Starting phenix.real_space_refine on Mon Jan 13 17:34:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gjn_40095/01_2025/8gjn_40095.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gjn_40095/01_2025/8gjn_40095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gjn_40095/01_2025/8gjn_40095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gjn_40095/01_2025/8gjn_40095.map" model { file = "/net/cci-nas-00/data/ceres_data/8gjn_40095/01_2025/8gjn_40095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gjn_40095/01_2025/8gjn_40095.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2102 2.51 5 N 550 2.21 5 O 652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3319 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.19, per 1000 atoms: 1.26 Number of scatterers: 3319 At special positions: 0 Unit cell: (86.625, 54.45, 107.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 652 8.00 N 550 7.00 C 2102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 115 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 108 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 408.9 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 13.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.719A pdb=" N TYR A 51 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 4.450A pdb=" N GLY A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.106A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.074A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.661A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.213A pdb=" N GLU A 29 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET A 53 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY A 69 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP A 55 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 42 Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 26 removed outlier: 4.157A pdb=" N VAL B 39 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.388A pdb=" N TRP B 55 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 33 Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 108 hydrogen bonds defined for protein. 249 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: 0.88 Time building geometry restraints manager: 0.97 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: 801 1.33 - 1.46: 791 1.46 - 1.58: 1791 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3401 Sorted by residual: bond pdb=" N ILE C 472 " pdb=" CA ILE C 472 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N CYS A 115 " pdb=" CA CYS A 115 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ARG C 457 " pdb=" CA ARG C 457 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.18e-02 7.18e+03 9.94e+00 bond pdb=" N VAL C 524 " pdb=" CA VAL C 524 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 9.93e+00 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 3361 1.75 - 3.50: 1059 3.50 - 5.25: 180 5.25 - 7.00: 13 7.00 - 8.75: 2 Bond angle restraints: 4615 Sorted by residual: angle pdb=" N PHE C 490 " pdb=" CA PHE C 490 " pdb=" C PHE C 490 " ideal model delta sigma weight residual 109.24 100.49 8.75 1.39e+00 5.18e-01 3.96e+01 angle pdb=" N CYS C 488 " pdb=" CA CYS C 488 " pdb=" C CYS C 488 " ideal model delta sigma weight residual 109.54 101.74 7.80 1.37e+00 5.33e-01 3.25e+01 angle pdb=" N TYR C 489 " pdb=" CA TYR C 489 " pdb=" C TYR C 489 " ideal model delta sigma weight residual 110.43 116.65 -6.22 1.31e+00 5.83e-01 2.25e+01 angle pdb=" C GLY A 27 " pdb=" N PRO A 28 " pdb=" CA PRO A 28 " ideal model delta sigma weight residual 119.90 124.65 -4.75 1.02e+00 9.61e-01 2.16e+01 angle pdb=" C LYS B 80 " pdb=" CA LYS B 80 " pdb=" CB LYS B 80 " ideal model delta sigma weight residual 116.54 111.44 5.10 1.15e+00 7.56e-01 1.97e+01 ... (remaining 4610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 1851 17.49 - 34.98: 134 34.98 - 52.47: 21 52.47 - 69.95: 21 69.95 - 87.44: 2 Dihedral angle restraints: 2029 sinusoidal: 809 harmonic: 1220 Sorted by residual: dihedral pdb=" CA ASP B 61 " pdb=" C ASP B 61 " pdb=" N GLY B 62 " pdb=" CA GLY B 62 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER B 97 " pdb=" C SER B 97 " pdb=" N PRO B 98 " pdb=" CA PRO B 98 " ideal model delta harmonic sigma weight residual 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N VAL A 112 " pdb=" CA VAL A 112 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 2026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 226 0.060 - 0.120: 168 0.120 - 0.180: 80 0.180 - 0.240: 17 0.240 - 0.300: 5 Chirality restraints: 496 Sorted by residual: chirality pdb=" CA PHE C 464 " pdb=" N PHE C 464 " pdb=" C PHE C 464 " pdb=" CB PHE C 464 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA PRO A 33 " pdb=" N PRO A 33 " pdb=" C PRO A 33 " pdb=" CB PRO A 33 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA LEU C 461 " pdb=" N LEU C 461 " pdb=" C LEU C 461 " pdb=" CB LEU C 461 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 493 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 601 " -0.104 2.00e-02 2.50e+03 8.66e-02 9.37e+01 pdb=" C7 NAG C 601 " 0.024 2.00e-02 2.50e+03 pdb=" C8 NAG C 601 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG C 601 " 0.142 2.00e-02 2.50e+03 pdb=" O7 NAG C 601 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 380 " -0.094 2.00e-02 2.50e+03 5.01e-02 5.01e+01 pdb=" CG TYR C 380 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 380 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR C 380 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR C 380 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR C 380 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR C 380 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 380 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 69 " -0.071 2.00e-02 2.50e+03 4.07e-02 3.31e+01 pdb=" CG TYR B 69 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR B 69 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR B 69 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 69 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR B 69 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR B 69 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 69 " -0.063 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1409 2.92 - 3.42: 3062 3.42 - 3.91: 5638 3.91 - 4.41: 6166 4.41 - 4.90: 10475 Nonbonded interactions: 26750 Sorted by model distance: nonbonded pdb=" O TYR B 111 " pdb=" OG1 THR C 478 " model vdw 2.431 3.040 nonbonded pdb=" OG1 THR C 333 " pdb=" N ASN C 334 " model vdw 2.451 3.120 nonbonded pdb=" O GLN A 24 " pdb=" N LYS A 42 " model vdw 2.470 3.120 nonbonded pdb=" OH TYR C 453 " pdb=" OE1 GLN C 493 " model vdw 2.482 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.506 3.040 ... (remaining 26745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.450 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.013 0.046 3401 Z= 0.832 Angle : 1.648 8.747 4615 Z= 1.119 Chirality : 0.093 0.300 496 Planarity : 0.013 0.098 595 Dihedral : 14.166 87.440 1237 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 1.10 % Allowed : 7.40 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.73 (0.37), residues: 415 helix: -3.89 (0.58), residues: 26 sheet: -1.56 (0.46), residues: 116 loop : -1.77 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.009 TRP C 353 HIS 0.001 0.000 HIS C 519 PHE 0.062 0.008 PHE C 464 TYR 0.094 0.014 TYR C 380 ARG 0.009 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.7469 (tttt) cc_final: 0.7225 (tttt) REVERT: C 367 VAL cc_start: 0.8406 (t) cc_final: 0.8095 (p) outliers start: 4 outliers final: 0 residues processed: 70 average time/residue: 0.1594 time to fit residues: 13.8574 Evaluate side-chains 62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 12 optimal weight: 0.0010 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 62 GLN B 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.164977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137899 restraints weight = 5802.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.142070 restraints weight = 3015.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.144777 restraints weight = 1844.462| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3401 Z= 0.196 Angle : 0.597 8.968 4615 Z= 0.313 Chirality : 0.043 0.196 496 Planarity : 0.004 0.032 595 Dihedral : 5.291 35.193 488 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.19 % Allowed : 10.68 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.85 (0.39), residues: 415 helix: -3.79 (0.62), residues: 27 sheet: -1.23 (0.45), residues: 133 loop : -0.87 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 353 HIS 0.001 0.000 HIS C 519 PHE 0.016 0.002 PHE C 497 TYR 0.017 0.002 TYR C 380 ARG 0.004 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7140 (tttt) cc_final: 0.6866 (tttt) REVERT: B 83 SER cc_start: 0.6890 (p) cc_final: 0.6668 (p) REVERT: C 354 ASN cc_start: 0.8139 (m-40) cc_final: 0.7888 (m110) REVERT: C 423 TYR cc_start: 0.8263 (t80) cc_final: 0.8045 (t80) REVERT: C 492 LEU cc_start: 0.8414 (mp) cc_final: 0.8183 (mp) REVERT: C 508 TYR cc_start: 0.8626 (m-10) cc_final: 0.8357 (m-10) outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 0.1275 time to fit residues: 12.2875 Evaluate side-chains 74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.0040 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 32 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.2330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 57 GLN C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.164594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.137766 restraints weight = 5829.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.141822 restraints weight = 3127.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144431 restraints weight = 1975.771| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3401 Z= 0.158 Angle : 0.530 7.484 4615 Z= 0.275 Chirality : 0.042 0.209 496 Planarity : 0.004 0.038 595 Dihedral : 4.683 34.631 488 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.64 % Allowed : 14.52 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.50 (0.39), residues: 415 helix: -3.12 (0.79), residues: 27 sheet: -1.00 (0.44), residues: 139 loop : -0.66 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.011 0.001 PHE C 497 TYR 0.011 0.001 TYR C 380 ARG 0.002 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 367 VAL cc_start: 0.8405 (t) cc_final: 0.8199 (p) REVERT: C 423 TYR cc_start: 0.8381 (t80) cc_final: 0.8109 (t80) REVERT: C 438 SER cc_start: 0.8654 (m) cc_final: 0.8025 (p) REVERT: C 508 TYR cc_start: 0.8630 (m-10) cc_final: 0.8351 (m-10) REVERT: C 514 SER cc_start: 0.8523 (t) cc_final: 0.8191 (p) outliers start: 6 outliers final: 5 residues processed: 83 average time/residue: 0.1141 time to fit residues: 12.5652 Evaluate side-chains 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.158583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132130 restraints weight = 5833.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136261 restraints weight = 3070.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138834 restraints weight = 1902.873| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 3401 Z= 0.375 Angle : 0.641 9.039 4615 Z= 0.333 Chirality : 0.046 0.222 496 Planarity : 0.005 0.041 595 Dihedral : 5.571 37.963 488 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.64 % Allowed : 16.71 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.63 (0.39), residues: 415 helix: -3.02 (0.76), residues: 34 sheet: -0.68 (0.44), residues: 138 loop : -0.98 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 55 HIS 0.001 0.000 HIS C 519 PHE 0.012 0.002 PHE C 464 TYR 0.024 0.002 TYR B 111 ARG 0.003 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.8111 (p-80) REVERT: C 353 TRP cc_start: 0.8793 (p-90) cc_final: 0.8197 (p-90) REVERT: C 367 VAL cc_start: 0.8361 (t) cc_final: 0.8139 (p) REVERT: C 478 THR cc_start: 0.8165 (m) cc_final: 0.7895 (p) REVERT: C 503 VAL cc_start: 0.8452 (t) cc_final: 0.8118 (p) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.1094 time to fit residues: 11.6070 Evaluate side-chains 76 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.0980 chunk 32 optimal weight: 0.0050 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 5 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN C 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.161433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135235 restraints weight = 5850.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.139350 restraints weight = 3046.