Starting phenix.real_space_refine on Fri Dec 27 11:29:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfl_34722/12_2024/8hfl_34722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfl_34722/12_2024/8hfl_34722.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/8hfl_34722/12_2024/8hfl_34722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfl_34722/12_2024/8hfl_34722.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfl_34722/12_2024/8hfl_34722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfl_34722/12_2024/8hfl_34722.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= 0.140 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 S 20 5.16 5 Cl 2 4.86 5 C 2980 2.51 5 N 689 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4441 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4421 Classifications: {'peptide': 553} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 533} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 20 Unusual residues: {' CL': 1, '1XR': 1} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} Time building chain proxies: 3.37, per 1000 atoms: 0.76 Number of scatterers: 4441 At special positions: 0 Unit cell: (68.1975, 71.445, 98.5075, 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) Cl 2 17.00 S 20 16.00 O 750 8.00 N 689 7.00 C 2980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 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: 1.31 Conformation dependent library (CDL) restraints added in 622.5 milliseconds 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 80.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.515A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 4.367A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.629A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 151 through 166 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.590A pdb=" N LEU A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 283 Proline residue: A 270 - end of helix removed outlier: 4.106A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.744A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.700A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.758A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.523A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.719A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.554A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.774A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 292 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1297 1.34 - 1.46: 974 1.46 - 1.58: 2277 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4580 Sorted by residual: bond pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.95e+00 bond pdb=" C2 1XR A 701 " pdb=" N1 1XR A 701 " ideal model delta sigma weight residual 1.441 1.477 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C10 1XR A 701 " pdb=" N1 1XR A 701 " ideal model delta sigma weight residual 1.467 1.490 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.28e-02 6.10e+03 1.09e+00 bond pdb=" C1 1XR A 701 " pdb=" C2 1XR A 701 " ideal model delta sigma weight residual 1.542 1.522 0.020 2.00e-02 2.50e+03 9.88e-01 ... (remaining 4575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 6100 1.50 - 3.00: 111 3.00 - 4.50: 32 4.50 - 6.00: 4 6.00 - 7.50: 1 Bond angle restraints: 6248 Sorted by residual: angle pdb=" C GLY A 106 " pdb=" N MET A 107 " pdb=" CA MET A 107 " ideal model delta sigma weight residual 119.78 116.12 3.66 1.24e+00 6.50e-01 8.70e+00 angle pdb=" N VAL A 263 " pdb=" CA VAL A 263 " pdb=" C VAL A 263 " ideal model delta sigma weight residual 113.00 109.26 3.74 1.30e+00 5.92e-01 8.26e+00 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" C TYR A 205 " ideal model delta sigma weight residual 110.80 116.58 -5.78 2.13e+00 2.20e-01 7.36e+00 angle pdb=" C1 1XR A 701 " pdb=" C2 1XR A 701 " pdb=" N1 1XR A 701 " ideal model delta sigma weight residual 117.04 109.54 7.50 3.00e+00 1.11e-01 6.25e+00 angle pdb=" CA MET A 107 " pdb=" C MET A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 120.81 118.72 2.09 8.60e-01 1.35e+00 5.88e+00 ... (remaining 6243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 2237 16.52 - 33.04: 241 33.04 - 49.56: 62 49.56 - 66.08: 23 66.08 - 82.60: 2 Dihedral angle restraints: 2565 sinusoidal: 968 harmonic: 1597 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -133.33 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 132.57 -9.77 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 2562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 666 0.088 - 0.176: 28 0.176 - 0.264: 0 0.264 - 0.351: 0 0.351 - 0.439: 2 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA HIS A 372 " pdb=" N HIS A 372 " pdb=" C HIS A 372 " pdb=" CB HIS A 372 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C2 1XR A 701 " pdb=" C1 1XR A 701 " pdb=" C3 1XR A 701 " pdb=" N1 1XR A 701 " both_signs ideal model delta sigma weight residual False -2.43 -2.59 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 693 not shown) Planarity restraints: 759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ILE A 103 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 492 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C VAL A 492 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 492 " 0.015 2.00e-02 2.50e+03 pdb=" N SER A 493 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C LEU A 102 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 102 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 103 " 0.012 2.00e-02 2.50e+03 ... (remaining 756 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 26 2.56 - 3.15: 3663 3.15 - 3.73: 6973 3.73 - 4.32: 9679 4.32 - 4.90: 16767 Nonbonded interactions: 37108 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OG SER A 419 " model vdw 1.981 3.040 nonbonded pdb=" OG1 THR A 479 " pdb=" OG SER A 536 " model vdw 2.179 3.040 nonbonded pdb=" NZ LYS A 189 " pdb=" OE2 GLU A 371 " model vdw 2.195 3.120 nonbonded pdb=" O ALA A 328 " pdb=" OG SER A 331 " model vdw 2.236 3.040 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 283 " model vdw 2.303 3.040 ... (remaining 37103 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: 0.350 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.440 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.003 0.039 4580 Z= 0.188 Angle : 0.548 7.502 6248 Z= 0.296 Chirality : 0.044 0.439 696 Planarity : 0.004 0.037 759 Dihedral : 15.471 82.598 1546 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % Rotamer: Outliers : 1.72 % Allowed : 17.17 % Favored : 81.12 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.37), residues: 549 helix: 1.52 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.10 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.013 0.001 PHE A 403 TYR 0.014 0.001 TYR A 590 ARG 0.001 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.463 Fit side-chains REVERT: A 509 MET cc_start: 0.8973 (mtp) cc_final: 0.8715 (mtt) REVERT: A 606 ILE cc_start: 0.8230 (mm) cc_final: 0.8016 (mm) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.5877 time to fit residues: 32.6905 Evaluate side-chains 48 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 536 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4580 Z= 0.212 Angle : 0.517 6.793 6248 Z= 0.268 Chirality : 0.040 0.173 696 Planarity : 0.004 0.034 759 Dihedral : 6.023 47.869 615 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.37 % Favored : 97.45 % Rotamer: Outliers : 2.79 % Allowed : 14.81 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.37), residues: 549 helix: 1.37 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.01 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.003 0.001 HIS A 370 PHE 0.015 0.001 PHE A 110 TYR 0.016 0.001 TYR A 590 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.538 Fit side-chains REVERT: A 271 TYR cc_start: 0.8564 (m-80) cc_final: 0.8237 (m-80) REVERT: A 377 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: A 421 MET cc_start: 0.7916 (mtp) cc_final: 0.7680 (mtm) REVERT: A 434 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8655 (m-30) REVERT: A 509 MET cc_start: 0.9017 (mtp) cc_final: 0.8734 (mtt) REVERT: A 606 ILE cc_start: 0.8274 (mm) cc_final: 0.8040 (mm) outliers start: 13 outliers final: 3 residues processed: 63 average time/residue: 0.5767 time to fit residues: 39.4366 Evaluate side-chains 52 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 434 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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-5532/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-5532/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-5532/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-5532/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-5532/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-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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-5532/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-5532/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-5532/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-5532/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: 62.9104 > 50: distance: 50 - 72: 27.025 distance: 55 - 79: 31.014 distance: 61 - 90: 34.592 distance: 66 - 72: 28.218 distance: 72 - 73: 53.675 distance: 73 - 74: 34.158 distance: 73 - 76: 24.579 distance: 74 - 79: 13.744 distance: 76 - 77: 17.050 distance: 76 - 78: 22.948 distance: 79 - 80: 28.306 distance: 80 - 83: 39.375 distance: 81 - 90: 36.423 distance: 84 - 85: 40.825 distance: 85 - 87: 8.544 distance: 86 - 88: 16.640 distance: 87 - 89: 49.282 distance: 88 - 89: 13.790 distance: 91 - 94: 20.046 distance: 96 - 97: 21.294 distance: 97 - 98: 6.731 distance: 97 - 100: 35.903 distance: 100 - 101: 41.446 distance: 101 - 102: 34.687 distance: 102 - 103: 33.308 distance: 102 - 104: 13.012 distance: 103 - 125: 55.459 distance: 104 - 105: 32.816 distance: 105 - 106: 34.131 distance: 105 - 108: 34.109 distance: 106 - 107: 6.262 distance: 106 - 111: 34.909 distance: 107 - 133: 41.769 distance: 108 - 109: 12.234 distance: 108 - 110: 31.905 distance: 111 - 112: 36.573 distance: 112 - 113: 17.397 distance: 112 - 115: 37.994 distance: 113 - 114: 19.290 distance: 114 - 144: 29.707 distance: 115 - 116: 39.399 distance: 118 - 119: 3.945 distance: 119 - 120: 35.383 distance: 119 - 125: 3.265 distance: 120 - 149: 36.582 distance: 121 - 123: 44.201 distance: 122 - 124: 37.791 distance: 126 - 127: 35.151 distance: 126 - 129: 22.802 distance: 127 - 128: 35.338 distance: 127 - 133: 26.421 distance: 128 - 156: 28.859 distance: 129 - 130: 19.222 distance: 130 - 132: 30.348 distance: 133 - 134: 29.888 distance: 134 - 135: 7.120 distance: 134 - 137: 7.236 distance: 135 - 136: 17.481 distance: 135 - 144: 26.263 distance: 136 - 163: 30.318 distance: 137 - 138: 30.251 distance: 138 - 139: 33.269 distance: 138 - 140: 29.521 distance: 139 - 141: 4.169 distance: 140 - 142: 44.838 distance: 141 - 143: 11.553 distance: 142 - 143: 22.641