Starting phenix.real_space_refine on Sat Apr 26 22:06:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irx_60824/04_2025/9irx_60824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irx_60824/04_2025/9irx_60824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9irx_60824/04_2025/9irx_60824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irx_60824/04_2025/9irx_60824.map" model { file = "/net/cci-nas-00/data/ceres_data/9irx_60824/04_2025/9irx_60824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irx_60824/04_2025/9irx_60824.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.143 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 Br 2 7.06 5 S 27 5.16 5 C 2305 2.51 5 N 586 2.21 5 O 589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3509 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3487 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 26, 'TRANS': 442} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'R75': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.95, per 1000 atoms: 0.84 Number of scatterers: 3509 At special positions: 0 Unit cell: (106.7, 55.484, 66.154, 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) Br 2 34.99 S 27 16.00 O 589 8.00 N 586 7.00 C 2305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 391.9 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 856 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 82.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.504A pdb=" N SER A 141 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 170 removed outlier: 3.626A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 192 Processing helix chain 'A' and resid 195 through 223 removed outlier: 3.603A pdb=" N GLY A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.506A pdb=" N PHE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.034A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.549A pdb=" N LEU A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 377 through 403 removed outlier: 3.733A pdb=" N GLY A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Proline residue: A 391 - end of helix removed outlier: 4.011A pdb=" N SER A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 Processing helix chain 'A' and resid 430 through 456 Processing helix chain 'A' and resid 464 through 486 Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.563A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.199A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 266 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 803 1.33 - 1.48: 1220 1.48 - 1.64: 1526 1.64 - 1.79: 0 1.79 - 1.94: 44 Bond restraints: 3593 Sorted by residual: bond pdb=" CAO R75 A 601 " pdb=" CAS R75 A 601 " ideal model delta sigma weight residual 1.382 1.571 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" CAP R75 A 601 " pdb=" CAV R75 A 601 " ideal model delta sigma weight residual 1.396 1.569 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" CAD R75 A 601 " pdb=" CAE R75 A 601 " ideal model delta sigma weight residual 1.382 1.528 -0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" CAA R75 A 601 " pdb=" CAB R75 A 601 " ideal model delta sigma weight residual 1.378 1.519 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" CAC R75 A 601 " pdb=" CAD R75 A 601 " ideal model delta sigma weight residual 1.400 1.533 -0.133 2.00e-02 2.50e+03 4.46e+01 ... (remaining 3588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4808 1.56 - 3.12: 61 3.12 - 4.68: 28 4.68 - 6.24: 4 6.24 - 7.80: 5 Bond angle restraints: 4906 Sorted by residual: angle pdb=" CAJ R75 A 601 " pdb=" CAL R75 A 601 " pdb=" CAP R75 A 601 " ideal model delta sigma weight residual 129.37 121.57 7.80 3.00e+00 1.11e-01 6.76e+00 angle pdb=" CAQ R75 A 601 " pdb=" CAM R75 A 601 " pdb=" OAN R75 A 601 " ideal model delta sigma weight residual 116.30 124.01 -7.71 3.00e+00 1.11e-01 6.61e+00 angle pdb=" C VAL A 162 " pdb=" CA VAL A 162 " pdb=" CB VAL A 162 " ideal model delta sigma weight residual 111.94 108.87 3.07 1.26e+00 6.30e-01 5.92e+00 angle pdb=" CAS R75 A 601 " pdb=" CAO R75 A 601 " pdb=" OAN R75 A 601 " ideal model delta sigma weight residual 125.82 132.61 -6.79 3.00e+00 1.11e-01 5.13e+00 angle pdb=" CA TYR A 275 " pdb=" CB TYR A 275 " pdb=" CG TYR A 275 " ideal model delta sigma weight residual 113.90 117.90 -4.00 1.80e+00 3.09e-01 