Starting phenix.real_space_refine on Fri Aug 2 13:04:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/08_2024/8x64_38079.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/08_2024/8x64_38079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/08_2024/8x64_38079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/08_2024/8x64_38079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/08_2024/8x64_38079.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/08_2024/8x64_38079.cif" } resolution = 3.4 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= -0.001 sd= 0.056 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 1 4.86 5 C 1472 2.51 5 N 351 2.21 5 O 345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2189 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2167 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 3 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y5R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.37, per 1000 atoms: 1.08 Number of scatterers: 2189 At special positions: 0 Unit cell: (54.06, 73.14, 71.02, 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 1 17.00 S 20 16.00 O 345 8.00 N 351 7.00 C 1472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 360.5 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 81.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 27 through 53 removed outlier: 3.669A pdb=" N CYS B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 removed outlier: 3.909A pdb=" N ILE B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 69 " --> pdb=" O TYR B 65 " (cutoff:3.500A) Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 96 through 130 removed outlier: 3.825A pdb=" N CYS B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 165 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 187 through 220 removed outlier: 3.509A pdb=" N LYS B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 439 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 447 through 472 removed outlier: 3.644A pdb=" N MET B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix Processing helix chain 'B' and resid 475 through 480 151 hydrogen bonds defined for protein. 453 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: 0.55 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 305 1.30 - 1.43: 644 1.43 - 1.56: 1268 1.56 - 1.68: 2 1.68 - 1.81: 32 Bond restraints: 2251 Sorted by residual: bond pdb=" C PHE B 424 " pdb=" N ILE B 425 " ideal model delta sigma weight residual 1.332 1.257 0.075 1.36e-02 5.41e+03 3.04e+01 bond pdb=" C PHE B 424 " pdb=" O PHE B 424 " ideal model delta sigma weight residual 1.235 1.172 0.064 1.26e-02 6.30e+03 2.55e+01 bond pdb=" CA PHE B 424 " pdb=" CB PHE B 424 " ideal model delta sigma weight residual 1.530 1.447 0.084 1.69e-02 3.50e+03 2.44e+01 bond pdb=" CA PHE B 424 " pdb=" C PHE B 424 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.34e-02 5.57e+03 2.32e+01 bond pdb=" N PHE B 424 " pdb=" CA PHE B 424 " ideal model delta sigma weight residual 1.457 1.396 0.061 1.29e-02 6.01e+03 2.27e+01 ... (remaining 2246 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.27: 59 106.27 - 113.20: 1220 113.20 - 120.13: 839 120.13 - 127.07: 906 127.07 - 134.00: 30 Bond angle restraints: 3054 Sorted by residual: angle pdb=" CA ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 117.30 124.60 -7.30 1.16e+00 7.43e-01 3.96e+01 angle pdb=" O ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 122.12 116.20 5.92 1.06e+00 8.90e-01 3.12e+01 angle pdb=" N PHE B 424 " pdb=" CA PHE B 424 " pdb=" C PHE B 424 " ideal model delta sigma weight residual 110.80 102.52 8.28 2.13e+00 2.20e-01 1.51e+01 angle pdb=" CA ILE B 115 " pdb=" C ILE B 115 " pdb=" N PHE B 116 " ideal model delta sigma weight residual 116.60 121.79 -5.19 1.45e+00 4.76e-01 1.28e+01 angle pdb=" N ALA B 423 " pdb=" CA ALA B 423 " pdb=" C ALA B 423 " ideal model delta sigma weight residual 111.28 114.76 -3.48 1.09e+00 