Starting phenix.real_space_refine on Fri Dec 8 06:59:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkh_40184/12_2023/8gkh_40184_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkh_40184/12_2023/8gkh_40184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkh_40184/12_2023/8gkh_40184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkh_40184/12_2023/8gkh_40184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkh_40184/12_2023/8gkh_40184_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkh_40184/12_2023/8gkh_40184_neut.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 125 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 4337 2.51 5 N 1358 2.21 5 O 1715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 7570 Number of models: 1 Model: "" Number of chains: 7 Chain: "N" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "P" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4946 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 25, 'TRANS': 574} Chain breaks: 1 Chain: "T" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 695 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain breaks: 1 Chain: "W" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1615 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 35} Link IDs: {'rna2p': 11, 'rna3p': 64} Chain breaks: 1 Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4558 SG CYS P 548 32.953 45.640 21.668 1.00 51.02 S ATOM 4582 SG CYS P 551 30.062 44.068 19.775 1.00 57.06 S ATOM 4875 SG CYS P 586 33.492 42.516 19.547 1.00 52.44 S ATOM 4911 SG CYS P 591 32.800 45.814 17.814 1.00 44.29 S Time building chain proxies: 4.98, per 1000 atoms: 0.66 Number of scatterers: 7570 At special positions: 0 Unit cell: (75.9, 107.25, 139.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 125 15.00 Mg 2 11.99 O 1715 8.00 N 1358 7.00 C 4337 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: 4.15 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 703 " pdb="ZN ZN P 703 " - pdb=" SG CYS P 551 " pdb="ZN ZN P 703 " - pdb=" SG CYS P 586 " pdb="ZN ZN P 703 " - pdb=" SG CYS P 591 " pdb="ZN ZN P 703 " - pdb=" SG CYS P 548 " Number of angles added : 6 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 61.0% alpha, 7.7% beta 52 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 35 through 68 Processing helix chain 'P' and resid 76 through 90 Processing helix chain 'P' and resid 91 through 93 No H-bonds generated for 'chain 'P' and resid 91 through 93' Processing helix chain 'P' and resid 97 through 119 Proline residue: P 109 - end of helix removed outlier: 4.072A pdb=" N GLN P 112 " --> pdb=" O LEU P 108 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG P 113 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 151 Processing helix chain 'P' and resid 151 through 164 Processing helix chain 'P' and resid 164 through 172 Processing helix chain 'P' and resid 176 through 194 removed outlier: 3.630A pdb=" N PHE P 182 " --> pdb=" O ALA P 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER P 191 " --> pdb=" O ARG P 187 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL P 192 " --> pdb=" O TYR P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 200 through 207 Processing helix chain 'P' and resid 208 through 220 Processing helix chain 'P' and resid 230 through 238 Processing helix chain 'P' and resid 239 through 241 No H-bonds generated for 'chain 'P' and resid 239 through 241' Processing helix chain 'P' and resid 242 through 257 Processing helix chain 'P' and resid 279 through 286 Processing helix chain 'P' and resid 290 through 296 removed outlier: 3.847A pdb=" N THR P 296 " --> pdb=" O ARG P 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 305 removed outlier: 3.601A pdb=" N ARG P 305 " --> pdb=" O ASP P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 311 through 315 Processing helix chain 'P' and resid 365 through 368 Processing helix chain 'P' and resid 369 through 376 Processing helix chain 'P' and resid 403 through 412 Processing helix chain 'P' and resid 412 through 428 Processing helix chain 'P' and resid 428 through 435 removed outlier: 3.730A pdb=" N ARG P 435 " --> pdb=" O