 0.003 TYR H 175 ARG 0.011 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 230 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 SER cc_start: 0.5579 (t) cc_final: 0.5323 (m) REVERT: B 26 ASP cc_start: 0.7878 (m-30) cc_final: 0.7571 (m-30) REVERT: B 60 ARG cc_start: 0.6721 (ttp80) cc_final: 0.6093 (mmm160) REVERT: B 83 ILE cc_start: 0.6982 (mp) cc_final: 0.6749 (mp) REVERT: B 259 ILE cc_start: 0.7714 (pt) cc_final: 0.7487 (pt) REVERT: B 322 LYS cc_start: 0.7322 (mtpp) cc_final: 0.6755 (tptt) REVERT: B 332 THR cc_start: 0.7611 (t) cc_final: 0.7183 (m) REVERT: B 348 ILE cc_start: 0.6745 (mm) cc_final: 0.6509 (mt) outliers start: 19 outliers final: 3 residues processed: 246 average time/residue: 1.1128 time to fit residues: 292.8540 Evaluate side-chains 146 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 296 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 HIS B 336 ASN C 75 GLN C 88 ASN C 142 HIS H 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 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 : 0.004 0.050 9440 Z= 0.278 Angle : 0.682 9.432 12799 Z= 0.359 Chirality : 0.045 0.287 1439 Planarity : 0.005 0.046 1630 Dihedral : 5.475 46.732 1303 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.36 % Allowed : 13.75 % Favored : 80.89 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1162 helix: 1.59 (0.24), residues: 413 sheet: 0.26 (0.31), residues: 286 loop : -0.95 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 82 HIS 0.006 0.002 HIS B 218 PHE 0.022 0.002 PHE C 253 TYR 0.045 0.002 TYR H 235 ARG 0.008 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 143 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6991 (tt) REVERT: B 23 LYS cc_start: 0.7539 (mptt) cc_final: 0.7223 (mttp) REVERT: B 60 ARG cc_start: 0.6930 (ttp80) cc_final: 0.6186 (mmp-170) REVERT: B 282 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6922 (tttt) REVERT: B 322 LYS cc_start: 0.7418 (mtpp) cc_final: 0.6707 (tptt) REVERT: C 228 ASP cc_start: 0.6432 (OUTLIER) cc_final: 0.5689 (m-30) REVERT: C 269 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6711 (mm) REVERT: H 235 TYR cc_start: 0.4303 (OUTLIER) cc_final: 0.3949 (t80) outliers start: 53 outliers final: 24 residues processed: 180 average time/residue: 1.3025 time to fit residues: 249.5567 Evaluate side-chains 149 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN B 327 HIS ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9440 Z= 0.200 Angle : 0.606 8.324 12799 Z= 0.316 Chirality : 0.043 0.240 1439 Planarity : 0.004 0.050 1630 Dihedral : 5.290 52.611 1303 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.45 % Allowed : 17.69 % Favored : 77.86 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.80 (0.24), residues: 1162 helix: 2.13 (0.25), residues: 412 sheet: 0.44 (0.31), residues: 281 loop : -0.86 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.002 PHE B 201 TYR 0.031 0.001 TYR H 235 ARG 0.006 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7550 (tptt) cc_final: 0.7228 (tptm) REVERT: B 38 ARG cc_start: 0.6866 (mtp-110) cc_final: 0.6635 (mtp85) REVERT: B 60 ARG cc_start: 0.6915 (ttp80) cc_final: 0.6175 (mmm160) REVERT: C 228 ASP cc_start: 0.6379 (OUTLIER) cc_final: 0.5600 (m-30) REVERT: C 269 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6622 (mm) REVERT: H 6 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5893 (pm20) REVERT: H 235 TYR cc_start: 0.4005 (OUTLIER) cc_final: 0.3729 (t80) outliers start: 44 outliers final: 23 residues processed: 162 average time/residue: 1.3774 time to fit residues: 236.6224 Evaluate side-chains 140 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 179 GLN H 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9440 Z= 0.204 Angle : 0.599 7.529 12799 Z= 0.309 Chirality : 0.042 0.223 1439 Planarity : 0.004 0.058 1630 Dihedral : 5.196 54.899 1303 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.95 % Allowed : 18.40 % Favored : 76.