4.95e+00 ... (remaining 4901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.60: 2043 27.60 - 55.19: 37 55.19 - 82.79: 4 82.79 - 110.39: 0 110.39 - 137.99: 1 Dihedral angle restraints: 2085 sinusoidal: 758 harmonic: 1327 Sorted by residual: dihedral pdb=" CAL R75 A 601 " pdb=" CAM R75 A 601 " pdb=" CAQ R75 A 601 " pdb=" CAR R75 A 601 " ideal model delta sinusoidal sigma weight residual 263.96 125.97 137.99 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" SG CYS A 49 " pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " pdb=" CA CYS A 116 " ideal model delta sinusoidal sigma weight residual 79.00 26.30 52.70 1 2.00e+01 2.50e-03 9.46e+00 dihedral pdb=" N LEU A 437 " pdb=" CA LEU A 437 " pdb=" CB LEU A 437 " pdb=" CG LEU A 437 " ideal model delta sinusoidal sigma weight residual -60.00 -110.18 50.18 3 1.50e+01 4.44e-03 8.87e+00 ... (remaining 2082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 381 0.026 - 0.051: 137 0.051 - 0.077: 42 0.077 - 0.102: 25 0.102 - 0.128: 8 Chirality restraints: 593 Sorted by residual: chirality pdb=" CA ILE A 77 " pdb=" N ILE A 77 " pdb=" C ILE A 77 " pdb=" CB ILE A 77 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CB VAL A 210 " pdb=" CA VAL A 210 " pdb=" CG1 VAL A 210 " pdb=" CG2 VAL A 210 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA VAL A 121 " pdb=" N VAL A 121 " pdb=" C VAL A 121 " pdb=" CB VAL A 121 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 590 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 275 " 0.008 2.00e-02 2.50e+03 7.55e-03 1.14e+00 pdb=" CG TYR A 275 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 275 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 275 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 275 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 275 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 275 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 275 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 51 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 52 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 44 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.79e-01 pdb=" N PRO A 45 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.014 5.00e-02 4.00e+02 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 371 2.74 - 3.28: 3735 3.28 - 3.82: 6332 3.82 - 4.36: 7404 4.36 - 4.90: 12697 Nonbonded interactions: 30539 Sorted by model distance: nonbonded pdb=" OE1 GLN A 149 " pdb=" NH2 ARG A 487 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG A 349 " pdb=" O LEU A 459 " model vdw 2.237 3.120 nonbonded pdb=" O ALA A 335 " pdb=" OG1 THR A 467 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG A 173 " pdb=" O LEU A 279 " model vdw 2.282 3.120 nonbonded pdb=" N GLU A 281 " pdb=" OE2 GLU A 298 " model vdw 2.285 3.120 ... (remaining 30534 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.220 Find NCS groups from input model: 0.030 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:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.009 0.189 3595 Z= 0.428 Angle : 0.583 7.803 4910 Z= 0.275 Chirality : 0.035 0.128 593 Planarity : 0.003 0.026 598 Dihedral : 11.281 137.986 1223 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.56 % Allowed : 3.89 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.40), residues: 457 helix: 1.76 (0.28), residues: 348 sheet: None (None), residues: 0 loop : 0.96 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 357 HIS 0.002 0.001 HIS A 47 PHE 0.012 0.001 PHE A 360 TYR 0.018 0.002 TYR A 275 ARG 0.002 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.11788 ( 266) hydrogen bonds : angle 5.49077 ( 786) SS BOND : bond 0.00688 ( 2) SS BOND : angle 1.71300 ( 4) covalent geometry : bond 0.00866 ( 3593) covalent geometry : angle 0.58119 ( 4906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.381 Fit side-chains REVERT: A 37 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8253 (tp) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.8964 time to fit residues: 56.1024 Evaluate side-chains 47 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 210 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.143773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116487 restraints weight = 2990.962| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.36 