Starting phenix.real_space_refine on Mon Jan 13 20:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjg_37579/01_2025/8wjg_37579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjg_37579/01_2025/8wjg_37579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wjg_37579/01_2025/8wjg_37579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjg_37579/01_2025/8wjg_37579.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjg_37579/01_2025/8wjg_37579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjg_37579/01_2025/8wjg_37579.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.167 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 31 5.16 5 C 2569 2.51 5 N 672 2.21 5 O 680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3952 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 3952 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 29, 'TRANS': 503} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 2.86, per 1000 atoms: 0.72 Number of scatterers: 3952 At special positions: 0 Unit cell: (104.86, 85.6, 64.2, 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 31 16.00 O 680 8.00 N 672 7.00 C 2569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " 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: 0.94 Conformation dependent library (CDL) restraints added in 499.3 milliseconds 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 2 sheets defined 83.3% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.732A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 42 removed outlier: 4.754A pdb=" N GLU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.776A pdb=" N ARG A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 171 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 192 removed outlier: 3.550A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.829A pdb=" N PHE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.922A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.785A pdb=" N ASP A 313 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.742A pdb=" N LEU A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 368 removed outlier: 3.950A pdb=" N PHE A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.754A pdb=" N GLY A 375 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.751A pdb=" N THR A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 460 removed outlier: 3.889A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 490 removed outlier: 4.476A pdb=" N MET A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 495 through 513 Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 526 through 538 removed outlier: 3.535A pdb=" N VAL A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 305 hydrogen bonds defined for protein. 882 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: 1.15 Time building geometry restraints manager: 1.12 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: 1252 1.34 - 1.47: 984 1.47 - 1.59: 1761 1.59 - 1.71: 0 1.71 - 1.84: 50 Bond restraints: 4047 Sorted by residual: bond pdb=" C MET A 36 " pdb=" O MET A 36 " ideal model delta sigma weight residual 1.235 1.263 -0.028 1.38e-02 5.25e+03 4.04e+00 bond pdb=" CG PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 1.503 1.438 0.065 3.40e-02 8.65e+02 3.64e+00 bond pdb=" N PRO A 194 " pdb=" CA PRO A 194 " ideal model delta sigma weight residual 1.469 1.445 0.024 1.28e-02 6.10e+03 3.47e+00 bond pdb=" N PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 1.473 1.498 -0.025 1.40e-02 5.10e+03 3.25e+00 bond pdb=" CB MET A 222 " pdb=" CG MET A 222 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.75e+00 ... (remaining 4042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 5385 3.17 - 6.34: 113 6.34 - 9.51: 17 9.51 - 12.68: 6 12.68 - 15.85: 5 Bond angle restraints: 5526 Sorted by residual: angle pdb=" CA PRO A 194 " pdb=" N PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 112.00 97.41 14.59 1.40e+00 5.10e-01 1.09e+02 angle pdb=" C ALA A 323 " pdb=" N MET A 324 " pdb=" CA MET A 324 " ideal model delta sigma weight residual 121.66 109.91 11.75 1.76e+00 3.23e-01 4.45e+01 angle pdb=" CB MET A 222 " pdb=" CG MET A 222 " pdb=" SD MET A 222 " ideal model delta sigma weight residual 112.70 97.37 15.33 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C THR A 518 " pdb=" N GLN A 519 " pdb=" CA GLN A 519 " ideal model delta sigma weight residual 125.66 134.53 -8.87 1.85e+00 2.92e-01 2.30e+01 angle pdb=" CB MET A 324 " pdb=" CG MET A 324 " pdb=" SD MET A 324 " ideal model delta sigma weight residual 112.70 125.54 -12.84 3.00e+00 1.11e-01 1.83e+01 ... (remaining 5521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 2132 17.27 - 34.55: 160 34.55 - 51.82: 51 51.82 - 69.09: 19 69.09 - 86.36: 4 Dihedral angle restraints: 2366 sinusoidal: 849 harmonic: 1517 Sorted by residual: dihedral pdb=" CA GLY A 375 " pdb=" C GLY A 375 " pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta harmonic sigma weight residual -180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 135.06 -42.06 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CD ARG A 487 " pdb=" NE ARG A 487 " pdb=" CZ ARG A 487 " pdb=" NH1 ARG A 487 " ideal model delta sinusoidal sigma weight residual 0.00 -28.91 28.91 1 1.00e+01 1.00e-02 1.20e+01 ... (remaining 2363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 459 0.051 - 0.101: 135 0.101 - 0.152: 45 0.152 - 0.202: 12 0.202 - 0.252: 4 Chirality restraints: 655 Sorted by residual: chirality pdb=" CA MET A 466 " pdb=" N MET A 466 " pdb=" C MET A 466 " pdb=" CB MET A 466 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU A 13 " pdb=" CB LEU A 13 " pdb=" CD1 LEU A 13 " pdb=" CD2 LEU A 13 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ARG