Starting phenix.real_space_refine (version: dev) on Mon Mar 13 22:01:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2023/6snh_10257_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2023/6snh_10257.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2023/6snh_10257_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2023/6snh_10257_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2023/6snh_10257_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2023/6snh_10257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2023/6snh_10257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2023/6snh_10257_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6snh_10257/03_2023/6snh_10257_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3122 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "X PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 129": "NH1" <-> "NH2" Residue "X ASP 150": "OD1" <-> "OD2" Residue "X PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 167": "NH1" <-> "NH2" Residue "X TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 250": "NH1" <-> "NH2" Residue "X PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 169": "OD1" <-> "OD2" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 7315 Number of models: 1 Model: "" Number of chains: 4 Chain: "X" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3924 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 25, 'TRANS': 453} Chain breaks: 1 Chain: "H" Number of atoms: 1690 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Conformer: "B" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} bond proxies already assigned to first conformer: 1721 Chain: "L" Number of atoms: 1659 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1654 Chain: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'LMH': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 6.19, per 1000 atoms: 0.85 Number of scatterers: 7315 At special positions: 0 Unit cell: (110.04, 84.84, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 1 15.00 O 1326 8.00 N 1156 7.00 C 4801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS X 314 " - pdb=" SG CYS X 515 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.05 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 38.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'X' and resid 41 through 53 removed outlier: 4.335A pdb=" N VAL X 47 " --> pdb=" O PHE X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 81 removed outlier: 3.931A pdb=" N GLN X 81 " --> pdb=" O MET X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 87 No H-bonds generated for 'chain 'X' and resid 85 through 87' Processing helix chain 'X' and resid 102 through 118 Processing helix chain 'X' and resid 121 through 123 No H-bonds generated for 'chain 'X' and resid 121 through 123' Processing helix chain 'X' and resid 139 through 153 Processing helix chain 'X' and resid 155 through 169 Processing helix chain 'X' and resid 173 through 185 removed outlier: 4.045A pdb=" N ILE X 183 " --> pdb=" O ALA X 179 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE X 185 " --> pdb=" O SER X 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 193 Processing helix chain 'X' and resid 200 through 215 Processing helix chain 'X' and resid 219 through 232 removed outlier: 3.818A pdb=" N VAL X 224 " --> pdb=" O ALA X 220 " (cutoff:3.500A) Processing helix chain 'X' and resid 234 through 252 removed outlier: 3.862A pdb=" N TYR X 238 " --> pdb=" O MET X 235 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR X 239 " --> pdb=" O ALA X 236 " (cutoff:3.500A) Proline residue: X 241 - end of helix removed outlier: 4.750A pdb=" N PHE X 244 " --> pdb=" O PRO X 241 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU X 247 " --> pdb=" O PHE X 244 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER X 251 " --> pdb=" O LEU X 248 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU X 252 " --> pdb=" O SER X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 260 through 281 Proline residue: X 279 - end of helix Processing helix chain 'X' and resid 286 through 297 removed outlier: 3.515A pdb=" N HIS X 295 " --> pdb=" O GLN X 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 320 removed outlier: 4.535A pdb=" N VAL X 318 " --> pdb=" O CYS X 314 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE X 319 " --> pdb=" O VAL X 315 " (cutoff:3.500A) Processing helix chain 'X' and resid 322 through 325 No H-bonds generated for 'chain 'X' and resid 322 through 325' Processing helix chain 'X' and resid 329 through 352 removed outlier: 3.545A pdb=" N LEU X 336 " --> pdb=" O GLN X 332 " (cutoff:3.500A) Proline residue: X 345 - end of helix Processing helix chain 'X' and resid 356 through 373 removed outlier: 3.661A pdb=" N LEU X 359 " --> pdb=" O LYS X 356 " (cutoff:3.500A) Proline residue: X 360 - end of helix removed outlier: 3.514A pdb=" N LEU X 363 " --> pdb=" O PRO X 360 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER X 367 " --> pdb=" O ILE X 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU X 372 " --> pdb=" O SER X 369 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE X 373 " --> pdb=" O PHE X 370 " (cutoff:3.500A) Processing