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.141900 restraints weight = 1881.143| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3401 Z= 0.158 Angle : 0.534 7.305 4615 Z= 0.270 Chirality : 0.042 0.222 496 Planarity : 0.004 0.039 595 Dihedral : 4.893 35.244 488 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.74 % Allowed : 19.45 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.47 (0.40), residues: 415 helix: -2.95 (0.74), residues: 34 sheet: -0.70 (0.43), residues: 140 loop : -0.77 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS A 60 PHE 0.009 0.001 PHE C 497 TYR 0.013 0.001 TYR C 380 ARG 0.002 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 353 TRP cc_start: 0.8800 (p-90) cc_final: 0.8196 (p-90) REVERT: C 394 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7874 (m-40) REVERT: C 478 THR cc_start: 0.8169 (m) cc_final: 0.7832 (p) REVERT: C 503 VAL cc_start: 0.8295 (t) cc_final: 0.7899 (p) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.1034 time to fit residues: 10.5609 Evaluate side-chains 76 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.159227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133097 restraints weight = 5879.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137387 restraints weight = 3048.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140064 restraints weight = 1872.680| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3401 Z= 0.318 Angle : 0.611 7.158 4615 Z= 0.315 Chirality : 0.044 0.235 496 Planarity : 0.004 0.043 595 Dihedral : 5.437 35.666 488 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.66 % Allowed : 17.26 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.59 (0.40), residues: 415 helix: -3.09 (0.71), residues: 34 sheet: -0.84 (0.43), residues: 142 loop : -0.80 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 436 HIS 0.001 0.000 HIS A 60 PHE 0.010 0.002 PHE A 54 TYR 0.023 0.002 TYR B 111 ARG 0.003 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 HIS cc_start: 0.8451 (OUTLIER) cc_final: 0.8219 (p-80) REVERT: C 353 TRP cc_start: 0.8806 (p-90) cc_final: 0.8183 (p-90) REVERT: C 478 THR cc_start: 0.8095 (m) cc_final: 0.7817 (p) REVERT: C 487 ASN cc_start: 0.8010 (m-40) cc_final: 0.7774 (m110) REVERT: C 503 VAL cc_start: 0.8271 (t) cc_final: 0.7891 (p) outliers start: 17 outliers final: 13 residues processed: 77 average time/residue: 0.1302 time to fit residues: 12.9164 Evaluate side-chains 76 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 62.5039 > 50: distance: 68 - 90: 23.653 distance: 86 - 90: 25.610 distance: 90 - 91: 11.318 distance: 91 - 92: 24.503 distance: 91 - 94: 18.366 distance: 92 - 93: 3.326 distance: 92 - 98: 36.049 distance: 94 - 95: 19.552 distance: 95 - 96: 23.660 distance: 95 - 97: 20.845 distance: 98 - 99: 4.912 distance: 99 - 100: 17.316 distance: 99 - 102: 7.600 distance: 100 - 101: 10.559 distance: 100 - 110: 11.845 distance: 102 - 103: 7.034 distance: 103 - 105: 12.634 distance: 104 - 106: 8.747 distance: 105 - 107: 11.026 distance: 106 - 108: 13.311 distance: 107 - 108: 7.615 distance: 108 - 109: 10.086 distance: 110 - 111: 15.844 distance: 111 - 112: 32.202 distance: 111 - 114: 25.065 distance: 112 - 113: 39.986 distance: 114 - 115: 7.527 distance: 115 - 116: 15.941 distance: 116 - 117: 22.141 distance: 117 - 118: 14.709 distance: 119 - 120: 4.219 distance: 120 - 121: 45.273 distance: 120 - 123: 45.800 distance: 121 - 122: 17.323 distance: 121 - 127: 15.200 distance: 123 - 124: 12.448 distance: 124 - 125: 25.989 distance: 124 - 126: 32.381 distance: 127 - 128: 8.623 distance: 127 - 133: 37.940 distance: 128 - 129: 21.522 distance: 128 - 131: 18.310 distance: 129 - 130: 12.343 distance: 129 - 134: 46.012 distance: 131 - 132: 11.673 distance: 132 - 133: 43.730 distance: 134 - 135: 26.638 distance: 135 - 136: 19.811 distance: 135 - 138: 11.450 distance: 136 - 137: 23.834 distance: 136 - 142: 24.133 distance: 138 - 139: 10.753 distance: 139 - 140: 3.387 distance: 139 - 141: 14.892 distance: 142 - 143: 14.043 distance: 143 - 144: 19.129 distance: 143 - 146: 9.227 distance: 144 - 145: 36.663 distance: 144 - 150: 7.541 distance: 146 - 147: 7.306 distance: 147 - 148: 17.643 distance: 147 - 149: 12.256 distance: 150 - 151: 24.601 distance: 151 - 152: 7.857 distance: 151 - 154: 26.608 distance: 152 - 153: 26.140 distance: 152 - 161: 31.167 distance: 154 - 155: 13.981 distance: 155 - 156: 5.893 distance: 156 - 158: 10.290 distance: 157 - 159: 5.164 distance: 158 - 160: 7.681 distance: 159 - 160: 8.826 distance: 161 - 162: 36.520 distance: 162 - 163: 20.195 distance: 162 - 165: 20.865 distance: 163 - 164: 8.327 distance: 163 - 168: 40.848 distance: 165 - 166: 18.699 distance: 165 - 167: 11.186 distance: 168 - 169: 30.328 distance: 169 - 170: 46.292 distance: 170 - 171: 11.533 distance: 170 - 172: 26.663