LEU P 431 " (cutoff:3.500A) Processing helix chain 'P' and resid 443 through 457 removed outlier: 3.741A pdb=" N ASP P 457 " --> pdb=" O VAL P 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 457 through 466 Processing helix chain 'P' and resid 468 through 497 Processing helix chain 'P' and resid 523 through 532 removed outlier: 4.036A pdb=" N THR P 527 " --> pdb=" O LYS P 523 " (cutoff:3.500A) Processing helix chain 'P' and resid 568 through 575 Processing helix chain 'P' and resid 588 through 592 Processing helix chain 'P' and resid 605 through 622 Processing sheet with id=AA1, first strand: chain 'P' and resid 21 through 27 removed outlier: 4.929A pdb=" N SER P 325 " --> pdb=" O TYR P 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 400 through 402 Processing sheet with id=AA3, first strand: chain 'P' and resid 557 through 559 removed outlier: 3.642A pdb=" N GLY P 585 " --> pdb=" O GLU P 558 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 563 through 565 271 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 4.23 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: 1900 1.34 - 1.45: 2153 1.45 - 1.57: 3645 1.57 - 1.69: 245 1.69 - 1.81: 48 Bond restraints: 7991 Sorted by residual: bond pdb=" O3' DG T -17 " pdb=" P DA T -16 " ideal model delta sigma weight residual 1.607 1.625 -0.018 1.50e-02 4.44e+03 1.37e+00 bond pdb=" C1' A W 16 " pdb=" N9 A W 16 " ideal model delta sigma weight residual 1.465 1.480 -0.015 1.50e-02 4.44e+03 1.07e+00 bond pdb=" C1' U W 15 " pdb=" N1 U W 15 " ideal model delta sigma weight residual 1.470 1.484 -0.014 1.50e-02 4.44e+03 8.77e-01 bond pdb=" C3' DC T -6 " pdb=" O3' DC T -6 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.52e-01 bond pdb=" C3' DA T -8 " pdb=" O3' DA T -8 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 7.82e-01 ... (remaining 7986 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.13: 791 106.13 - 113.10: 4332 113.10 - 120.06: 2908 120.06 - 127.03: 3008 127.03 - 134.00: 331 Bond angle restraints: 11370 Sorted by residual: angle pdb=" O3' DG T -17 " pdb=" P DA T -16 " pdb=" OP1 DA T -16 " ideal model delta sigma weight residual 108.00 131.22 -23.22 3.00e+00 1.11e-01 5.99e+01 angle pdb=" OP1 DA T -16 " pdb=" P DA T -16 " pdb=" OP2 DA T -16 " ideal model delta sigma weight residual 120.00 103.13 16.87 3.00e+00 1.11e-01 3.16e+01 angle pdb=" O3' C W 19 " pdb=" C3' C W 19 " pdb=" C2' C W 19 " ideal model delta sigma weight residual 109.50 116.88 -7.38 1.50e+00 4.44e-01 2.42e+01 angle pdb=" C4' U W 76 " pdb=" C3' U W 76 " pdb=" O3' U W 76 " ideal model delta sigma weight residual 109.40 116.64 -7.24 1.50e+00 4.44e-01 2.33e+01 angle pdb=" C4' U W 15 " pdb=" C3' U W 15 " pdb=" O3' U W 15 " ideal model delta sigma weight residual 109.40 115.86 -6.46 1.50e+00 4.44e-01 1.85e+01 ... (remaining 11365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 4365 35.94 - 71.88: 310 71.88 - 107.82: 31 107.82 - 143.76: 8 143.76 - 179.70: 11 Dihedral angle restraints: 4725 sinusoidal: 2947 harmonic: 1778 Sorted by residual: dihedral pdb=" C4' U W 76 " pdb=" C3' U W 76 " pdb=" C2' U W 76 " pdb=" C1' U W 76 " ideal model delta sinusoidal sigma weight residual -35.00 36.12 -71.12 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' A W 16 " pdb=" C3' A W 16 " pdb=" C2' A W 16 " pdb=" C1' A W 16 " ideal model delta sinusoidal sigma weight residual -35.00 35.70 -70.70 1 8.00e+00 1.56e-02 1.00e+02 dihedral pdb=" C4' C W 19 " pdb=" C3' C W 19 " pdb=" C2' C W 19 " pdb=" C1' C W 19 " ideal model delta sinusoidal sigma weight residual -35.00 35.27 -70.27 1 8.00e+00 1.56e-02 9.94e+01 ... (remaining 4722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1215 0.149 - 0.299: 39 0.299 - 0.448: 52 0.448 - 0.598: 0 0.598 - 0.747: 1 Chirality restraints: 1307 Sorted by residual: chirality pdb=" P DA T -16 " pdb=" OP1 DA T -16 " pdb=" OP2 DA T -16 " pdb=" O5' DA T -16 " both_signs ideal model delta sigma weight residual True 2.35 -3.09 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" P DC T 7 " pdb=" OP1 DC T 7 " pdb=" OP2 DC T 7 " pdb=" O5' DC T 7 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" P DA T -4 " pdb=" OP1 DA