Starting phenix.real_space_refine on Sat Aug 3 01:38:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gea_29962/08_2024/8gea_29962.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gea_29962/08_2024/8gea_29962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gea_29962/08_2024/8gea_29962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gea_29962/08_2024/8gea_29962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gea_29962/08_2024/8gea_29962.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gea_29962/08_2024/8gea_29962.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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 42 5.16 5 C 4221 2.51 5 N 1140 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6551 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1751 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2392 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 116 Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 335 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2058 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.59, per 1000 atoms: 0.70 Number of scatterers: 6551 At special positions: 0 Unit cell: (68.9, 97.52, 128.26, 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 42 16.00 O 1148 8.00 N 1140 7.00 C 4221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 48.6% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.967A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.642A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.418A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.510A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.669A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.777A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.295A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix removed outlier: 3.566A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.711A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.879A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 4.136A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.597A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.514A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.065A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.533A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.843A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.793A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.708A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.537A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1134 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: 1.96 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2117 1.34 - 1.46: 1403 1.46 - 1.58: 3114 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6692 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.568 -0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.438 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.563 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.483 -0.032 2.00e-02 2.50e+03 2.59e+00 ... (remaining 6687 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.93: 135 106.93 - 113.71: 3800 113.71 - 120.49: 2571 120.49 - 127.27: 2566 127.27 - 134.05: 73 Bond angle restraints: 9145 Sorted by residual: angle pdb=" N GLY A 329 " pdb=" CA GLY A 329 " pdb=" C GLY A 329 " ideal model delta sigma weight residual 113.18 107.88 5.30 2.37e+00 1.78e-01 5.01e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.49 -5.86 3.00e+00 1.11e-01 3.81e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.72 117.50 3.22 1.67e+00 3.59e-01 3.71e+00 angle pdb=" N ILE R 55 " pdb=" CA ILE R 55 " pdb=" CB ILE R 55 " ideal model delta sigma weight residual 110.54 112.95 -2.41 1.36e+00 5.41e-01 3.15e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 116.05 -5.16 3.00e+00 1.11e-01 2.96e+00 ... (remaining 9140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3566 17.97 - 35.94: 284 35.94 - 53.91: 23 53.91 - 71.87: 3 71.87 - 89.84: 4 Dihedral angle restraints: 3880 sinusoidal: 1249 harmonic: 2631 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CG ARG A 336 " pdb=" CD ARG A 336 " pdb=" NE ARG A 336 " pdb=" CZ ARG A 336 " ideal model delta sinusoidal sigma weight residual 90.00 133.08 -43.08 2 1.50e+01 4.44e-03 9.95e+00 dihedral pdb=" CA ALA R 85 " pdb=" C ALA R 85 " pdb=" N VAL R 86 " pdb=" CA VAL R 86 " ideal model delta harmonic sigma weight residual -180.00 -164.76 -15.24 0 5.00e+00 4.00e-02 9.29e+00 ... (remaining 3877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 704 0.030 - 0.061: 264 0.061 - 0.091: 74 0.091 - 0.121: 48 0.121 - 0.151: 5 Chirality restraints: 1095 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CB THR A 263 " pdb=" CA THR A 263 " pdb=" OG1 THR A 263 " pdb=" CG2 THR A 263 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 1092 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.22e+00 pdb=" CG TYR B 59 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.017 5.00e-02 4.00e+02 2.53e-02 1.02e+00 pdb=" N PRO B 194 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.016 5.00e-02 4.00e+02 2.50e-02 9.96e-01 pdb=" N PRO B 236 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.014 5.00e-02 4.00e+02 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1600 2.80 - 3.32: 6354 3.32 - 3.85: 10867 3.85 - 4.37: 11896 4.37 - 4.90: 21791 Nonbonded interactions: 52508 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" O HIS G 44 " model vdw 2.269 3.040 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.299 3.120 nonbonded pdb=" OE1 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.313 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.316 3.120 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.327 3.040 ... (remaining 52503 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 ========== 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=0.00 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: 4.720 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: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 22.170 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6692 Z= 0.215 Angle : 0.476 5.858 9145 Z= 0.255 Chirality : 0.039 0.151 1095 Planarity : 0.003 0.025 1150 Dihedral : 12.734 89.842 2169 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.28), residues: 888 helix: 2.33 (0.26), residues: 396 sheet: 0.02 (0.40), residues: 171 loop : -0.83 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 281 HIS 0.005 0.001 HIS A 220 PHE 0.010 0.001 PHE R 289 TYR 0.026 0.001 TYR B 59 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.729 Fit side-chains REVERT: R 277 ILE cc_start: 0.7992 (tt) cc_final: 0.7757 (tp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1751 time to fit residues: 21.0580 Evaluate side-chains 68 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 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: 0.7838 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6692 Z= 0.211 Angle : 0.478 5.342 9145 Z= 0.266 Chirality : 0.040 0.178 1095 Planarity : 0.003 0.026 1150 Dihedral : 3.915 30.645 976 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.67 % Allowed : 9.03 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.28), residues: 888 helix: 2.42 (0.26), residues: 400 sheet: -0.05 (0.39), residues: 174 loop : -0.78 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE R 289 TYR 0.020 0.001 TYR B 59 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.753 Fit side-chains REVERT: R 36 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6710 (ttp) REVERT: R 58 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7862 (mp) REVERT: R 277 ILE cc_start: 0.7959 (tt) cc_final: 0.7705 (tp) outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.1562 time to fit residues: 18.3103 Evaluate side-chains 77 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 159 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 0.0170 chunk 80 optimal weight: 0.0970 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6692 Z= 0.154 Angle : 0.437 5.139 9145 Z= 0.241 Chirality : 0.039 0.183 1095 Planarity : 0.003 0.028 1150 Dihedral : 3.761 30.555 976 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.67 % Allowed : 12.21 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.28), residues: 888 helix: 2.57 (0.26), residues: 400 sheet: 0.13 (0.39), residues: 171 loop : -0.73 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.013 0.001 PHE R 289 TYR 0.015 0.001 TYR B 59 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.765 Fit side-chains REVERT: R 36 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6869 (ttp) REVERT: R 58 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7937 (mp) REVERT: R 277 ILE cc_start: 0.7780 (tt) cc_final: 0.7560 (tp) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.1415 time to fit residues: 16.8384 Evaluate side-chains 78 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.0030 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6692 Z= 0.172 Angle : 0.435 5.272 9145 Z= 0.241 Chirality : 0.039 0.151 1095 Planarity : 0.003 0.027 1150 Dihedral : 3.726 29.184 976 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.84 % Allowed : 14.05 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.28), residues: 888 helix: 2.53 (0.26), residues: 400 sheet: 0.01 (0.39), residues: 171 loop : -0.75 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS A 220 PHE 0.013 0.001 PHE B 199 TYR 0.016 0.001 TYR B 59 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.763 Fit side-chains REVERT: B 211 TRP cc_start: 0.8983 (m100) cc_final: 0.8677 (m100) REVERT: R 36 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6845 (ttp) REVERT: R 58 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7913 (mp) REVERT: R 277 ILE cc_start: 0.7729 (tt) cc_final: 0.7521 (tp) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.1459 time to fit residues: 17.9828 Evaluate side-chains 82 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.0040 overall best weight: 0.