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.91 (0.24), residues: 1162 helix: 2.26 (0.25), residues: 413 sheet: 0.32 (0.30), residues: 290 loop : -0.74 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.014 0.002 PHE B 201 TYR 0.028 0.002 TYR H 235 ARG 0.005 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 125 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5479 (ttp) cc_final: 0.5236 (ttm) REVERT: A 298 MET cc_start: 0.5621 (tpp) cc_final: 0.5382 (tpt) REVERT: B 60 ARG cc_start: 0.6963 (ttp80) cc_final: 0.6181 (mmm160) REVERT: B 202 ARG cc_start: 0.6836 (mtp85) cc_final: 0.6491 (ptm160) REVERT: B 335 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6670 (tp30) REVERT: C 269 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6541 (mm) REVERT: H 235 TYR cc_start: 0.3981 (OUTLIER) cc_final: 0.3684 (t80) outliers start: 49 outliers final: 26 residues processed: 160 average time/residue: 1.3367 time to fit residues: 227.5197 Evaluate side-chains 145 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.543 > 50: distance: 78 - 166: 31.659 distance: 81 - 163: 34.074 distance: 92 - 150: 25.786 distance: 95 - 147: 25.634 distance: 103 - 133: 33.030 distance: 105 - 109: 33.684 distance: 110 - 111: 42.645 distance: 111 - 112: 48.845 distance: 111 - 118: 42.598 distance: 113 - 114: 63.069 distance: 114 - 115: 23.791 distance: 115 - 116: 56.882 distance: 115 - 117: 3.400 distance: 118 - 119: 40.295 distance: 119 - 120: 40.229 distance: 119 - 122: 40.981 distance: 120 - 121: 40.418 distance: 122 - 123: 14.662 distance: 123 - 124: 26.058 distance: 123 - 125: 46.616 distance: 126 - 127: 33.981 distance: 127 - 128: 39.407 distance: 128 - 129: 24.020 distance: 128 - 130: 46.054 distance: 132 - 133: 40.277 distance: 132 - 139: 18.793 distance: 134 - 135: 40.491 distance: 135 - 136: 40.938 distance: 136 - 137: 34.173 distance: 137 - 138: 57.004 distance: 139 - 140: 36.377 distance: 139 - 249: 26.195 distance: 140 - 141: 13.569 distance: 140 - 143: 21.668 distance: 141 - 142: 28.203 distance: 141 - 147: 45.082 distance: 142 - 246: 36.481 distance: 143 - 144: 28.115 distance: 144 - 145: 29.830 distance: 144 - 146: 19.589 distance: 147 - 148: 31.379 distance: 148 - 149: 26.567 distance: 148 - 151: 4.536 distance: 149 - 150: 27.957 distance: 149 - 155: 44.445 distance: 151 - 152: 57.802 distance: 151 - 153: 30.943 distance: 152 - 154: 55.383 distance: 155 - 156: 39.764 distance: 155 - 237: 33.524 distance: 156 - 157: 15.757 distance: 156 - 159: 47.941 distance: 157 - 158: 14.787 distance: 157 - 163: 25.883 distance: 158 - 234: 36.337 distance: 159 - 160: 20.271 distance: 159 - 161: 4.077 distance: 160 - 162: 47.231 distance: 163 - 164: 11.666 distance: 164 - 165: 12.574 distance: 164 - 167: 11.491 distance: 165 - 166: 31.969 distance: 167 - 168: 4.373 distance: 168 - 169: 6.323 distance: 168 - 170: 21.692 distance: 169 - 171: 17.540 distance: 170 - 172: 55.358 distance: 170 - 173: 32.188 distance: 171 - 172: 55.859 distance: 172 - 174: 32.481 distance: 173 - 175: 22.749 distance: 174 - 176: 42.155 distance: 175 - 176: 23.726 distance: 177 - 178: 4.453 distance: 178 - 179: 41.815 distance: 178 - 181: 34.535 distance: 179 - 180: 43.036 distance: 179 - 185: 47.879 distance: 181 - 182: 39.175 distance: 185 - 186: 39.572 distance: 186 - 187: 18.098 distance: 187 - 188: 15.967 distance: 187 - 191: 29.008 distance: 189 - 190: 67.087