Starting phenix.real_space_refine on Sat Apr 26 20:20:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qdo_13922/04_2025/7qdo_13922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdo_13922/04_2025/7qdo_13922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qdo_13922/04_2025/7qdo_13922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdo_13922/04_2025/7qdo_13922.map" model { file = "/net/cci-nas-00/data/ceres_data/7qdo_13922/04_2025/7qdo_13922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdo_13922/04_2025/7qdo_13922.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.096 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 12 5.16 5 C 2080 2.51 5 N 564 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3304 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1652 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 194} Restraints were copied for chains: B Time building chain proxies: 2.86, per 1000 atoms: 0.87 Number of scatterers: 3304 At special positions: 0 Unit cell: (84.739, 52.857, 80.544, 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 12 16.00 O 648 8.00 N 564 7.00 C 2080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 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: 0.96 Conformation dependent library (CDL) restraints added in 409.5 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 12 sheets defined 11.3% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 414 through 421 removed outlier: 4.006A pdb=" N TRP B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 414 through 421 removed outlier: 4.006A pdb=" N TRP A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 Processing sheet with id=AA1, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.641A pdb=" N ARG B 346 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 363 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 411 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS B 367 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 409 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 380 through 383 removed outlier: 3.704A pdb=" N VAL B 428 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 399 through 400 removed outlier: 3.966A pdb=" N THR B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 453 through 457 removed outlier: 6.202A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 453 through 457 removed outlier: 6.202A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.595A pdb=" N CYS B 536 " --> pdb=" O ARG B 550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.641A pdb=" N ARG A 346 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR A 363 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 411 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS A 367 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 409 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 380 through 383 removed outlier: 3.705A pdb=" N VAL A 428 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.966A pdb=" N THR A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 457 removed outlier: 6.202A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 453 through 457 removed outlier: 6.202A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.595A pdb=" N CYS A 536 " --> pdb=" O ARG A 550 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 348 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: 1.16 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: 1072 1.34 - 1.46: 706 1.46 - 1.58: 1596 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3390 Sorted by residual: bond pdb=" N VAL B 447 " pdb=" CA VAL B 447 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.27e-02 6.20e+03 7.10e+00 bond pdb=" N THR A 533 " pdb=" CA THR A 533 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.89e+00 bond pdb=" N THR B 533 " pdb=" CA THR B 533 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.79e+00 bond pdb=" N VAL A 447 " pdb=" CA VAL A 447 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.27e-02 6.20e+03 6.76e+00 bond pdb=" N SER A 442 " pdb=" CA SER A 442 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.64e+00 ... (remaining 3385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 4228 1.29 - 2.58: 321 2.58 - 3.86: 75 3.86 - 5.15: 8 5.15 - 6.44: 12 Bond angle restraints: 4644 Sorted by residual: angle pdb=" N ASN A 465 " pdb=" CA