Starting phenix.real_space_refine on Thu Dec 7 16:53:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/12_2023/8jtc_36640_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/12_2023/8jtc_36640.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/12_2023/8jtc_36640_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/12_2023/8jtc_36640_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/12_2023/8jtc_36640_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/12_2023/8jtc_36640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/12_2023/8jtc_36640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/12_2023/8jtc_36640_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtc_36640/12_2023/8jtc_36640_updated.pdb" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.068 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 27 5.16 5 C 1963 2.51 5 N 452 2.21 5 O 499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2941 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2897 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.73 Number of scatterers: 2941 At special positions: 0 Unit cell: (56.16, 67.6, 73.84, 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 27 16.00 O 499 8.00 N 452 7.00 C 1963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.26 Conformation dependent library (CDL) restraints added in 588.3 milliseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 0 sheets defined 87.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 19 through 53 removed outlier: 4.013A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 122 through 156 removed outlier: 3.887A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 158 through 178 Processing helix chain 'A' and resid 182 through 210 Processing helix chain 'A' and resid 214 through 245 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 269 removed outlier: 4.555A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 292 through 322 removed outlier: 4.143A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 329 through 355 removed outlier: 4.169A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 4.381A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 377 Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 385 through 413 Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 446 removed outlier: 4.556A pdb=" N TYR A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.027A pdb=" N ALA A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 468 Proline residue: A 465 - end of helix removed outlier: 4.427A pdb=" N PHE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 717 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: 0.80 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 441 1.30 - 1.43: 776 1.43 - 1.56: 1753 1.56 - 1.68: 0 1.68 - 1.81: 46 Bond restraints: 3016 Sorted by residual: bond pdb=" C12 YHR A 501 " pdb=" N21 YHR A 501 " ideal model delta sigma weight residual 1.363 1.217 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C13 YHR A 501 " pdb=" N8 YHR A 501 " ideal model delta sigma weight residual 1.514 1.407 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C22 YHR A 501 " pdb=" N21 YHR A 501 " ideal model delta sigma weight residual 1.389 1.283 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C11 YHR A 501 " pdb=" C23 YHR A 501 " ideal model delta sigma weight residual 1.373 1.477 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" N ILE A 223 " pdb=" CA ILE A 223 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.19e-02 7.06e+03 1.00e+01 ... (remaining 3011 not shown) Histogram of bond angle deviations from ideal: 97.90 - 106.16: 115 106.16 - 114.41: 1792 114.41 - 122.67: 2057 122.67 - 130.92: 137 130.92 - 139.17: 12 Bond angle restraints: 4113 Sorted by residual: angle pdb=" C27 YHR A 501 " pdb=" C26 YHR A 501 " pdb=" O28 YHR A 501 " ideal model delta sigma weight residual 101.89 119.99 -18.10 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C25 YHR A 501 " pdb=" C26 YHR A 501 " pdb=" O28 YHR A 501 " ideal model delta sigma weight residual 137.71 120.12 17.59 3.00e+00 1.11e-01 3.44e+01 angle pdb=" C12 YHR A 501 " pdb=" N21 YHR A 501 " pdb=" C22 YHR A 501 " ideal model delta sigma weight residual 108.09 123.97 -15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C7 YHR A 501 " pdb=" N8 YHR A 501 " pdb=" C9 YHR A 501 " ideal model delta sigma weight residual 99.45 115.07 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C11 YHR A 501 " pdb=" C10 YHR A 501 " pdb=" C9 YHR A 501 " ideal model delta sigma weight residual 118.10 103.47 14.63 3.00e+00 1.11e-01 2.38e+01 ... (remaining 4108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 1544 17.25 - 34.50: 176 34.50 - 51.75: 28 51.75 - 69.00: 3 69.00 - 86.25: 2 Dihedral angle restraints: 1753 sinusoidal: 645 harmonic: 1108 Sorted by residual: dihedral pdb=" CA GLN A 271 " pdb=" C GLN A 271 " pdb=" N PRO A 272 " pdb=" CA PRO A 272 " ideal model delta harmonic sigma weight residual 180.00 -149.93 -30.07 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA PHE A 348 " pdb=" C PHE A 348 " pdb=" N GLY A 349 " pdb=" CA GLY A 349 " ideal model delta harmonic sigma weight residual 180.00 164.02 15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA SER A 416 " pdb=" C SER A 416 " pdb=" N VAL A 417 " pdb=" CA VAL A 417 " ideal model delta harmonic sigma weight residual 180.00 164.34 15.66 0 5.00e+00 4.00e-02 9.80e+00 ... (remaining 1750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 332 0.041 - 0.082: 118 0.082 - 0.122: 28 0.122 - 0.163: 9 0.163 - 0.204: 6 Chirality restraints: 493 Sorted by residual: chirality pdb=" C16 YHR A 501 " pdb=" C15 YHR A 501 " pdb=" C17 YHR A 501 " pdb=" C3 YHR A 501 " both_signs ideal model delta sigma weight residual False 2.75 2.55 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA TYR A 243 " pdb=" N TYR A 243 " pdb=" C TYR A 243 " pdb=" CB TYR A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CA LEU A 452 " pdb=" N LEU A 452 " pdb=" C LEU A 452 " pdb=" CB LEU A 452 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 490 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 236 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 222 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C GLY A 222 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY A 222 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 223 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 432 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C GLY A 432 " -0.028 2.00e-02 2.50e+03 pdb=" O GLY A 432 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 433 " 0.009 2.00e-02 2.50e+03 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 640 2.77 - 3.30: 3061 3.30 - 3.84: 5160 3.84 - 4.37: 5661 4.37 - 4.90: 10012 Nonbonded interactions: 24534 Sorted by model distance: nonbonded pdb=" OG SER A 325 " pdb=" OE1 GLN A 329 " model vdw 2.240 2.440 nonbonded pdb=" OG SER A 200 " pdb=" OH TYR A 422 " model vdw 2.398 2.440 nonbonded pdb=" OH TYR A 408 " pdb=" OG SER A 472 " model vdw 2.476 2.440 nonbonded pdb=" O MET A 402 " pdb=" N MET A 406 " model vdw 2.528 2.520 nonbonded pdb=" O MET A 397 " pdb=" OG SER A 401 " model vdw 2.534 2.440 ... (remaining 24529 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 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.660 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.170 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.007 0.146 3016 Z= 0.472 Angle : 1.064 18.102 4113 Z= 0.515 Chirality : 0.049 0.204 493 Planarity : 0.006 0.066 500 Dihedral : 14.571 86.250 1047 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.33 % Allowed : 22.37 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: 1.13 (0.43), residues: 387 helix: 1.16 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.21 (0.77), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 451 HIS 0.002 0.001 HIS A 53 PHE 0.020 0.001 PHE A 348 TYR 0.016 0.001 TYR A 243 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.305 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.1643 time to fit residues: 12.2925 Evaluate side-chains 58 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.431 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0399 time to fit residues: 0.5039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.0470 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3016 Z= 0.220 Angle : 0.702 9.807 4113 Z= 0.329 Chirality : 0.042 0.200 493 Planarity : 0.005 0.047 500 Dihedral : 5.920 76.477 427 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.30 % Allowed : 21.05 % Favored : 76.64 % 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: 1.90 (0.43), residues: 387 helix: 1.71 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.20 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.001 0.000 HIS A 53 PHE 0.020 0.001 PHE A 348 TYR 0.006 0.001 TYR A 49 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.277 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.1430 