8.42e-01 1.02e+01 ... (remaining 3049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.25: 1116 14.25 - 28.50: 145 28.50 - 42.74: 52 42.74 - 56.99: 7 56.99 - 71.24: 1 Dihedral angle restraints: 1321 sinusoidal: 538 harmonic: 783 Sorted by residual: dihedral pdb=" CB CYS B 441 " pdb=" SG CYS B 441 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual -86.00 -142.50 56.50 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" C ILE B 115 " pdb=" N ILE B 115 " pdb=" CA ILE B 115 " pdb=" CB ILE B 115 " ideal model delta harmonic sigma weight residual -122.00 -134.73 12.73 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CA ILE B 115 " pdb=" CB ILE B 115 " ideal model delta harmonic sigma weight residual 123.40 135.77 -12.37 0 2.50e+00 1.60e-01 2.45e+01 ... (remaining 1318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 328 0.085 - 0.169: 20 0.169 - 0.254: 0 0.254 - 0.339: 0 0.339 - 0.423: 1 Chirality restraints: 349 Sorted by residual: chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA MET B 81 " pdb=" N MET B 81 " pdb=" C MET B 81 " pdb=" CB MET B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CB ILE B 115 " pdb=" CA ILE B 115 " pdb=" CG1 ILE B 115 " pdb=" CG2 ILE B 115 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 346 not shown) Planarity restraints: 358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 424 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C PHE B 424 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE B 424 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE B 425 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C SER B 114 " 0.052 2.00e-02 2.50e+03 pdb=" O SER B 114 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 115 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 78 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C ALA B 78 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA B 78 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 79 " -0.015 2.00e-02 2.50e+03 ... (remaining 355 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 609 2.81 - 3.33: 2228 3.33 - 3.86: 3460 3.86 - 4.38: 3778 4.38 - 4.90: 6258 Nonbonded interactions: 16333 Sorted by model distance: nonbonded pdb=" OG1 THR B 41 " pdb=" OG1 THR B 462 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP B 73 " pdb=" OG SER B 461 " model vdw 2.296 3.040 nonbonded pdb=" O PHE B 424 " pdb=" C ILE B 425 " model vdw 2.317 3.270 nonbonded pdb=" O ALA B 423 " pdb=" ND2 ASN B 460 " model vdw 2.380 3.120 nonbonded pdb=" OH TYR B 214 " pdb=" NZ LYS B 218 " model vdw 2.384 3.120 ... (remaining 16328 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=0.00 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.890 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 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 : 0.006 0.084 2251 Z= 0.385 Angle : 0.789 8.277 3054 Z= 0.428 Chirality : 0.048 0.423 349 Planarity : 0.007 0.047 358 Dihedral : 14.113 71.238 805 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.42 % Allowed : 0.00 % Favored : 99.58 % Cbeta Deviations : 0.39 % 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: -0.76 (0.53), residues: 255 helix: 0.47 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -3.69 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 455 HIS 0.003 0.001 HIS B 450 PHE 0.010 0.001 PHE B 435 TYR 0.018 0.001 TYR B 200 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.237 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1397 time to fit residues: 7.1954 Evaluate side-chains 36 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.0010 chunk 23 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2251 Z= 0.225 Angle : 0.659 7.450 3054 Z= 0.334 Chirality : 0.041 0.125 349 Planarity : 0.005 0.041 358 Dihedral : 5.577 50.887 299 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.67 % Allowed : 14.23 % Favored : 84.10 % 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: -0.10 (0.53), residues: 255 helix: 0.95 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -3.52 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 455 HIS 0.001 0.001 HIS B 167 PHE 0.012 0.001 PHE B 435 TYR 0.010 0.001 TYR B 126 ARG 0.001 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.225 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1383 time to fit residues: 6.3387 Evaluate side-chains 34 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2251 Z= 0.184 Angle : 0.600 7.278 3054 Z= 0.304 Chirality : 0.039 0.117 349 Planarity : 0.005 0.042 358 Dihedral : 5.332 48.761 299 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.77 % Allowed : 14.64 % Favored : 81.59 % 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: 0.36 (0.54), residues: 255 helix: 1.32 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -3.46 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 455 HIS 0.001 0.000 HIS B 450 PHE 0.010 0.001 PHE B 435 TYR 0.009 0.001 TYR B 200 ARG 0.001 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.233 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 41 average time/residue: 0.1239 time to fit residues: 6.1754 Evaluate side-chains 39 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 438 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.6138 > 50: distance: 62 - 69: 21.097 distance: 69 - 70: 49.972 distance: 70 - 71: 6.529 distance: 70 - 73: 33.238 distance: 73 - 74: 12.119 distance: 74 - 75: 27.580 distance: 74 - 76: 11.368 distance: 75 - 77: 22.804 distance: 77 - 78: 45.029 distance: 79 - 80: 14.056 distance: 80 - 81: 24.923 distance: 80 - 83: 16.457 distance: 81 - 82: 6.211 distance: 81 - 87: 14.005 distance: 83 - 84: 42.318 distance: 84 - 85: 19.710 distance: 84 - 86: 39.891 distance: 87 - 88: 19.507 distance: 88 - 89: 33.877 distance: 88 - 91: 20.728 distance: 89 - 90: 11.925 distance: 89 - 97: 28.059 distance: 90 - 123: 53.899 distance: 91 - 92: 8.996 distance: 92 - 93: 10.934 distance: 92 - 94: 22.048 distance: 93 - 95: 9.955 distance: 94 - 96: 32.819 distance: 95 - 96: 10.525 distance: 97 - 98: 15.514 distance: 98 - 99: 14.602 distance: 98 - 101: 26.223 distance: 99 - 100: 13.011 distance: 99 - 105: 14.502 distance: 100 - 131: 26.014 distance: 101 - 102: 41.787 distance: 102 - 103: 43.744 distance: 103 - 104: 44.988 distance: 105 - 106: 11.667 distance: 106 - 107: 17.138 distance: 106 - 109: 26.611 distance: 107 - 108: 40.101 distance: 107 - 116: 10.772 distance: 109 - 110: 30.486 distance: 110 - 111: 11.632 distance: 110 - 112: 30.393 distance: 111 - 113: 57.078 distance: 113 - 115: 45.067 distance: 114 - 115: 24.452 distance: 116 - 117: 27.182 distance: 117 - 118: 21.059 distance: 117 - 120: 10.692 distance: 118 - 119: 24.089 distance: 118 - 123: 11.759 distance: 119 - 153: 38.777 distance: 120 - 121: 22.569 distance: 120 - 122: 17.439 distance: 123 - 124: 9.281 distance: 124 - 127: 33.958 distance: 125 - 126: 16.489 distance: 125 - 131: 33.283 distance: 126 - 157: 17.559 distance: 127 - 128: 12.020 distance: 127 - 129: 39.257 distance: 128 - 130: 28.423 distance: 131 - 132: 19.310 distance: 132 - 133: 14.654 distance: 132 - 135: 16.165 distance: 133 - 134: 13.658 distance: 133 - 145: 27.242 distance: 134 - 169: 21.626 distance: 135 - 136: 16.193 distance: 136 - 137: 14.290 distance: 136 - 138: 16.591 distance: 137 - 139: 7.331 distance: 138 - 140: 13.163 distance: 138 - 141: 28.322 distance: 139 - 140: 17.090 distance: 140 - 142: 13.872 distance: 141 - 143: 28.321 distance: 142 - 144: 21.516 distance: 143 - 144: 15.340 distance: 145 - 146: 12.204 distance: 146 - 147: 34.864 distance: 146 - 149: 12.822 distance: 147 - 148: 16.543 distance: 147 - 153: 22.677 distance: 148 - 177: 24.552 distance: 149 - 150: 35.460 distance: 150 - 151: 47.200 distance: 150 - 152: 48.455 distance: 153 - 154: 46.952 distance: 154 - 155: 41.665 distance: 155 - 156: 7.402 distance: 155 - 157: 28.645 distance: 156 - 184: 29.780