ASN A 465 " pdb=" C ASN A 465 " ideal model delta sigma weight residual 114.56 108.69 5.87 1.27e+00 6.20e-01 2.14e+01 angle pdb=" N ASN B 465 " pdb=" CA ASN B 465 " pdb=" C ASN B 465 " ideal model delta sigma weight residual 114.56 108.69 5.87 1.27e+00 6.20e-01 2.14e+01 angle pdb=" N LYS A 445 " pdb=" CA LYS A 445 " pdb=" C LYS A 445 " ideal model delta sigma weight residual 114.56 110.31 4.25 1.27e+00 6.20e-01 1.12e+01 angle pdb=" CA ARG B 491 " pdb=" C ARG B 491 " pdb=" O ARG B 491 " ideal model delta sigma weight residual 122.03 118.12 3.91 1.17e+00 7.31e-01 1.11e+01 angle pdb=" N LYS B 445 " pdb=" CA LYS B 445 " pdb=" C LYS B 445 " ideal model delta sigma weight residual 114.56 110.33 4.23 1.27e+00 6.20e-01 1.11e+01 ... (remaining 4639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1872 15.93 - 31.87: 142 31.87 - 47.80: 34 47.80 - 63.73: 0 63.73 - 79.66: 2 Dihedral angle restraints: 2050 sinusoidal: 802 harmonic: 1248 Sorted by residual: dihedral pdb=" CB CYS B 367 " pdb=" SG CYS B 367 " pdb=" SG CYS B 426 " pdb=" CB CYS B 426 " ideal model delta sinusoidal sigma weight residual 93.00 137.25 -44.25 1 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" CB CYS B 474 " pdb=" SG CYS B 474 " pdb=" SG CYS B 536 " pdb=" CB CYS B 536 " ideal model delta sinusoidal sigma weight residual 93.00 65.87 27.13 1 1.00e+01 1.00e-02 1.06e+01 dihedral pdb=" CA MET B 506 " pdb=" C MET B 506 " pdb=" N PRO B 507 " pdb=" CA PRO B 507 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 344 0.037 - 0.074: 119 0.074 - 0.112: 65 0.112 - 0.149: 14 0.149 - 0.186: 2 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA VAL B 447 " pdb=" N VAL B 447 " pdb=" C VAL B 447 " pdb=" CB VAL B 447 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA VAL A 447 " pdb=" N VAL A 447 " pdb=" C VAL A 447 " pdb=" CB VAL A 447 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA LEU A 449 " pdb=" N LEU A 449 " pdb=" C LEU A 449 " pdb=" CB LEU A 449 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 541 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 451 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 452 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 451 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.49e+00 pdb=" N PRO B 452 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 452 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 452 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 382 " 0.007 2.00e-02 2.50e+03 7.53e-03 1.42e+00 pdb=" CG TRP A 382 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 382 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 382 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 382 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 382 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 382 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 382 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 382 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 382 " 0.000 2.00e-02 2.50e+03 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 28 2.61 - 3.18: 2840 3.18 - 3.76: 4774 3.76 - 4.33: 6386 4.33 - 4.90: 10535 Nonbonded interactions: 24563 Sorted by model distance: nonbonded pdb=" SG CYS A 367 " pdb=" SG CYS A 426 " model vdw 2.038 3.760 nonbonded pdb=" SG CYS A 474 " pdb=" SG CYS A 536 " model vdw 2.041 3.760 nonbonded pdb=" OD1 ASP A 553 " pdb=" OG1 THR A 556 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP B 553 " pdb=" OG1 THR B 556 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 363 " pdb=" O ILE B 413 " model vdw 2.270 3.040 ... (remaining 24558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.990 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.960 Find NCS groups from input model: 0.050 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 0.037 3392 Z= 0.318 Angle : 0.824 6.438 4648 Z= 0.510 Chirality : 0.049 0.186 544 Planarity : 0.005 0.031 598 Dihedral : 11.618 79.664 1228 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.82 (0.40), residues: 420 helix: -0.82 (0.83), residues: 44 sheet: 1.32 (0.37), residues: 180 loop : -2.45 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 382 HIS 0.004 0.001 HIS A 540 PHE 0.013 0.003 PHE A 479 TYR 0.011 0.002 TYR A 500 ARG 0.004 0.001 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.25403 ( 106) hydrogen bonds : angle 9.34136 ( 348) SS BOND : bond 0.00817 ( 2) SS BOND : angle 1.37041 ( 4) covalent geometry : bond 0.00512 ( 3390) covalent geometry : angle 0.82287 ( 4644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1648 time to fit residues: 18.9645 Evaluate side-chains 67 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.185682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.135652 restraints weight = 5150.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140524 restraints weight = 2878.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143538 restraints weight = 2037.656| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3392 Z= 0.150 Angle : 0.678 6.186 4648 Z= 0.359 Chirality : 0.046 0.161 544 Planarity : 0.005 0.036 598 Dihedral : 4.223 16.559 454 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.59 % Allowed : 10.85 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.39 (0.41), residues: 420 helix: -0.44 (0.74), residues: 44 sheet: 1.35 (0.40), residues: 174 loop : -1.78 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 528 HIS 0.007 0.001 HIS A 518 PHE 0.016 0.002 PHE A 479 TYR 0.005 0.001 TYR A 534 ARG 0.004 0.001 ARG A 491 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 106) hydrogen bonds : angle 6.40618 ( 348) SS BOND : bond 0.01086 ( 2) SS BOND : angle 1.36324 ( 4) covalent geometry : bond 0.00332 ( 3390) covalent geometry : angle 0.67729 ( 4644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: B 417 ASP cc_start: 0.8471 (p0) cc_final: 0.8163 (p0) REVERT: B 506 MET cc_start: 0.6712 (mmm) cc_final: 0.6012 (ptt) REVERT: A 367 CYS cc_start: 0.7601 (p) cc_final: 0.7193 (p) REVERT: A 417 ASP cc_start: 0.8405 (p0) cc_final: 0.8173 (p0) REVERT: A 506 MET cc_start: 0.6748 (mmm) cc_final: 0.6012 (ptt) outliers start: 6 outliers final: 6 residues processed: 84 average time/residue: 0.1672 time to fit residues: 16.7835 Evaluate side-chains 62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.184563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133746 restraints weight = 5116.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138646 restraints weight = 2946.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141904 restraints weight = 2099.006| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3392 Z= 0.140 Angle : 0.644 5.889 4648 Z= 0.337 Chirality : 0.045 0.152 544 Planarity : 0.004 0.031 598 Dihedral : 4.203 15.559 454 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.17 % Allowed : 14.55 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.54 (0.40), residues: 420 helix: -0.39 (0.75), residues: 44 sheet: 1.38 (0.40), residues: 160 loop : -1.83 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 528 HIS 0.006 0.001 HIS B 518 PHE 0.016 0.002 PHE B 479 TYR 0.016 0.002 TYR A 500 ARG 0.003 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.04473 ( 106) hydrogen bonds : angle 5.66462 ( 348) SS BOND : bond 0.00922 ( 2) SS BOND : angle 1.40551 ( 4) covalent geometry : bond 0.00317 ( 3390) covalent geometry : angle 0.64275 ( 4644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.342 Fit side-chains REVERT: B 506 MET cc_start: 0.6845 (mmm) cc_final: 0.5793 (ptp) REVERT: A 367 CYS cc_start: 0.7709 (p) cc_final: 0.7164 (p) REVERT: A 489 MET cc_start: 0.8008 (tpp) cc_final: 0.7264 (mmm) REVERT: A 506 MET cc_start: 0.6807 (mmm) cc_final: 0.5990 (ptt) outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 0.1623 time to fit residues: 13.6430 Evaluate side-chains 61 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.184146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133467 restraints weight = 5181.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138246 restraints weight = 2996.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141371 restraints weight = 2146.653| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3392 Z= 0.127 Angle : 0.643 6.064 4648 Z= 0.333 Chirality : 0.044 0.150 544 Planarity : 0.004 0.033 598 Dihedral : 4.113 15.105 454 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.91 % Allowed : 18.52 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.54 (0.40), residues: 420 helix: -0.74 (0.74), residues: 44 sheet: 1.45 (0.40), residues: 160 loop : -1.81 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 528 HIS 0.005 0.001 HIS B 518 PHE 0.016 0.002 PHE A 405 TYR 0.011 0.001 TYR B 500 ARG 0.003 0.000 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 106) hydrogen bonds : angle 5.41718 ( 348) SS BOND : bond 0.00933 ( 2) SS BOND : angle 1.52795 ( 4) covalent geometry : bond 0.00282 ( 3390) covalent geometry : angle 0.64122 ( 4644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.414 Fit side-chains REVERT: B 489 MET cc_start: 0.8098 (tpp) cc_final: 0.7286 (mmm) REVERT: B 493 GLN cc_start: 0.8692 (mm110) cc_final: 0.8486 (mm110) REVERT: A 367 CYS cc_start: 0.7820 (p) cc_final: 0.7231 (p) REVERT: A 489 MET cc_start: 0.8078 (tpp) cc_final: 0.7241 (mmm) REVERT: A 506 MET cc_start: 0.6827 (mmm) cc_final: 0.5847 (ptp) REVERT: A 536 CYS cc_start: 0.8390 (p) cc_final: 0.8068 (t) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.1832 time to fit residues: 14.5695 Evaluate side-chains 62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.180868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130477 restraints weight = 5129.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135036 restraints weight = 3028.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137912 restraints weight = 2198.892| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3392 Z= 0.173 Angle : 0.682 7.468 4648 Z= 0.354 Chirality : 0.045 0.206 544 Planarity : 0.004 0.033 598 Dihedral : 4.211 16.318 454 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.76 % Allowed : 17.72 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.51 (0.41), residues: 420 helix: -0.75 (0.77), residues: 44 sheet: 1.52 (0.41), residues: 160 loop : -1.83 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 528 HIS 0.007 0.001 HIS A 518 PHE 0.020 0.003 PHE A 479 TYR 0.009 0.001 TYR B 500 ARG 0.006 0.000 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 106) hydrogen bonds : angle 5.37826 ( 348) SS BOND : bond 0.01079 ( 2) SS BOND : angle 1.87028 ( 4) covalent geometry : bond 0.00406 ( 3390) covalent geometry : angle 0.68024 ( 4644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.338 Fit side-chains REVERT: B 489 MET cc_start: 0.8056 (tpp) cc_final: 0.7301 (mmm) REVERT: B 506 MET cc_start: 0.6824 (mmm) cc_final: 0.5624 (mtm) REVERT: A 367 CYS cc_start: 0.7752 (p) cc_final: 0.7082 (p) REVERT: A 489 MET cc_start: 0.8036 (tpp) cc_final: 0.7814 (mtp) REVERT: A 536 CYS cc_start: 0.8416 (p) cc_final: 0.8092 (t) outliers start: 18 outliers final: 9 residues processed: 74 average time/residue: 0.1865 time to fit residues: 16.3899 Evaluate side-chains 70 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 53.147 > 50: distance: 20 - 24: 25.372 distance: 24 - 25: 33.512 distance: 25 - 26: 46.014 distance: 25 - 28: 45.839 distance: 26 - 27: 14.546 distance: 26 - 29: 36.282 distance: 29 - 30: 39.680 distance: 29 - 35: 21.124 distance: 30 - 31: 21.404 distance: 30 - 33: 38.659 distance: 31 - 32: 19.795 distance: 31 - 36: 22.817 distance: 33 - 34: 19.840 distance: 34 - 35: 3.906 distance: 36 - 37: 22.966 distance: 36 - 113: 15.089 distance: 37 - 38: 34.050 distance: 37 - 40: 11.137 distance: 38 - 39: 39.540 distance: 38 - 44: 44.700 distance: 39 - 110: 15.839 distance: 40 - 41: 15.574 distance: 41 - 42: 4.866 distance: 44 - 45: 26.693 distance: 44 - 50: 27.000 distance: 45 - 46: 3.783 distance: 45 - 48: 6.777 distance: 46 - 47: 7.856 distance: 46 - 51: 5.314 distance: 48 - 49: 8.154 distance: 49 - 50: 11.937 distance: 51 - 52: 16.924 distance: 52 - 53: 15.841 distance: 52 - 55: 12.204 distance: 53 - 54: 26.822 distance: 53 - 60: 37.097 distance: 55 - 56: 8.950 distance: 60 - 61: 20.813 distance: 60 - 66: 22.438 distance: 61 - 62: 13.928 distance: 61 - 64: 31.448 distance: 62 - 63: 30.908 distance: 62 - 67: 38.788 distance: 64 - 65: 25.504 distance: 65 - 66: 19.083 distance: 67 - 68: 26.725 distance: 68 - 69: 31.686 distance: 68 - 71: 19.130 distance: 69 - 70: 31.237 distance: 69 - 76: 17.564 distance: 71 - 72: 6.312 distance: 72 - 73: 7.723 distance: 73 - 74: 4.298 distance: 73 - 75: 3.578 distance: 76 - 77: 16.164 distance: 77 - 78: 33.207 distance: 77 - 80: 13.270 distance: 78 - 79: 51.517 distance: 78 - 81: 53.147 distance: 81 - 82: 32.718 distance: 81 - 87: 38.467 distance: 82 - 83: 7.588 distance: 82 - 85: 11.857 distance: 83 - 84: 12.546 distance: 83 - 88: 12.626 distance: 85 - 86: 7.831 distance: 86 - 87: 17.713 distance: 88 - 89: 8.636 distance: 89 - 90: 3.240 distance: 90 - 91: 4.779