r_work: 0.3060 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3595 Z= 0.197 Angle : 0.638 6.430 4910 Z= 0.308 Chirality : 0.041 0.198 593 Planarity : 0.004 0.031 598 Dihedral : 8.053 118.721 501 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.44 % Allowed : 7.78 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.40), residues: 457 helix: 1.69 (0.28), residues: 352 sheet: None (None), residues: 0 loop : 1.27 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 PHE 0.015 0.002 PHE A 360 TYR 0.017 0.002 TYR A 275 ARG 0.005 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 266) hydrogen bonds : angle 4.55375 ( 786) SS BOND : bond 0.00880 ( 2) SS BOND : angle 1.52102 ( 4) covalent geometry : bond 0.00482 ( 3593) covalent geometry : angle 0.63683 ( 4906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.381 Fit side-chains REVERT: A 37 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 222 MET cc_start: 0.7032 (mmt) cc_final: 0.6816 (mmt) REVERT: A 430 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.5768 (mmt) outliers start: 16 outliers final: 4 residues processed: 64 average time/residue: 0.8790 time to fit residues: 58.7099 Evaluate side-chains 50 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 262 GLN A 473 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.136869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.108362 restraints weight = 3096.094| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.44 r_work: 0.3036 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3595 Z= 0.166 Angle : 0.601 6.483 4910 Z= 0.288 Chirality : 0.039 0.178 593 Planarity : 0.004 0.029 598 Dihedral : 7.797 107.850 501 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.06 % Allowed : 11.39 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.39), residues: 457 helix: 1.59 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 1.18 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 PHE 0.014 0.002 PHE A 360 TYR 0.016 0.002 TYR A 275 ARG 0.005 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 266) hydrogen bonds : angle 4.40339 ( 786) SS BOND : bond 0.00738 ( 2) SS BOND : angle 1.32154 ( 4) covalent geometry : bond 0.00402 ( 3593) covalent geometry : angle 0.59994 ( 4906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.350 Fit side-chains REVERT: A 430 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.5726 (mmt) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.8606 time to fit residues: 51.2970 Evaluate side-chains 52 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112241 restraints weight = 3104.529| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.42 r_work: 0.3041 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3595 Z= 0.175 Angle : 0.609 7.666 4910 Z= 0.291 Chirality : 0.040 0.184 593 Planarity : 0.004 0.051 598 Dihedral : 7.689 99.359 501 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.61 % Allowed : 13.06 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.40), residues: 457 helix: 1.50 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 1.38 (0.69), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 PHE 0.014 0.002 PHE A 360 TYR 0.017 0.002 TYR A 275 ARG 0.013 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 266) hydrogen bonds : angle 4.41005 ( 786) SS BOND : bond 0.00788 ( 2) SS BOND : angle 1.25554 ( 4) covalent geometry : bond 0.00428 ( 3593) covalent geometry : angle 0.60866 ( 4906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.342 Fit side-chains REVERT: A 430 MET cc_start: 0.6519 (OUTLIER) cc_final: 0.6316 (mmm) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.8693 time to fit residues: 50.0945 Evaluate side-chains 54 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 30 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.139100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110739 restraints weight = 3184.135| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.47 r_work: 0.3078 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3595 Z= 0.127 Angle : 0.562 6.830 4910 Z= 0.266 Chirality : 0.037 0.167 593 Planarity : 0.004 0.058 598 Dihedral : 7.336 83.405 501 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.61 % Allowed : 15.56 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.40), residues: 457 helix: 1.65 