Starting phenix.real_space_refine on Thu Dec 7 22:07:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2023/7slp_25197_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2023/7slp_25197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2023/7slp_25197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2023/7slp_25197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2023/7slp_25197_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slp_25197/12_2023/7slp_25197_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 15 5.16 5 C 3151 2.51 5 N 912 2.21 5 O 1061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ASP 593": "OD1" <-> "OD2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ARG 565": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5176 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1887 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2481 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 782 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 10, 'rna3p_pyr': 14} Link IDs: {'rna2p': 12, 'rna3p': 24} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 3.72, per 1000 atoms: 0.72 Number of scatterers: 5176 At special positions: 0 Unit cell: (81.32, 78.11, 101.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 37 15.00 O 1061 8.00 N 912 7.00 C 3151 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: 2.32 Conformation dependent library (CDL) restraints added in 893.6 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 3 sheets defined 42.4% alpha, 9.3% beta 8 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 433 through 436 No H-bonds generated for 'chain 'A' and resid 433 through 436' Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 456 through 464 Processing helix chain 'A' and resid 477 through 492 removed outlier: 4.035A pdb=" N SER A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 584 through 591 Processing helix chain 'A' and resid 594 through 606 Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.582A pdb=" N THR A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 78 through 81 No H-bonds generated for 'chain 'B' and resid 78 through 81' Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 122 through 125 No H-bonds generated for 'chain 'B' and resid 122 through 125' Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 177 through 185 removed outlier: 3.502A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 412 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.967A pdb=" N ILE B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 527 through 544 Processing helix chain 'B' and resid 553 through 570 Processing sheet with id= A, first strand: chain 'A' and resid 660 through 662 removed outlier: 3.528A pdb=" N CYS A 580 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 616 " --> pdb=" O CYS A 580 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 581 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 554 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASP A 474 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 556 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.749A pdb=" N TYR B 153 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 519 through 523 167 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1067 1.33 - 1.45: 1463 1.45 - 1.57: 2736 1.57 - 1.70: 73 1.70 - 1.82: 21 Bond restraints: 5360 Sorted by residual: bond pdb=" N GLU A 574 " pdb=" CA GLU A 574 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.00e-02 1.00e+04 9.22e+00 bond pdb=" C2 SAH A 701 " pdb=" N3 SAH A 701 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" N LYS A 625 " pdb=" CA LYS A 625 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.37e+00 bond pdb=" N SER A 622 " pdb=" CA SER A 622 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.89e+00 bond pdb=" N LYS B 112 " pdb=" CA LYS B 112 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.23e+00 ... (remaining 5355 not shown) Histogram of bond angle deviations from ideal: 93.07 - 101.29: 21 101.29 - 109.52: 1077 109.52 - 117.74: 3128 117.74 - 125.97: 3014 125.97 - 134.19: 196 Bond angle restraints: 7436 Sorted by residual: angle pdb=" N LEU B 131 " pdb=" CA LEU B 131 " pdb=" C LEU B 131 " ideal model delta sigma weight residual 110.91 120.44 -9.53 1.17e+00 7.31e-01 6.64e+01 angle pdb=" C PRO A 573 " pdb=" CA PRO A 573 " pdb=" CB PRO A 573 " ideal model delta sigma weight residual 111.11 102.94 8.17 1.17e+00 7.31e-01 4.88e+01 angle pdb=" C4' G R 300 " pdb=" C3' G R 300 " pdb=" O3' G R 300 " ideal model delta sigma weight residual 109.40 119.08 -9.68 1.50e+00 4.44e-01 4.16e+01 angle pdb=" N GLU B 480 " pdb=" CA GLU B 480 " pdb=" C GLU B 480 " ideal model delta sigma weight residual 109.15 118.31 -9.16 1.44e+00 4.82e-01 4.05e+01 angle pdb=" C SER B 479 " pdb=" CA SER B 479 " pdb=" CB SER B 479 " ideal model delta sigma weight residual 112.78 101.99 10.79 2.18e+00 2.10e-01 2.45e+01 ... (remaining 7431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 2873 21.54 - 43.07: 251 43.07 - 64.60: 69 64.60 - 86.14: 24 86.14 - 107.67: 7 Dihedral angle restraints: 3224 sinusoidal: 1589 harmonic: 1635 Sorted by residual: dihedral pdb=" CA ASN A 426 " pdb=" C ASN A 426 " pdb=" N PRO A 427 " pdb=" CA PRO A 427 " ideal model delta harmonic sigma weight residual 180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA HIS A 682 " pdb=" C HIS A 682 " pdb=" N LYS A 683 " pdb=" CA LYS A 683 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ARG B 55 " pdb=" C ARG B 55 " pdb=" N PHE B 56 " pdb=" CA PHE B 56 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 3221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 733 0.086 - 0.173: 115 0.173 - 0.259: 16 0.259 - 0.345: 1 0.345 - 0.432: 2 Chirality restraints: 867 Sorted by residual: chirality pdb=" CB VAL B 99 " pdb=" CA VAL B 99 " pdb=" CG1 VAL B 99 " pdb=" CG2 VAL B 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA PHE A 523 " pdb=" N PHE A 523 " pdb=" C PHE A 523 " pdb=" CB PHE A 523 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA LEU B 131 " pdb=" N LEU B 131 " pdb=" C LEU B 131 " pdb=" CB LEU B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 864 not shown) Planarity restraints: 807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 643 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 644 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 539 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C VAL A 539 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL A 539 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO A 540 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 588 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C HIS A 588 " -0.042 2.00e-02 2.50e+03 pdb=" O HIS A 588 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 589 " 0.014 2.00e-02 2.50e+03 ... (remaining 804 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 817 2.76 - 3.29: 4655 3.29 - 3.83: 9056 3.83 - 4.36: 9885 4.36 - 4.90: 15915 Nonbonded interactions: 40328 Sorted by model distance: nonbonded pdb=" O2' C R 320 " pdb=" OP1 C R 323 " model vdw 2.221 2.440 nonbonded pdb=" O2' U R 327 " pdb=" O2 U R 327 " model vdw 2.233 2.440 nonbonded pdb=" O GLN B 470 " pdb=" OG1 THR B 474 " model vdw 2.298 2.440 nonbonded pdb=" NH2 ARG B 552 " pdb=" N7 G R 303 " model vdw 2.303 2.600 nonbonded pdb=" O ARG A 425 " pdb=" OH TYR A 490 " model vdw 2.306 2.440 ... (remaining 40323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 2.000 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.730 Find NCS groups from input model: 0.130 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 5360 Z= 0.525 Angle : 1.220 10.794 7436 Z= 0.688 Chirality : 0.067 0.432 867 Planarity : 0.008 0.065 807 Dihedral : 18.737 107.672 2166 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.20 % Favored : 95.26 % Rotamer: Outliers : 1.77 % Allowed : 9.49 % Favored : 88.74 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.00 % 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: -3.76 (0.27), residues: 548 helix: -3.01 (0.21), residues: 266 sheet: 0.07 (0.64), residues: 60 loop : -2.38 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 384 HIS 0.009 0.003 HIS B 494 PHE 0.033 0.004 PHE A 442 TYR 0.029 0.005 TYR A 661 ARG 0.010 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 158 average time/residue: 0.1864 time to fit residues: 36.7533 Evaluate side-chains 85 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.587 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0580 time to fit residues: 1.1617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5360 Z= 0.233 Angle : 0.670 7.230 7436 Z= 0.343 Chirality : 0.039 0.245 867 Planarity : 0.007 0.085 807 Dihedral : 18.238 101.238 1149 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.77 (0.32), residues: 548 helix: -0.89 (0.29), residues: 256 sheet: -0.24 (0.71), residues: 50 loop : -1.60 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 586 HIS 0.006 0.002 HIS A 588 PHE 0.011 0.002 PHE B 46 TYR 0.016 0.002 TYR B 159 ARG 0.006 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1880 time to fit residues: 26.4983 Evaluate side-chains 71 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 481 HIS ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN B 508 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.8336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5360 Z= 0.291 Angle : 0.758 8.931 7436 Z= 0.383 Chirality : 0.042 0.216 867 Planarity : 0.007 0.101 807 Dihedral : 18.282 104.474 1149 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.29 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.44 (0.33), residues: 548 helix: -0.54 (0.30), residues: 255 sheet: -0.01 (0.89), residues: 40 loop : -1.49 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 519 HIS 0.012 0.002 HIS B 517 PHE 0.033 0.003 PHE A 523 TYR 0.019 0.002 TYR A 415 ARG 0.007 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1625 time to fit residues: 21.3393 Evaluate side-chains 69 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 HIS ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN B 508 ASN ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 1.