helix chain 'X' and resid 382 through 392 Proline residue: X 388 - end of helix removed outlier: 4.359A pdb=" N LEU X 392 " --> pdb=" O PRO X 388 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 422 removed outlier: 3.536A pdb=" N LEU X 415 " --> pdb=" O ALA X 411 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP X 416 " --> pdb=" O LEU X 412 " (cutoff:3.500A) Proline residue: X 417 - end of helix Processing helix chain 'X' and resid 427 through 438 Processing helix chain 'X' and resid 477 through 498 removed outlier: 3.730A pdb=" N PHE X 495 " --> pdb=" O GLY X 491 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU X 496 " --> pdb=" O PHE X 492 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP X 497 " --> pdb=" O TYR X 493 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN X 498 " --> pdb=" O HIS X 494 " (cutoff:3.500A) Processing helix chain 'X' and resid 510 through 535 removed outlier: 3.742A pdb=" N PHE X 519 " --> pdb=" O CYS X 515 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE X 520 " --> pdb=" O ALA X 516 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS X 521 " --> pdb=" O VAL X 517 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 195 through 198 No H-bonds generated for 'chain 'H' and resid 195 through 198' Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 185 through 190 Processing sheet with id= A, first strand: chain 'H' and resid 5 through 7 Processing sheet with id= B, first strand: chain 'H' and resid 116 through 118 removed outlier: 3.912A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 129 through 133 removed outlier: 4.278A pdb=" N SER H 188 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE H 175 " --> pdb=" O SER H 188 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 159 through 163 Processing sheet with id= E, first strand: chain 'L' and resid 5 through 7 Processing sheet with id= F, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.048A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 116 through 120 Processing sheet with id= H, first strand: chain 'L' and resid 146 through 152 306 hydrogen bonds defined for protein. 808 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: 1.92 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1506 1.33 - 1.46: 2404 1.46 - 1.58: 3589 1.58 - 1.71: 2 1.71 - 1.84: 44 Bond restraints: 7545 Sorted by residual: bond pdb=" C SER L 10 " pdb=" O SER L 10 " ideal model delta sigma weight residual 1.235 1.344 -0.109 1.18e-02 7.18e+03 8.52e+01 bond pdb=" C33 LMH X 601 " pdb=" C34 LMH X 601 " ideal model delta sigma weight residual 1.419 1.510 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C33 LMH X 601 " pdb=" O32 LMH X 601 " ideal model delta sigma weight residual 1.550 1.464 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C SER L 10 " pdb=" CA ASER L 10 " ideal model delta sigma weight residual 1.520 1.558 -0.038 1.12e-02 7.97e+03 1.15e+01 bond pdb=" C SER L 10 " pdb=" CA BSER L 10 " ideal model delta sigma weight residual 1.520 1.558 -0.038 1.12e-02 7.97e+03 1.15e+01 ... (remaining 7540 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.45: 166 105.45 - 112.60: 3991 112.60 - 119.75: 2369 119.75 - 126.90: 3639 126.90 - 134.05: 127 Bond angle restraints: 10292 Sorted by residual: angle pdb=" C16 LMH X 601 " pdb=" C17 LMH X 601 " pdb=" C18 LMH X 601 " ideal model delta sigma weight residual 74.50 120.05 -45.55 3.00e+00 1.11e-01 2.31e+02 angle pdb=" C11 LMH X 601 " pdb=" C12 LMH X 601 " pdb=" C13 LMH X 601 " ideal model delta sigma weight residual 74.50 119.89 -45.39 3.00e+00 1.11e-01 2.29e+02 angle pdb=" C06 LMH X 601 " pdb=" C07 LMH X 601 " pdb=" C08 LMH X 601 " ideal model delta sigma weight residual 74.51 119.88 -45.37 3.00e+00 1.11e-01 2.29e+02 angle pdb=" CA SER H 188 " pdb=" C SER H 188 " pdb=" O SER H 188 " ideal model delta sigma weight residual 120.89 131.05 -10.16 1.10e+00 8.26e-01 8.53e+01 angle pdb=" N SER L 10 " pdb=" CA ASER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 108.13 123.32 -15.19 1.72e+00 3.38e-01 7.80e+01 ... (remaining 10287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 4039 19.94 - 39.89: 284 39.89 - 59.83: 51 59.83 - 79.77: 9 79.77 - 99.71: 4 Dihedral angle restraints: 4387 sinusoidal: 1664 harmonic: 2723 Sorted by residual: dihedral pdb=" N HIS X 378 " pdb=" C HIS X 378 " pdb=" CA HIS X 378 " pdb=" CB HIS X 378 " ideal model delta harmonic sigma weight residual 122.80 149.53 -26.73 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C HIS X 378 " pdb=" N HIS X 378 " pdb=" CA HIS X 378 " pdb=" CB HIS X 378 " ideal model delta harmonic sigma weight residual -122.60 -149.26 26.66 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" CB CYS X 314 " pdb=" SG CYS X 314 " pdb=" SG CYS X 515 " pdb=" CB CYS X 515 " ideal model delta sinusoidal sigma weight residual -86.00 -153.31 67.31 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 4384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 1137 0.218 - 0.435: 1 0.435 - 0.653: 2 0.653 - 0.871: 0 0.871 - 1.088: 1 Chirality restraints: 1141 Sorted by residual: chirality pdb=" CA HIS X 378 " pdb=" N HIS X 378 " pdb=" C HIS X 378 " pdb=" CB HIS X 378 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA ASER L 10 " pdb=" N SER L 10 " pdb=" C SER L 10 " pdb=" CB ASER L 10 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA BSER L 10 " pdb=" N SER L 10 " pdb=" C SER L 10 " pdb=" CB BSER L 10 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 1138 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE X 384 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.90e+00 pdb=" N PRO X 385 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO X 385 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO X 385 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 165 " 0.013 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C VAL L 165 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL L 165 " 0.016 2.00e-02 2.50e+03 pdb=" N THR L 166 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 160 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C THR H 160 " 0.042 2.00e-02 2.50e+03 pdb=" O THR H 160 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL H 161 " -0.014 2.00e-02 2.50e+03 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 653 2.72 - 3.27: 8138 3.27 - 3.81: 11947 3.81 - 4.36: 14257 4.36 - 4.90: 24172 Nonbonded interactions: 59167 Sorted by model distance: nonbonded pdb=" NH1 ARG L 110 " pdb=" O THR L 111 " model vdw 2.181 2.520 nonbonded pdb=" N VAL H 2 " pdb=" O SER H 25 " model vdw 2.212 2.520 nonbonded pdb=" O HIS L 191 " pdb=" NH1 ARG L 213 " model vdw 2.215 2.520 nonbonded pdb=" OH TYR H 59 " pdb=" N ILE H 69 " model vdw 2.230 2.520 nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.236 2.440 ... (remaining 59162 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 4801 2.51 5 N 1156 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 6.290 Check model and map are aligned: 0.110 Process input model: 25.050 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 Set scattering table: 0.060 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 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 : 0.008 0.109 7545 Z= 0.509 Angle : 1.237 45.552 10292 Z= 0.619 Chirality : 0.062 1.088 1141 Planarity : 0.005 0.070 1267 Dihedral : 14.342 99.714 2636 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.99 % Favored : 88.90 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 8.33 % 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: -4.30 (0.23), residues: 918 helix: -1.92 (0.24), residues: 352 sheet: -2.67 (0.29), residues: 202 loop : -3.80 (0.26), residues: 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.887 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.1704 time to fit residues: 16.8444 Evaluate side-chains 43 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1781 time to fit residues: 2.2399 ------------------------------------------------------------------------------- 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: 8.9990 chunk 68 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 82 HIS ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 194 HIS X 198 GLN X 200 ASN X 295 HIS X 408 ASN X 441 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 GLN L 37 GLN L 79 GLN L 191 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7545 Z= 0.211 Angle : 0.879 25.221 10292 Z= 0.375 Chirality : 0.042 0.167 1141 Planarity : 0.005 0.058 1267 Dihedral : 7.186 86.387 1024 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.46 (0.26), residues: 918 helix: -0.19 (0.28), residues: 350 sheet: -2.05 (0.30), residues: 205 loop : -2.77 (0.31), residues: 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.792 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.1510 time to fit residues: 13.3732 Evaluate side-chains 49 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0807 time to fit residues: 2.1827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 68 optimal weight: 0.0770 chunk 55 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 81 optimal weight: 0.0000 chunk 88 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 7545 Z= 0.152 Angle : 0.837 22.390 10292 Z= 0.349 Chirality : 0.041 0.172 1141 Planarity : 0.004 0.045 1267 Dihedral : 6.915 105.378 1024 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.47 (0.28), residues: 918 helix: 0.69 (0.30), residues: 349 sheet: -1.32 (0.32), residues: 202 loop : -2.41 (0.31), residues: 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 1.161 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 58 average time/residue: 0.1970 time to fit residues: 18.1074 Evaluate side-chains 45 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 107 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7545 Z= 0.167 Angle : 0.827 22.343 10292 Z= 0.342 Chirality : 0.040 0.168 1141 Planarity : 0.004 0.043 1267 Dihedral : 6.782 115.446 1024 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.03 (0.28), residues: 918 helix: 0.87 (0.29), residues: 351 sheet: -0.79 (0.34), residues: 202 loop : -2.17 (0.32), residues: 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.860 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 0.1402 time to fit residues: 11.8675 Evaluate side-chains 50 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0807 time to fit residues: 1.7400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 