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6692 Z= 0.158 Angle : 0.432 7.012 9145 Z= 0.237 Chirality : 0.039 0.219 1095 Planarity : 0.003 0.028 1150 Dihedral : 3.668 28.866 976 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.01 % Allowed : 13.04 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.29), residues: 888 helix: 2.48 (0.26), residues: 407 sheet: 0.03 (0.39), residues: 169 loop : -0.66 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS A 220 PHE 0.012 0.001 PHE B 199 TYR 0.016 0.001 TYR B 59 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.750 Fit side-chains REVERT: B 211 TRP cc_start: 0.9003 (m100) cc_final: 0.8767 (m100) REVERT: R 36 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6886 (ttp) REVERT: R 58 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7913 (mp) outliers start: 18 outliers final: 12 residues processed: 90 average time/residue: 0.1539 time to fit residues: 19.7064 Evaluate side-chains 86 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.0670 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6692 Z= 0.287 Angle : 0.493 5.733 9145 Z= 0.271 Chirality : 0.041 0.185 1095 Planarity : 0.003 0.026 1150 Dihedral : 3.897 29.468 976 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.84 % Allowed : 13.71 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.29), residues: 888 helix: 2.33 (0.26), residues: 401 sheet: -0.20 (0.37), residues: 175 loop : -0.62 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.022 0.002 PHE B 199 TYR 0.021 0.001 TYR B 59 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 0.743 Fit side-chains REVERT: R 58 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7927 (mp) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.1428 time to fit residues: 17.3073 Evaluate side-chains 83 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 86 optimal weight: 0.0050 chunk 54 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6692 Z= 0.160 Angle : 0.441 6.257 9145 Z= 0.242 Chirality : 0.040 0.244 1095 Planarity : 0.003 0.027 1150 Dihedral : 3.793 31.455 976 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.34 % Allowed : 16.05 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.29), residues: 888 helix: 2.45 (0.26), residues: 401 sheet: -0.18 (0.38), residues: 175 loop : -0.65 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR R 199 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.943 Fit side-chains REVERT: A 236 GLN cc_start: 0.8049 (pt0) cc_final: 0.7780 (pt0) REVERT: B 58 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8445 (mp) REVERT: B 59 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: R 36 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6881 (ttp) REVERT: R 58 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7933 (mp) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.1448 time to fit residues: 17.6102 Evaluate side-chains 83 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.2980 chunk 17 optimal weight: 0.0170 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6692 Z= 0.155 Angle : 0.442 6.133 9145 Z= 0.243 Chirality : 0.040 0.214 1095 Planarity : 0.003 0.027 1150 Dihedral : 3.739 32.431 976 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.68 % Allowed : 16.22 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.29), residues: 888 helix: 2.45 (0.26), residues: 406 sheet: -0.20 (0.38), residues: 175 loop : -0.69 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR R 199 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.722 Fit side-chains REVERT: B 58 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8454 (mp) REVERT: B 59 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: R 36 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6883 (ttp) REVERT: R 58 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7962 (mp) outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 0.1400 time to fit residues: 17.5687 Evaluate side-chains 91 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9274 > 50: distance: 2 - 19: 12.091 distance: 6 - 26: 32.748 distance: 13 - 34: 27.600 distance: 16 - 19: 8.724 distance: 17 - 39: 22.695 distance: 19 - 20: 11.121 distance: 20 - 21: 25.757 distance: 20 - 23: 22.322 distance: 21 - 22: 21.416 distance: 21 - 26: 29.931 distance: 22 - 44: 16.120 distance: 23 - 24: 24.971 distance: 23 - 25: 16.091 distance: 26 - 27: 35.885 distance: 27 - 28: 7.383 distance: 27 - 30: 9.234 distance: 28 - 29: 3.516 distance: 28 - 34: 9.225 distance: 30 - 31: 42.648 distance: 31 - 32: 18.786 distance: 32 - 33: 27.775 distance: 34 - 35: 16.474 distance: 35 - 36: 30.003 distance: 35 - 38: 17.942 distance: 36 - 37: 13.826 distance: 36 - 39: 25.364 distance: 37 - 59: 4.554 distance: 39 - 40: 3.513 distance: 40 - 41: 10.864 distance: 40 - 43: 16.027 distance: 41 - 44: 7.704 distance: 42 - 64: 38.043 distance: 44 - 45: 10.398 distance: 45 - 46: 21.840 distance: 45 - 48: 14.688 distance: 46 - 52: 22.292 distance: 47 - 69: 14.839 distance: 48 - 49: 4.600 distance: 48 - 50: 3.626 distance: 49 - 51: 11.548 distance: 52 - 53: 19.106 distance: 53 - 54: 19.852 distance: 53 - 56: 3.511 distance: 54 - 55: 4.747 distance: 54 - 59: 18.254 distance: 55 - 77: 35.606 distance: 56 - 57: 20.708 distance: 56 - 58: 19.246 distance: 59 - 60: 7.827 distance: 60 - 61: 11.021 distance: 60 - 63: 12.054 distance: 61 - 62: 12.667 distance: 61 - 64: 11.138 distance: 62 - 84: 16.989 distance: 64 - 65: 10.916 distance: 65 - 66: 12.761 distance: 65 - 68: 11.395 distance: 66 - 67: 8.961 distance: 66 - 69: 4.967 distance: 67 - 90: 23.973 distance: 69 - 70: 11.902 distance: 70 - 73: 19.702 distance: 71 - 72: 12.411 distance: 71 - 77: 9.611 distance: 72 - 93: 23.748 distance: 77 - 78: 5.936 distance: 78 - 79: 5.975 distance: 78 - 81: 16.402 distance: 79 - 80: 5.566 distance: 79 - 84: 6.262 distance: 80 - 100: 13.691 distance: 81 - 82: 15.942 distance: 81 - 83: 14.900