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 1.27 (0.71), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 357 HIS 0.001 0.000 HIS A 245 PHE 0.013 0.002 PHE A 360 TYR 0.015 0.001 TYR A 275 ARG 0.013 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 266) hydrogen bonds : angle 4.18869 ( 786) SS BOND : bond 0.00472 ( 2) SS BOND : angle 1.02848 ( 4) covalent geometry : bond 0.00292 ( 3593) covalent geometry : angle 0.56152 ( 4906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.386 Fit side-chains REVERT: A 278 TRP cc_start: 0.8115 (m100) cc_final: 0.7809 (m100) REVERT: A 300 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8140 (ttm110) REVERT: A 388 VAL cc_start: 0.8379 (p) cc_final: 0.8019 (t) REVERT: A 430 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5824 (mmt) outliers start: 13 outliers final: 5 residues processed: 60 average time/residue: 0.7513 time to fit residues: 47.4189 Evaluate side-chains 55 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.108761 restraints weight = 3221.496| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.48 r_work: 0.3047 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3595 Z= 0.160 Angle : 0.591 6.987 4910 Z= 0.281 Chirality : 0.040 0.240 593 Planarity : 0.004 0.044 598 Dihedral : 6.951 76.411 500 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.78 % Allowed : 17.50 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.40), residues: 457 helix: 1.69 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 1.27 (0.69), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 PHE 0.013 0.002 PHE A 362 TYR 0.017 0.002 TYR A 275 ARG 0.010 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 266) hydrogen bonds : angle 4.26422 ( 786) SS BOND : bond 0.00715 ( 2) SS BOND : angle 1.12572 ( 4) covalent geometry : bond 0.00386 ( 3593) covalent geometry : angle 0.59080 ( 4906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.349 Fit side-chains REVERT: A 388 VAL cc_start: 0.8434 (p) cc_final: 0.8078 (t) outliers start: 10 outliers final: 5 residues processed: 53 average time/residue: 0.8478 time to fit residues: 47.0101 Evaluate side-chains 52 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4083 > 50: distance: 33 - 53: 25.481 distance: 37 - 61: 14.800 distance: 45 - 72: 23.867 distance: 49 - 53: 28.092 distance: 50 - 77: 26.416 distance: 53 - 54: 22.062 distance: 54 - 55: 45.782 distance: 54 - 57: 27.486 distance: 55 - 56: 20.719 distance: 55 - 61: 13.976 distance: 56 - 84: 34.083 distance: 57 - 58: 31.260 distance: 58 - 59: 31.718 distance: 58 - 60: 16.299 distance: 61 - 62: 26.230 distance: 62 - 63: 38.122 distance: 62 - 65: 23.825 distance: 63 - 64: 52.700 distance: 63 - 72: 37.524 distance: 64 - 89: 46.278 distance: 65 - 66: 53.991 distance: 66 - 67: 20.853 distance: 67 - 68: 6.857 distance: 68 - 69: 5.240 distance: 69 - 70: 8.727 distance: 69 - 71: 17.037 distance: 72 - 73: 8.297 distance: 73 - 74: 38.352 distance: 73 - 76: 23.618 distance: 74 - 75: 7.820 distance: 74 - 77: 32.302 distance: 75 - 94: 43.320 distance: 77 - 78: 9.599 distance: 78 - 79: 8.602 distance: 78 - 81: 37.021 distance: 79 - 80: 39.444 distance: 79 - 84: 17.805 distance: 81 - 82: 30.146 distance: 81 - 83: 33.305 distance: 84 - 85: 22.741 distance: 85 - 86: 19.274 distance: 85 - 88: 24.373 distance: 86 - 87: 9.770 distance: 86 - 89: 48.031 distance: 89 - 90: 20.899 distance: 90 - 91: 42.395 distance: 90 - 93: 20.368 distance: 91 - 92: 17.872 distance: 91 - 94: 13.290 distance: 94 - 95: 41.645 distance: 95 - 96: 42.613 distance: 95 - 98: 16.865 distance: 96 - 97: 25.964 distance: 98 - 99: 32.205 distance: 98 - 100: 16.190 distance: 99 - 101: 46.513 distance: 102 - 103: 20.795 distance: 103 - 104: 18.850 distance: 103 - 106: 15.428 distance: 104 - 105: 20.574 distance: 104 - 110: 37.348 distance: 106 - 107: 11.610 distance: 107 - 108: 18.456 distance: 107 - 109: 32.946 distance: 110 - 111: 40.663 distance: 111 - 112: 16.416 distance: 111 - 114: 13.591 distance: 112 - 113: 11.575 distance: 112 - 117: 29.635 distance: 114 - 115: 29.507 distance: 114 - 116: 30.061 distance: 117 - 118: 30.060 distance: 117 - 123: 13.702 distance: 118 - 119: 26.538 distance: 118 - 121: 11.211 distance: 119 - 120: 43.139 distance: 119 - 124: 18.432 distance: 120 - 144: 31.639 distance: 121 - 122: 4.572 distance: 122 - 123: 15.777