409 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7545 Z= 0.199 Angle : 0.843 22.208 10292 Z= 0.350 Chirality : 0.041 0.157 1141 Planarity : 0.004 0.043 1267 Dihedral : 6.810 122.665 1024 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.28), residues: 918 helix: 0.96 (0.30), residues: 349 sheet: -0.56 (0.34), residues: 202 loop : -2.10 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.928 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.1412 time to fit residues: 11.5462 Evaluate side-chains 44 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0684 time to fit residues: 1.5119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7545 Z= 0.185 Angle : 0.834 22.143 10292 Z= 0.346 Chirality : 0.041 0.173 1141 Planarity : 0.004 0.044 1267 Dihedral : 6.724 125.040 1024 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.29), residues: 918 helix: 1.05 (0.30), residues: 350 sheet: -0.29 (0.35), residues: 202 loop : -1.98 (0.33), residues: 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.867 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.1455 time to fit residues: 11.1069 Evaluate side-chains 45 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0792 time to fit residues: 1.5501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.0470 chunk 49 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 40 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7545 Z= 0.137 Angle : 0.829 21.958 10292 Z= 0.340 Chirality : 0.040 0.166 1141 Planarity : 0.004 0.044 1267 Dihedral : 6.567 127.575 1024 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.29), residues: 918 helix: 1.22 (0.30), residues: 349 sheet: -0.11 (0.35), residues: 203 loop : -1.80 (0.33), residues: 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.882 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1456 time to fit residues: 11.5614 Evaluate side-chains 44 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.0470 chunk 68 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7545 Z= 0.216 Angle : 0.849 22.014 10292 Z= 0.354 Chirality : 0.041 0.168 1141 Planarity : 0.004 0.044 1267 Dihedral : 6.644 130.880 1024 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 918 helix: 1.31 (0.30), residues: 339 sheet: -0.11 (0.35), residues: 203 loop : -1.78 (0.32), residues: 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.939 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.1492 time to fit residues: 11.0294 Evaluate side-chains 43 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0839 time to fit residues: 1.3370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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-4893/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-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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: 59.4023 > 50: distance: 30 - 193: 30.518 distance: 33 - 190: 27.702 distance: 43 - 178: 17.614 distance: 46 - 175: 6.341 distance: 56 - 160: 24.299 distance: 59 - 157: 21.932 distance: 107 - 186: 30.441 distance: 110 - 183: 12.385 distance: 119 - 168: 10.248 distance: 144 - 149: 18.431 distance: 149 - 150: 18.974 distance: 150 - 151: 26.989 distance: 150 - 153: 21.669 distance: 151 - 157: 41.529 distance: 153 - 154: 19.912 distance: 154 - 155: 14.120 distance: 154 - 156: 16.578 distance: 157 - 158: 9.765 distance: 158 - 159: 14.589 distance: 158 - 161: 19.040 distance: 159 - 160: 23.238 distance: 159 - 168: 10.587 distance: 161 - 162: 5.253 distance: 162 - 163: 5.512 distance: 162 - 164: 5.825 distance: 164 - 166: 3.855 distance: 165 - 167: 4.002 distance: 166 - 167: 4.747 distance: 168 - 169: 4.749 distance: 169 - 170: 7.606 distance: 169 - 172: 12.434 distance: 170 - 171: 4.147 distance: 170 - 175: 9.472 distance: 175 - 176: 13.366 distance: 176 - 177: 13.420 distance: 176 - 179: 15.831 distance: 177 - 178: 13.716 distance: 177 - 183: 14.024 distance: 179 - 180: 5.897 distance: 180 - 181: 5.329 distance: 180 - 182: 6.109 distance: 183 - 184: 23.543 distance: 184 - 185: 31.732 distance: 184 - 187: 27.148 distance: 185 - 186: 8.771 distance: 185 - 190: 26.228 distance: 187 - 188: 27.672 distance: 187 - 189: 27.413 distance: 190 - 191: 39.971 distance: 191 - 192: 41.942 distance: 191 - 194: 27.789 distance: 192 - 193: 11.534 distance: 192 - 198: 39.423 distance: 194 - 195: 10.877 distance: 194 - 196: 40.312 distance: 195 - 197: 33.821 distance: 198 - 199: 17.419 distance: 199 - 200: 20.941 distance: 199 - 202: 12.345 distance: 200 - 201: 11.741 distance: 200 - 204: 31.337 distance: 202 - 203: 12.511 distance: 204 - 205: 13.320 distance: 205 - 206: 27.678 distance: 205 - 208: 19.066 distance: 206 - 207: 6.782 distance: 206 - 210: 18.439 distance: 208 - 209: 23.073 distance: 210 - 211: 26.673 distance: 211 - 212: 36.398 distance: 211 - 214: 22.129 distance: 212 - 213: 21.655 distance: 212 - 218: 4.098 distance: 214 - 215: 5.141 distance: 215 - 216: 33.712 distance: 215 - 217: 22.958 distance: 218 - 219: 16.881 distance: 219 - 220: 26.523 distance: 219 - 222: 34.295 distance: 220 - 221: 34.670 distance: 220 - 227: 28.938 distance: 222 - 223: 24.347 distance: 223 - 224: 34.360 distance: 224 - 225: 30.792 distance: 224 - 226: 21.284