A 89 " pdb=" N ARG A 89 " pdb=" C ARG A 89 " pdb=" CB ARG A 89 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 652 not shown) Planarity restraints: 691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 193 " -0.143 5.00e-02 4.00e+02 2.05e-01 6.75e+01 pdb=" N PRO A 194 " 0.354 5.00e-02 4.00e+02 pdb=" CA PRO A 194 " -0.119 5.00e-02 4.00e+02 pdb=" CD PRO A 194 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 487 " -0.387 9.50e-02 1.11e+02 1.75e-01 2.36e+01 pdb=" NE ARG A 487 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 487 " -0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 487 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 487 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 291 " 0.311 9.50e-02 1.11e+02 1.40e-01 1.49e+01 pdb=" NE ARG A 291 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 291 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG A 291 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 291 " 0.001 2.00e-02 2.50e+03 ... (remaining 688 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 386 2.75 - 3.29: 4110 3.29 - 3.82: 6933 3.82 - 4.36: 7768 4.36 - 4.90: 13339 Nonbonded interactions: 32536 Sorted by model distance: nonbonded pdb=" OH TYR A 455 " pdb=" O PRO A 516 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 412 " pdb=" O GLY A 444 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A 167 " pdb=" OD1 ASN A 216 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP A 257 " pdb=" OG1 THR A 259 " model vdw 2.291 3.040 nonbonded pdb=" O ALA A 359 " pdb=" OG1 THR A 363 " model vdw 2.297 3.040 ... (remaining 32531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.650 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 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 : 0.005 0.070 4047 Z= 0.334 Angle : 1.210 15.847 5526 Z= 0.659 Chirality : 0.059 0.252 655 Planarity : 0.014 0.205 691 Dihedral : 15.276 86.364 1382 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.03 % Allowed : 21.83 % Favored : 76.14 % 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: 0.84 (0.34), residues: 529 helix: 1.01 (0.25), residues: 391 sheet: None (None), residues: 0 loop : -0.54 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 294 HIS 0.004 0.001 HIS A 245 PHE 0.032 0.003 PHE A 208 TYR 0.030 0.008 TYR A 275 ARG 0.039 0.003 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.408 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 1.1222 time to fit residues: 74.5593 Evaluate side-chains 59 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.174281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131777 restraints weight = 3945.519| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.12 r_work: 0.3589 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4047 Z= 0.210 Angle : 0.673 11.273 5526 Z= 0.327 Chirality : 0.041 0.134 655 Planarity : 0.006 0.095 691 Dihedral : 5.100 50.618 571 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.81 % Allowed : 20.81 % Favored : 75.38 % 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: 1.70 (0.38), residues: 529 helix: 1.64 (0.26), residues: 399 sheet: -1.07 (1.35), residues: 10 loop : -0.29 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 294 HIS 0.004 0.001 HIS A 245 PHE 0.019 0.002 PHE A 208 TYR 0.017 0.003 TYR A 275 ARG 0.006 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.386 Fit side-chains REVERT: A 5 GLU cc_start: 0.6994 (mp0) cc_final: 0.6649 (mp0) REVERT: A 39 ASN cc_start: 0.8059 (t0) cc_final: 0.7822 (t0) REVERT: A 170 PHE cc_start: 0.8472 (m-80) cc_final: 0.8223 (m-80) REVERT: A 529 ASP cc_start: 0.6932 (t0) cc_final: 0.6690 (t0) outliers start: 15 outliers final: 4 residues processed: 80 average time/residue: 0.9533 time to fit residues: 79.5607 Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8278 > 50: distance: 91 - 94: 30.997 distance: 94 - 95: 39.749 distance: 95 - 96: 57.139 distance: 95 - 98: 40.825 distance: 96 - 97: 41.149 distance: 96 - 102: 39.027 distance: 98 - 99: 39.304 distance: 99 - 100: 40.197 distance: 99 - 101: 41.039 distance: 102 - 103: 57.567 distance: 102 - 108: 38.645 distance: 103 - 104: 46.610 distance: 103 - 106: 7.568 distance: 104 - 105: 41.010 distance: 104 - 109: 22.771 distance: 107 - 108: 40.180 distance: 109 - 110: 40.072 distance: 110 - 111: 32.739 distance: 110 - 113: 20.657 distance: 111 - 112: 42.075 distance: 111 - 118: 42.301 distance: 113 - 114: 39.644 distance: 114 - 115: 27.110 distance: 115 - 116: 19.345 distance: 115 - 117: 36.077 distance: 118 - 119: 47.422 distance: 119 - 120: 23.725 distance: 119 - 122: 50.926 distance: 120 - 121: 38.725 distance: 120 - 125: 55.441 distance: 122 - 123: 7.060 distance: 122 - 124: 57.024 distance: 125 - 126: 40.978 distance: 126 - 127: 30.878 distance: 126 - 129: 39.825 distance: 127 - 128: 32.589 distance: 127 - 134: 39.661 distance: 130 - 131: 40.500 distance: 131 - 133: 58.563 distance: 134 - 135: 27.412 distance: 135 - 136: 46.311 distance: 135 - 138: 47.400 distance: 136 - 137: 40.226 distance: 136 - 140: 57.312 distance: 138 - 139: 70.399 distance: 140 - 141: 38.798 distance: 141 - 144: 40.311 distance: 144 - 145: 34.581 distance: 145 - 146: 40.105 distance: 145 - 147: 34.068 distance: 148 - 149: 35.090 distance: 149 - 150: 56.829 distance: 149 - 152: 55.136 distance: 152 - 153: 39.096 distance: 153 - 154: 38.613 distance: 155 - 156: 58.044 distance: 156 - 157: 62.227 distance: 156 - 159: 18.765 distance: 157 - 158: 56.086 distance: 157 - 163: 41.160 distance: 159 - 160: 41.729 distance: 160 - 161: 42.734 distance: 160 - 162: 21.579 distance: 163 - 169: 39.067 distance: 165 - 166: 39.860 distance: 165 - 170: 35.306 distance: 167 - 168: 39.513