T -4 " pdb=" OP2 DA T -4 " pdb=" O5' DA T -4 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 1304 not shown) Planarity restraints: 1000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G W 20 " 0.014 2.00e-02 2.50e+03 7.39e-03 1.64e+00 pdb=" N9 G W 20 " -0.020 2.00e-02 2.50e+03 pdb=" C8 G W 20 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G W 20 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G W 20 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G W 20 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G W 20 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G W 20 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G W 20 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G W 20 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G W 20 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G W 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G W 70 " -0.016 2.00e-02 2.50e+03 7.29e-03 1.59e+00 pdb=" N9 G W 70 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G W 70 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G W 70 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G W 70 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G W 70 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G W 70 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G W 70 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G W 70 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G W 70 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G W 70 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G W 70 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U W 27 " -0.015 2.00e-02 2.50e+03 7.91e-03 1.41e+00 pdb=" N1 U W 27 " 0.017 2.00e-02 2.50e+03 pdb=" C2 U W 27 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U W 27 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U W 27 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U W 27 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U W 27 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U W 27 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U W 27 " 0.003 2.00e-02 2.50e+03 ... (remaining 997 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 63 2.48 - 3.09: 5215 3.09 - 3.69: 12649 3.69 - 4.30: 18239 4.30 - 4.90: 28379 Nonbonded interactions: 64545 Sorted by model distance: nonbonded pdb="MG MG P 702 " pdb=" O HOH P 801 " model vdw 1.881 2.170 nonbonded pdb=" OD1 ASN P 385 " pdb="MG MG P 701 " model vdw 1.886 2.170 nonbonded pdb=" OP1 DT T -19 " pdb="MG MG P 701 " model vdw 1.900 2.170 nonbonded pdb=" OP2 DT T -19 " pdb="MG MG P 702 " model vdw 1.902 2.170 nonbonded pdb=" O2' G W 20 " pdb=" OP1 C W 21 " model vdw 1.902 2.440 ... (remaining 64540 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.960 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 29.080 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 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 : 0.002 0.032 7991 Z= 0.130 Angle : 1.275 23.219 11370 Z= 0.504 Chirality : 0.096 0.747 1307 Planarity : 0.002 0.025 1000 Dihedral : 22.210 179.701 3569 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 3.05 (0.36), residues: 596 helix: 2.95 (0.29), residues: 331 sheet: 0.24 (0.83), residues: 41 loop : 1.06 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 93 HIS 0.002 0.001 HIS P 55 PHE 0.005 0.001 PHE P 151 TYR 0.016 0.001 TYR P 283 ARG 0.002 0.000 ARG P 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 128 average time/residue: 1.3780 time to fit residues: 184.9281 Evaluate side-chains 120 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1084 time to fit residues: 1.0019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN P 129 GLN P 308 ASN P 378 ASN P 393 GLN P 396 ASN P 482 GLN P 517 GLN P 581 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7991 Z= 0.318 Angle : 0.696 8.309 11370 Z= 0.374 Chirality : 0.043 0.236 1307 Planarity : 0.005 0.038 1000 Dihedral : 25.240 176.710 2333 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.95 % Allowed : 9.39 % Favored : 87.66 % 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: 1.65 (0.34), residues: 596 helix: 1.63 (0.28), residues: 340 sheet: -0.24 (0.77), residues: 46 loop : 0.72 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 570 HIS 0.008 0.002 HIS P 566 PHE 0.023 0.002 PHE P 62 TYR 0.020 0.002 TYR P 283 ARG 0.010 0.001 ARG P 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.657 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 125 average time/residue: 1.2969 time to fit residues: 170.6445 Evaluate side-chains 114 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.617 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 4 average time/residue: 0.0844 time to fit residues: 1.4112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN P 378 ASN P 396 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7991 Z= 0.193 Angle : 0.587 8.339 11370 Z= 0.319 Chirality : 0.037 0.187 1307 Planarity : 0.004 0.037 1000 Dihedral : 24.791 176.000 2333 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 2.95 % Allowed : 12.34 % Favored : 84.71 % 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: 1.66 (0.34), residues: 596 helix: 1.68 (0.27), residues: 338 sheet: -0.33 (0.74), residues: 46 loop : 0.69 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 570 HIS 0.005 0.001 HIS P 566 PHE 0.017 0.002 PHE P 630 TYR 0.017 0.001 TYR P 283 ARG 0.007 0.001 ARG P 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.895 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 120 average time/residue: 1.3663 time to fit residues: 172.5169 Evaluate side-chains 118 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.646 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 6 average time/residue: 0.3507 time to fit residues: 3.3285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.0050 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 378 ASN P 393 GLN P 396 ASN P 517 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7991 Z= 0.241 Angle : 0.619 9.883 11370 Z= 0.332 Chirality : 0.039 0.231 1307 Planarity : 0.005 0.040 1000 Dihedral : 24.738 177.459 2333 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.13 % Allowed : 12.89 % Favored : 83.98 % 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: 1.34 (0.34), residues: 596 helix: 1.40 (0.27), residues: 338 sheet: -0.25 (0.76), residues: 46 loop : 0.51 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 570 HIS 0.005 0.001 HIS P 566 PHE 0.018 0.002 PHE P 630 TYR 0.018 0.002 TYR P 283 ARG 0.008 0.001 ARG P 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.665 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 114 average time/residue: 1.2968 time to fit residues: 155.7429 Evaluate side-chains 118 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.617 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 6 average time/residue: 0.3199 time to fit residues: 3.0464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN P 58 HIS P 321 HIS P 378 ASN P 396 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7991 Z= 0.232 Angle : 0.614 8.505 11370 Z= 0.327 Chirality : 0.038 0.231 1307 Planarity : 0.005 0.045 1000 Dihedral : 24.512 177.305 2333 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.13 % Allowed : 13.08 % Favored : 83.79 % 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: 1.20 (0.34), residues: 596 helix: 1.35 (0.27), residues: 338 sheet: -0.43 (0.76), residues: 46 loop : 0.38 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 570 HIS 0.005 0.001 HIS P 566 PHE 0.021 0.002 PHE P 630 TYR 0.018 0.002 TYR P 283 ARG 0.009 0.001 ARG P 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.651 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 120 average time/residue: 1.2948 time to fit residues: 163.6306 Evaluate side-chains 115 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.646 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.0686 time to fit residues: 1.2396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN P 124 ASN P 129 GLN P 321 HIS P 378 ASN P 393 GLN P 396 ASN P 517 GLN ** P 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7991 Z= 0.255 Angle : 0.623 7.858 11370 Z= 0.334 Chirality : 0.039 0.240 1307 Planarity : 0.005 0.050 1000 Dihedral : 24.317 177.886 2333 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.76 % Allowed : 14.55 % Favored : 82.69 % 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: 1.01 (0.34), residues: 596 helix: 1.14 (0.27), residues: 338 sheet: -0.49 (0.70), residues: 56 loop : 0.45 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 570 HIS 0.006 0.001 HIS P 566 PHE 0.023 0.002 PHE P 630 TYR 0.018 0.002 TYR P 450 ARG 0.011 0.001 ARG P 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.651 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 118 average time/residue: 1.3268 time to fit residues: 164.6230 Evaluate side-chains 105 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0603 time to fit residues: 0.9609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 chunk 68 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN P 55 HIS P 321 HIS P 378 ASN P 393 GLN P 396 ASN P 517 GLN P 590 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7991 Z= 0.195 Angle : 0.583 7.520 11370 Z= 0.314 Chirality : 0.037 0.195 1307 Planarity : 0.005 0.046 1000 Dihedral : 24.221 176.090 2333 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.03 % Allowed : 15.65 % Favored : 82.32 % 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: 1.16 (0.34), residues: 596 helix: 1.32 (0.27), residues: 337 sheet: -0.56 (0.70), residues: 56 loop : 0.44 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 570 HIS 0.005 0.001 HIS P 566 PHE 0.021 0.002 PHE P 630 TYR 0.017 0.002 TYR P 283 ARG 0.010 0.000 ARG P 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.687 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 1.3244 time to fit residues: 152.0735 Evaluate side-chains 113 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.5680 time to fit residues: 2.6610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 51.6735 > 50: distance: 68 - 69: 17.510 distance: 68 - 219: 3.285 distance: 69 - 70: 13.813 distance: 69 - 72: 12.297 distance: 70 - 71: 4.978 distance: 70 - 76: 9.645 distance: 71 - 216: 11.620 distance: 72 - 74: 14.744 distance: 73 - 75: 15.182 distance: 76 - 77: 4.081 distance: 77 - 78: 4.269 distance: 77 - 80: 8.843 distance: 78 - 79: 15.910 distance: 78 - 84: 11.696 distance: 80 - 81: 14.788 distance: 81 - 82: 15.982 distance: 81 - 83: 16.828 distance: 84 - 85: 6.006 distance: 85 - 86: 9.790 distance: 85 - 88: 6.554 distance: 86 - 91: 18.298 distance: 87 - 115: 11.713 distance: 88 - 89: 29.482 distance: 88 - 90: 31.741 distance: 91 - 92: 10.761 distance: 92 - 93: 13.100 distance: 92 - 95: 4.234 distance: 93 - 94: 8.308 distance: 93 - 99: 4.027 distance: 94 - 127: 13.734 distance: 95 - 96: 8.250 distance: 95 - 97: 11.493 distance: 96 - 98: 10.685 distance: 99 - 100: 7.523 distance: 100 - 101: 13.259 distance: 100 - 103: 10.776 distance: 101 - 102: 8.792 distance: 101 - 107: 6.000 distance: 102 - 136: 15.559 distance: 103 - 104: 10.336 distance: 103 - 105: 9.626 distance: 104 - 106: 24.148 distance: 107 - 108: 4.883 distance: 108 - 111: 3.543 distance: 109 - 110: 9.237 distance: 109 - 115: 10.129 distance: 110 - 146: 23.124 distance: 111 - 112: 12.714 distance: 112 - 113: 17.534 distance: 112 - 114: 11.760 distance: 115 - 116: 8.123 distance: 116 - 117: 10.698 distance: 116 - 119: 9.577 distance: 117 - 118: 7.799 distance: 119 - 120: 4.733 distance: 120 - 122: 3.369 distance: 121 - 123: 9.821 distance: 122 - 124: 9.659 distance: 123 - 125: 7.409 distance: 124 - 125: 10.958 distance: 125 - 126: 11.361 distance: 127 - 128: 14.299 distance: 128 - 129: 14.160 distance: 128 - 131: 7.270 distance: 129 - 130: 12.016 distance: 129 - 136: 28.735 distance: 131 - 132: 18.977 distance: 132 - 133: 22.906 distance: 133 - 134: 18.386 distance: 133 - 135: 20.361 distance: 136 - 137: 14.389 distance: 137 - 138: 19.562 distance: 137 - 140: 16.297 distance: 138 - 139: 15.577 distance: 138 - 146: 11.015 distance: 140 - 141: 5.796 distance: 141 - 142: 13.234 distance: 141 - 143: 9.557 distance: 142 - 144: 10.460 distance: 143 - 145: 13.206 distance: 144 - 145: 13.012 distance: 147 - 148: 3.635 distance: 147 - 150: 4.358 distance: 148 - 149: 7.179 distance: 148 - 154: 17.188 distance: 150 - 151: 9.810 distance: 150 - 152: 10.439 distance: 151 - 153: 4.953