Starting phenix.real_space_refine on Thu Nov 14 12:14:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geb_29964/11_2024/8geb_29964.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geb_29964/11_2024/8geb_29964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geb_29964/11_2024/8geb_29964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geb_29964/11_2024/8geb_29964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geb_29964/11_2024/8geb_29964.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geb_29964/11_2024/8geb_29964.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 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 36 5.16 5 C 4017 2.51 5 N 1091 2.21 5 O 1079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6223 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1650 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 3 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 198 Chain: "B" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2301 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 6, 'ASP:plan': 19} Unresolved non-hydrogen planarities: 158 Chain: "G" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 319 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1938 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 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: 4.77, per 1000 atoms: 0.77 Number of scatterers: 6223 At special positions: 0 Unit cell: (68.9, 98.58, 127.2, 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 36 16.00 O 1079 8.00 N 1091 7.00 C 4017 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 47.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.420A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.043A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.735A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.641A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.522A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.546A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.683A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET R 40 " --> pdb=" O MET R 36 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.895A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.238A 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 140 through 145 Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix removed outlier: 3.506A 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 298 removed outlier: 4.111A pdb=" N CYS R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.169A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 Processing helix chain 'R' and resid 321 through 327 removed outlier: 3.611A pdb=" N ILE R 325 " --> pdb=" O PHE R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 6.848A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50 removed outlier: 5.914A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 329 " --> pdb=" O LYS B 337 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.102A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.092A 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: 3.507A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.317A 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: 6.523A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.807A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.790A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.272A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1086 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: 1.94 Time building geometry restraints manager: 1.82 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: 1987 1.34 - 1.45: 886 1.45 - 1.57: 3436 1.57 - 1.69: 1 1.69 - 1.81: 48 Bond restraints: 6358 Sorted by residual: bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.575 -0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.441 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" CA ALA B 73 " pdb=" CB ALA B 73 " ideal model delta sigma weight residual 1.532 1.496 0.035 1.82e-02 3.02e+03 3.79e+00 ... (remaining 6353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 8572 1.70 - 3.41: 121 3.41 - 5.11: 13 5.11 - 6.82: 6 6.82 - 8.52: 2 Bond angle restraints: 8714 Sorted by residual: angle pdb=" N ILE B 269 " pdb=" CA ILE B 269 " pdb=" C ILE B 269 " ideal model delta sigma weight residual 109.34 117.26 -7.92 2.08e+00 2.31e-01 1.45e+01 angle pdb=" CB MET B 188 " pdb=" CG MET B 188 " pdb=" SD MET B 188 " ideal model delta sigma weight residual 112.70 104.18 8.52 3.00e+00 1.11e-01 8.06e+00 angle pdb=" N CYS B 271 " pdb=" CA CYS B 271 " pdb=" C CYS B 271 " ideal model delta sigma weight residual 110.59 114.37 -3.78 1.45e+00 4.76e-01 6.79e+00 angle pdb=" N SER B 74 " pdb=" CA SER B 74 " pdb=" C SER B 74 " ideal model delta sigma weight residual 109.85 113.95 -4.10 1.58e+00 4.01e-01 6.73e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 121.14 116.74 4.40 1.75e+00 3.27e-01 6.31e+00 ... (remaining 8709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 3352 16.71 - 33.41: 249 33.41 - 50.12: 45 50.12 - 66.82: 9 66.82 - 83.53: 2 Dihedral angle restraints: 3657 sinusoidal: 1051 harmonic: 2606 Sorted by residual: dihedral pdb=" CA ILE R 298 " pdb=" C ILE R 298 " pdb=" N GLN R 299 " pdb=" CA GLN R 299 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA MET B 262 " pdb=" C MET B 262 " pdb=" N THR B 263 " pdb=" CA THR B 263 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 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 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 650 0.030 - 0.060: 273 0.060 - 0.090: 84 0.090 - 0.121: 41 0.121 - 0.151: 2 Chirality restraints: 1050 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 5.68e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1047 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO R 323 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO B 194 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 321 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.015 5.00e-02 4.00e+02 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2190 2.85 - 3.36: 5967 3.36 - 3.87: 10203 3.87 - 4.39: 10707 4.39 - 4.90: 19725 Nonbonded interactions: 48792 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.333 3.040 nonbonded pdb=" OG SER B 279 " pdb=" OD2 ASP G 48 " model vdw 2.336 3.040 nonbonded pdb=" NH1 ARG B 137 " pdb=" O ILE B 171 " model vdw 2.373 3.120 nonbonded pdb=" OD1 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.375 3.040 nonbonded pdb=" O ARG A 283 " pdb=" NH1 ARG A 356 " model vdw 2.380 3.120 ... (remaining 48787 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.270 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 0.052 6358 Z= 0.225 Angle : 0.520 8.519 8714 Z= 0.275 Chirality : 0.040 0.151 1050 Planarity : 0.003 0.044 1106 Dihedral : 12.499 83.527 1960 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 1.44 (0.29), residues: 875 helix: 2.72 (0.26), residues: 396 sheet: 0.15 (0.41), residues: 162 loop : -0.95 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 281 HIS 0.006 0.001 HIS B 266 PHE 0.007 0.001 PHE A 212 TYR 0.011 0.001 TYR R 199 ARG 0.007 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.705 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1196 time to fit residues: 14.6923 Evaluate side-chains 64 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: