Starting phenix.real_space_refine on Tue Jan 14 01:13:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8poc_17788/01_2025/8poc_17788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8poc_17788/01_2025/8poc_17788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8poc_17788/01_2025/8poc_17788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8poc_17788/01_2025/8poc_17788.map" model { file = "/net/cci-nas-00/data/ceres_data/8poc_17788/01_2025/8poc_17788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8poc_17788/01_2025/8poc_17788.cif" } resolution = 4.0 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= 0.000 sd= 0.027 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 28 5.16 5 C 3108 2.51 5 N 880 2.21 5 O 908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4924 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "B" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "C" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "D" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Time building chain proxies: 3.58, per 1000 atoms: 0.73 Number of scatterers: 4924 At special positions: 0 Unit cell: (86.49, 76.26, 77.19, 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 28 16.00 O 908 8.00 N 880 7.00 C 3108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.26 Conformation dependent library (CDL) restraints added in 559.0 milliseconds 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 60.1% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 20 through 37 Processing helix chain 'A' and resid 38 through 56 removed outlier: 3.539A pdb=" N ARG A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.100A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 131 removed outlier: 3.896A pdb=" N GLY A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 20 through 37 Processing helix chain 'B' and resid 38 through 56 removed outlier: 3.574A pdb=" N ARG B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 79 removed outlier: 4.039A pdb=" N LEU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 130 Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 20 through 37 Processing helix chain 'C' and resid 38 through 56 removed outlier: 3.596A pdb=" N ARG C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 removed outlier: 4.027A pdb=" N LEU C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 130 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 20 through 37 Processing helix chain 'D' and resid 38 through 56 removed outlier: 3.548A pdb=" N ARG D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 79 removed outlier: 4.039A pdb=" N LEU D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 131 removed outlier: 3.905A pdb=" N GLY D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 82 through 87 Processing sheet with id=AA3, first strand: chain 'C' and resid 82 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 82 through 87 336 hydrogen bonds defined for protein. 966 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: 1.31 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: 1.23 - 1.34: 1680 1.34 - 1.46: 1134 1.46 - 1.58: 2174 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 5036 Sorted by residual: bond pdb=" CG1 ILE A 94 " pdb=" CD1 ILE A 94 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.20e+00 bond pdb=" CB GLN B 14 " pdb=" CG GLN B 14 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CG1 ILE D 94 " pdb=" CD1 ILE D 94 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.13e+00 bond pdb=" CB GLN C 14 " pdb=" CG GLN C 14 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CG LEU A 85 " pdb=" CD2 LEU A 85 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.51e-01 ... (remaining 5031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6663 1.71 - 3.41: 129 3.41 - 5.12: 27 5.12 - 6.83: 10 6.83 - 8.53: 3 Bond angle restraints: 6832 Sorted by residual: angle pdb=" C GLN D 16 " pdb=" N LEU D 17 " pdb=" CA LEU D 17 " ideal model delta sigma weight residual 122.31 113.78 8.53 2.34e+00 1.83e-01 1.33e+01 angle pdb=" C GLN C 16 " pdb=" N LEU C 17 " pdb=" CA LEU C 17 " ideal model delta sigma weight residual 122.31 114.00 8.31 2.34e+00 1.83e-01 1.26e+01 angle pdb=" C GLN B 16 " pdb=" N LEU B 17 " pdb=" CA LEU B 17 " ideal model delta sigma weight residual 122.31 114.55 7.76 2.34e+00 1.83e-01 1.10e+01 angle pdb=" CA GLN C 14 " pdb=" CB GLN C 14 " pdb=" CG GLN C 14 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.32e+00 angle pdb=" CA GLN B 14 " pdb=" CB GLN B 14 " pdb=" CG GLN B 14 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.30e+00 ... (remaining 6827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2649 17.13 - 34.26: 276 34.26 - 51.39: 35 51.39 - 68.52: 6 68.52 - 85.65: 18 Dihedral angle restraints: 2984 sinusoidal: 1208 harmonic: 1776 Sorted by residual: dihedral pdb=" CA ASN B 35 " pdb=" C ASN B 35 " pdb=" N ALA B 36 " pdb=" CA ALA B 36 " ideal model delta harmonic sigma weight residual 180.00 -164.77 -15.23 0 5.00e+00 4.00e-02 9.27e+00 dihedral pdb=" CA ARG A 13 " pdb=" CB ARG A 13 " pdb=" CG ARG A 13 " pdb=" CD ARG A 13 " ideal model delta sinusoidal sigma weight residual -60.00 -113.88 53.88 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" CA ARG B 13 " pdb=" CB ARG B 13 " pdb=" CG ARG B 13 " pdb=" CD ARG B 13 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 2981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 569 0.038 - 0.075: 151 0.075 - 0.113: 4 0.113 - 0.150: 0 0.150 - 0.188: 4 Chirality restraints: 728 Sorted by residual: chirality pdb=" CA ILE A 94 " pdb=" N ILE A 94 " pdb=" C ILE A 94 " pdb=" CB ILE A 94 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA ILE D 94 " pdb=" N ILE D 94 " pdb=" C ILE D 94 " pdb=" CB ILE D 94 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA ILE C 94 " pdb=" N ILE C 94 " pdb=" C ILE C 94 " pdb=" CB ILE C 94 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 725 not shown) Planarity restraints: 896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 99 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO C 100 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 100 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 100 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 11 " 0.008 2.00e-02 2.50e+03 1.03e-02 2.11e+00 pdb=" CG TYR B 11 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 11 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 11 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 11 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 11 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 11 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 11 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 99 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO B 100 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " 0.020 5.00e-02 4.00e+02 ... (remaining 893 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1472 2.84 - 3.35: 4800 3.35 - 3.87: 7565 3.87 - 4.38: 7525 4.38 - 4.90: 14384 Nonbonded interactions: 35746 Sorted by model distance: nonbonded pdb=" O GLU D 68 " pdb=" ND2 ASN D 72 " model vdw 2.324 3.120 nonbonded pdb=" N GLU A 89 " pdb=" OE1 GLU A 89 " model vdw 2.340 3.120 nonbonded pdb=" N GLU C 89 " pdb=" OE1 GLU C 89 " model vdw 2.343 3.120 nonbonded pdb=" O GLU B 68 " pdb=" ND2 ASN B 72 " model vdw 2.346 3.120 nonbonded pdb=" NH2 ARG C 112 " pdb=" OE1 GLU C 142 " model vdw 2.382 3.120 ... (remaining 35741 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.350 Find NCS groups from input model: 0.160 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 0.043 5036 Z= 0.221 Angle : 0.667 8.532 6832 Z= 0.349 Chirality : 0.034 0.188 728 Planarity : 0.004 0.037 896 Dihedral : 14.858 85.653 1848 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 2.14 (0.33), residues: 608 helix: 2.97 (0.27), residues: 344 sheet: 0.47 (0.44), residues: 96 loop : -1.49 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 126 HIS 0.006 0.002 HIS A 96 PHE 0.007 0.001 PHE D 44 TYR 0.025 0.001 TYR B 11 ARG 0.009 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.519 Fit side-chains REVERT: C 93 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8035 (mt-10) REVERT: D 1 MET cc_start: 0.7142 (mpp) cc_final: 0.6579 (mpp) REVERT: D 89 GLU cc_start: 0.8233 (pm20) cc_final: 0.7990 (pm20) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1594 time to fit residues: 27.3547 Evaluate side-chains 108 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS B 104 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.157915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114054 restraints weight = 6710.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.116002 restraints weight = 5703.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.117602 restraints weight = 5141.115| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5036 Z= 0.272 Angle : 0.588 5.074 6832 Z= 0.298 Chirality : 0.035 0.181 728 Planarity : 0.004 0.034 896 Dihedral : 3.466 15.374 692 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.46 % Allowed : 11.15 % Favored : 85.38 % 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 (0.34), residues: 608 helix: 2.93 (0.27), residues: 356 sheet: 0.75 (0.48), residues: 96 loop : -1.59 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 126 HIS 0.003 0.001 HIS B 96 PHE 0.009 0.002 PHE B 25 TYR 0.006 0.001 TYR B 95 ARG 0.003 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.599 Fit side-chains REVERT: A 93 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8134 (mt-10) REVERT: B 1 MET cc_start: 0.7281 (mmm) cc_final: 0.7072 (mpp) REVERT: B 68 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8166 (pt0) REVERT: B 93 GLU cc_start: 0.8481 (tt0) cc_final: 0.7918 (mt-10) REVERT: C 93 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8039 (mt-10) outliers start: 18 outliers final: 11 residues processed: 135 average time/residue: 0.1773 time to fit residues: 30.1228 Evaluate side-chains 134 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 52.1667 > 50: distance: 23 - 39: 4.080 distance: 27 - 43: 4.067 distance: 33 - 52: 7.343 distance: 37 - 39: 3.211 distance: 38 - 60: 5.507 distance: 40 - 41: 6.384 distance: 41 - 42: 5.597 distance: 41 - 43: 6.039 distance: 42 - 65: 10.951 distance: 43 - 44: 3.656 distance: 44 - 45: 4.440 distance: 44 - 47: 7.112 distance: 45 - 46: 7.596 distance: 45 - 52: 3.424 distance: 47 - 48: 9.916 distance: 48 - 49: 4.224 distance: 49 - 50: 3.407 distance: 49 - 51: 6.205 distance: 52 - 53: 7.222 distance: 53 - 54: 5.241 distance: 53 - 56: 9.963 distance: 54 - 55: 13.315 distance: 56 - 57: 6.215 distance: 57 - 58: 12.444 distance: 57 - 59: 6.910 distance: 60 - 61: 6.840 distance: 61 - 62: 8.988 distance: 61 - 64: 12.884 distance: 62 - 63: 16.500 distance: 62 - 65: 3.902 distance: 65 - 66: 9.583 distance: 66 - 67: 3.653 distance: 66 - 69: 6.409 distance: 67 - 68: 5.563 distance: 67 - 74: 7.853 distance: 69 - 70: 10.418 distance: 70 - 71: 6.244 distance: 71 - 72: 6.644 distance: 74 - 75: 3.804 distance: 75 - 76: 12.208 distance: 75 - 78: 6.348 distance: 76 - 77: 13.856 distance: 76 - 85: 8.752 distance: 78 - 79: 7.699 distance: 79 - 80: 7.896 distance: 80 - 81: 5.596 distance: 82 - 83: 3.674 distance: 86 - 87: 12.881 distance: 86 - 89: 11.013 distance: 87 - 88: 15.059 distance: 87 - 97: 5.955 distance: 90 - 91: 7.270 distance: 90 - 92: 3.633 distance: 91 - 93: 6.124 distance: 92 - 94: 6.078 distance: 93 - 95: 3.905 distance: 94 - 95: 5.839 distance: 95 - 96: 3.621 distance: 97 - 98: 3.928 distance: 97 - 103: 9.872 distance: 98 - 99: 13.218 distance: 98 - 101: 6.283 distance: 99 - 100: 15.922 distance: 99 - 104: 13.359 distance: 102 - 103: 3.207 distance: 104 - 105: 11.645 distance: 105 - 106: 8.286 distance: 105 - 108: 5.372 distance: 106 - 107: 6.097 distance: 106 - 112: 11.475 distance: 108 - 109: 25.221 distance: 109 - 110: 12.820 distance: 109 - 111: 43.813 distance: 112 - 113: 13.407 distance: 112 - 118: 21.227 distance: 113 - 114: 14.851 distance: 113 - 116: 23.179 distance: 114 - 115: 15.126 distance: 114 - 119: 8.442 distance: 116 - 117: 13.094 distance: 117 - 118: 21.297 distance: 148 - 160: 3.009