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5360 Z= 0.400 Angle : 0.838 8.929 7436 Z= 0.431 Chirality : 0.046 0.166 867 Planarity : 0.007 0.094 807 Dihedral : 18.852 99.330 1149 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.33), residues: 548 helix: -0.67 (0.30), residues: 253 sheet: -0.79 (0.70), residues: 53 loop : -1.55 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP B 519 HIS 0.010 0.003 HIS A 489 PHE 0.025 0.003 PHE A 523 TYR 0.018 0.003 TYR B 532 ARG 0.004 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1383 time to fit residues: 15.3975 Evaluate side-chains 59 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 HIS A 588 HIS A 682 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN B 517 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 1.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5360 Z= 0.152 Angle : 0.565 7.115 7436 Z= 0.283 Chirality : 0.037 0.153 867 Planarity : 0.005 0.083 807 Dihedral : 17.750 93.968 1149 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.34), residues: 548 helix: 0.20 (0.32), residues: 255 sheet: -0.18 (0.78), residues: 47 loop : -1.43 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 519 HIS 0.005 0.001 HIS A 606 PHE 0.010 0.001 PHE A 523 TYR 0.018 0.002 TYR A 661 ARG 0.002 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.568 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1942 time to fit residues: 21.1495 Evaluate side-chains 60 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.0370 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS A 486 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 1.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5360 Z= 0.132 Angle : 0.546 7.172 7436 Z= 0.271 Chirality : 0.037 0.167 867 Planarity : 0.005 0.085 807 Dihedral : 17.500 94.477 1149 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.22 % Allowed : 1.77 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.35), residues: 548 helix: 0.48 (0.32), residues: 260 sheet: 0.59 (0.87), residues: 42 loop : -1.54 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 586 HIS 0.003 0.001 HIS B 494 PHE 0.038 0.002 PHE A 600 TYR 0.019 0.001 TYR A 604 ARG 0.001 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.501 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 78 average time/residue: 0.1676 time to fit residues: 17.3192 Evaluate side-chains 61 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0516 time to fit residues: 0.7540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 1.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5360 Z= 0.199 Angle : 0.590 7.128 7436 Z= 0.296 Chirality : 0.038 0.166 867 Planarity : 0.006 0.083 807 Dihedral : 17.575 94.550 1149 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 548 helix: 0.61 (0.32), residues: 260 sheet: 0.58 (0.84), residues: 42 loop : -1.47 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 519 HIS 0.006 0.002 HIS A 489 PHE 0.019 0.002 PHE A 523 TYR 0.016 0.002 TYR A 604 ARG 0.003 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.549 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1528 time to fit residues: 15.1419 Evaluate side-chains 59 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7675 ------------------------------------------------------------------------------- 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: 67.5943 > 50: distance: 88 - 93: 17.957 distance: 93 - 94: 19.086 distance: 94 - 95: 14.085 distance: 94 - 97: 22.104 distance: 95 - 96: 42.956 distance: 95 - 104: 19.092 distance: 97 - 98: 8.542 distance: 98 - 99: 9.873 distance: 99 - 100: 12.595 distance: 100 - 101: 18.321 distance: 101 - 102: 11.849 distance: 101 - 103: 18.044 distance: 104 - 105: 16.014 distance: 105 - 106: 19.740 distance: 105 - 108: 12.596 distance: 106 - 107: 12.147 distance: 106 - 112: 16.185 distance: 108 - 109: 29.736 distance: 108 - 110: 18.041 distance: 112 - 113: 23.245 distance: 113 - 114: 21.158 distance: 113 - 116: 26.719 distance: 114 - 115: 6.876 distance: 114 - 117: 20.916 distance: 117 - 118: 18.519 distance: 118 - 119: 20.808 distance: 118 - 121: 10.030 distance: 119 - 120: 7.297 distance: 119 - 122: 25.130 distance: 122 - 123: 23.007 distance: 123 - 124: 22.267 distance: 123 - 126: 27.950 distance: 124 - 125: 3.897 distance: 124 - 131: 36.180 distance: 126 - 127: 25.544 distance: 127 - 128: 22.296 distance: 128 - 129: 10.611 distance: 129 - 130: 13.769 distance: 131 - 132: 21.309 distance: 132 - 133: 11.164 distance: 132 - 135: 11.695 distance: 133 - 134: 28.865 distance: 133 - 140: 27.921 distance: 135 - 136: 42.853 distance: 136 - 137: 13.720 distance: 137 - 138: 34.261 distance: 138 - 139: 39.763 distance: 140 - 141: 16.298 distance: 140 - 146: 31.255 distance: 141 - 144: 3.406 distance: 142 - 143: 6.340 distance: 142 - 147: 5.501 distance: 144 - 145: 23.717 distance: 145 - 146: 24.712 distance: 147 - 148: 35.950 distance: 148 - 149: 20.822 distance: 148 - 151: 40.067 distance: 149 - 150: 17.540 distance: 151 - 152: 14.981 distance: 152 - 153: 19.074 distance: 152 - 154: 21.975 distance: 155 - 156: 23.569 distance: 156 - 157: 20.381 distance: 157 - 158: 3.459 distance: 157 - 159: 23.281 distance: 159 - 160: 17.139 distance: 160 - 161: 12.171 distance: 160 - 163: 19.748 distance: 161 - 162: 15.546 distance: 161 - 168: 28.377 distance: 163 - 164: 22.257 distance: 164 - 165: 15.434 distance: 165 - 166: 22.237 distance: 165 - 167: 20.696