time to fit residues: 12.5228 Evaluate side-chains 64 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0320 time to fit residues: 0.6267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3016 Z= 0.269 Angle : 0.707 9.966 4113 Z= 0.333 Chirality : 0.042 0.154 493 Planarity : 0.005 0.042 500 Dihedral : 5.547 68.057 427 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.32 % Allowed : 24.34 % Favored : 74.34 % 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: 2.12 (0.43), residues: 387 helix: 1.90 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.36 (0.77), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.018 0.001 PHE A 348 TYR 0.009 0.001 TYR A 211 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.324 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 70 average time/residue: 0.1520 time to fit residues: 12.8442 Evaluate side-chains 64 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0326 time to fit residues: 0.4888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3016 Z= 0.220 Angle : 0.694 9.776 4113 Z= 0.325 Chirality : 0.041 0.150 493 Planarity : 0.005 0.039 500 Dihedral : 5.347 63.308 427 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.97 % Allowed : 26.64 % Favored : 71.38 % 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: 2.22 (0.44), residues: 387 helix: 1.96 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.34 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.018 0.001 PHE A 348 TYR 0.008 0.001 TYR A 211 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.319 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 68 average time/residue: 0.1554 time to fit residues: 12.7484 Evaluate side-chains 67 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0315 time to fit residues: 0.5398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.0770 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3016 Z= 0.205 Angle : 0.680 9.735 4113 Z= 0.319 Chirality : 0.041 0.166 493 Planarity : 0.005 0.038 500 Dihedral : 5.245 59.411 427 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.97 % Allowed : 26.97 % Favored : 71.05 % 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: 2.19 (0.44), residues: 387 helix: 1.94 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.30 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 414 PHE 0.016 0.001 PHE A 348 TYR 0.007 0.001 TYR A 211 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.310 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.1503 time to fit residues: 12.9243 Evaluate side-chains 68 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.304 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0408 time to fit residues: 0.6795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 70.0008 > 50: distance: 42 - 47: 10.070 distance: 47 - 48: 20.544 distance: 48 - 49: 11.438 distance: 48 - 51: 7.388 distance: 49 - 50: 15.451 distance: 49 - 53: 11.322 distance: 51 - 52: 29.990 distance: 53 - 54: 14.008 distance: 54 - 55: 26.137 distance: 54 - 57: 12.562 distance: 55 - 56: 17.738 distance: 55 - 64: 41.074 distance: 57 - 58: 25.076 distance: 58 - 59: 13.621 distance: 64 - 65: 21.299 distance: 65 - 66: 46.389 distance: 65 - 68: 30.233 distance: 66 - 67: 40.224 distance: 66 - 71: 30.212 distance: 68 - 69: 8.327 distance: 68 - 70: 6.423 distance: 71 - 72: 28.099 distance: 72 - 73: 51.709 distance: 72 - 75: 33.855 distance: 73 - 74: 35.964 distance: 73 - 80: 4.736 distance: 75 - 76: 30.576 distance: 76 - 77: 17.785 distance: 77 - 78: 22.952 distance: 77 - 79: 10.106 distance: 80 - 81: 30.808 distance: 80 - 86: 35.434 distance: 81 - 82: 27.763 distance: 81 - 84: 21.404 distance: 82 - 83: 12.421 distance: 82 - 87: 13.627 distance: 84 - 85: 41.044 distance: 85 - 86: 43.329 distance: 87 - 88: 30.472 distance: 88 - 89: 13.384 distance: 88 - 91: 30.530 distance: 89 - 90: 23.663 distance: 89 - 92: 9.591 distance: 92 - 93: 16.050 distance: 93 - 94: 11.606 distance: 93 - 96: 13.653 distance: 94 - 95: 17.060 distance: 94 - 97: 25.402 distance: 97 - 98: 28.946 distance: 98 - 99: 9.514 distance: 98 - 101: 15.860 distance: 99 - 100: 41.520 distance: 99 - 106: 39.337 distance: 101 - 102: 16.636 distance: 102 - 103: 9.079 distance: 103 - 104: 6.502 distance: 103 - 105: 9.558 distance: 106 - 107: 27.164 distance: 107 - 110: 34.935 distance: 108 - 111: 30.750 distance: 111 - 112: 33.908 distance: 112 - 113: 35.471 distance: 113 - 114: 41.120 distance: 113 - 115: 34.277