Starting phenix.real_space_refine on Wed Jan 17 14:37:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/01_2024/6i52_4410.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/01_2024/6i52_4410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/01_2024/6i52_4410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/01_2024/6i52_4410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/01_2024/6i52_4410.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/01_2024/6i52_4410.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.012 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 P 20 5.49 5 S 16 5.16 5 C 2377 2.51 5 N 635 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 91": "OD1" <-> "OD2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C ASP 465": "OD1" <-> "OD2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "C ARG 582": "NH1" <-> "NH2" Residue "C ARG 605": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3856 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 966 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1041 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1449 Classifications: {'peptide': 178} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 171} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 400 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 2.68, per 1000 atoms: 0.70 Number of scatterers: 3856 At special positions: 0 Unit cell: (82.68, 65.72, 107.06, 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) S 16 16.00 P 20 15.00 O 808 8.00 N 635 7.00 C 2377 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 - 3.50 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: 1.53 Conformation dependent library (CDL) restraints added in 704.7 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 22.9% alpha, 24.1% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 3.969A pdb=" N ILE A 13 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 14 " --> pdb=" O THR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.682A pdb=" N LYS A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.704A pdb=" N LEU B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 455 removed outlier: 3.590A pdb=" N GLN C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 450 through 455' Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.646A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 557 Processing helix chain 'C' and resid 561 through 571 Processing helix chain 'C' and resid 604 through 617 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 6.827A pdb=" N ARG A 78 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 89 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.877A pdb=" N ILE A 37 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.712A pdb=" N SER B 61 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.131A pdb=" N GLY B 73 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B 134 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 80 Processing sheet with id=AA6, first strand: chain 'C' and resid 468 through 476 removed outlier: 4.815A pdb=" N ILE C 473 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE C 526 " --> pdb=" O ILE C 473 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N GLN C 531 " --> pdb=" O ILE C 592 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N TYR C 594 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP C 533 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL C 596 " --> pdb=" O TRP C 533 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR C 535 " --> pdb=" O VAL C 596 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASN C 598 " --> pdb=" O THR C 535 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 591 " --> pdb=" O ASP C 584 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP C 584 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 580 " --> pdb=" O THR C 595 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG C 578 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C 599 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP C 576 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 482 through 484 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 497 108 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1129 1.34 - 1.45: 627 1.45 - 1.57: 2136 1.57 - 1.69: 39 1.69 - 1.81: 23 Bond restraints: 3954 Sorted by residual: bond pdb=" C THR B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.49e+00 bond pdb=" C ALA C 482 " pdb=" N TYR C 483 " ideal model delta sigma weight residual 1.331 1.356 -0.025 2.07e-02 2.33e+03 1.40e+00 bond pdb=" C3' DT D 11 " pdb=" O3' DT D 11 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" N ARG C 460 " pdb=" CA ARG C 460 " ideal model delta sigma weight residual 1.458 1.477 -0.019 1.90e-02 2.77e+03 1.04e+00 bond pdb=" N ALA B 177 " pdb=" CA ALA B 177 " ideal model delta sigma weight residual 1.468 1.457 0.012 1.24e-02 6.50e+03 8.68e-01 ... (remaining 3949 not shown) Histogram of bond angle deviations from ideal: 100.90 - 107.53: 206 107.53 - 114.15: 2239 114.15 - 120.78: 1583 120.78 - 127.41: 1373 127.41 - 134.03: 28 Bond angle restraints: 5429 Sorted by residual: angle pdb=" C GLY C 459 " pdb=" N ARG C 460 " pdb=" CA ARG C 460 " ideal model delta sigma weight residual 121.70 128.65 -6.95 1.80e+00 3.09e-01 1.49e+01 angle pdb=" C GLU C 462 " pdb=" N LYS C 463 " pdb=" CA LYS C 463 " ideal model delta sigma weight residual 123.05 117.73 5.32 1.40e+00 5.10e-01 1.45e+01 angle pdb=" C PHE C 466 " pdb=" N PHE C 467 " pdb=" CA PHE C 467 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.55e+00 angle pdb=" C ILE B 85 " pdb=" N PHE B 86 " pdb=" CA PHE B 86 " ideal model delta sigma weight residual 122.67 118.18 4.49 1.73e+00 3.34e-01 6.74e+00 angle pdb=" C ASP C 465 " pdb=" N PHE C 466 " pdb=" CA PHE C 466 " ideal model delta sigma weight residual 121.54 126.29 -4.75 1.91e+00 2.74e-01 6.18e+00 ... (remaining 5424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.30: 2228 29.30 - 58.61: 90 58.61 - 87.91: 15 87.91 - 117.21: 2 117.21 - 146.51: 3 Dihedral angle restraints: 2338 sinusoidal: 1070 harmonic: 1268 Sorted by residual: dihedral pdb=" CA GLU C 462 " pdb=" C GLU C 462 " pdb=" N LYS C 463 " pdb=" CA LYS C 463 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PHE C 466 " pdb=" C PHE C 466 " pdb=" N PHE C 467 " pdb=" CA PHE C 467 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DT D 11 " pdb=" C3' DT D 11 " pdb=" O3' DT D 11 " pdb=" P DT D 12 " ideal model delta sinusoidal sigma weight residual 220.00 73.49 146.51 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 2335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 396 0.027 - 0.054: 137 0.054 - 0.081: 40 0.081 - 0.109: 31 0.109 - 0.136: 14 Chirality restraints: 618 Sorted by residual: chirality pdb=" CA THR B 79 " pdb=" N THR B 79 " pdb=" C THR B 79 " pdb=" CB THR B 79 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE A 24 " pdb=" N ILE A 24 " pdb=" C ILE A 24 " pdb=" CB ILE A 24 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 615 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 79 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C THR B 79 " 0.043 2.00e-02 2.50e+03 pdb=" O THR B 79 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP B 80 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 30 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 31 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 118 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 119 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.019 5.00e-02 4.00e+02 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1101 2.82 - 3.34: 3351 3.34 - 3.86: 6120 3.86 - 4.38: 6724 4.38 - 4.90: 11453 Nonbonded interactions: 28749 Sorted by model distance: nonbonded pdb=" OD2 ASP A 9 " pdb=" OG1 THR A 11 " model vdw 2.303 2.440 nonbonded pdb=" ND1 HIS B 68 " pdb=" O GLY B 138 " model vdw 2.326 2.520 nonbonded pdb=" OD1 ASP C 500 " pdb=" N GLY C 501 " model vdw 2.330 2.520 nonbonded pdb=" OG SER C 474 " pdb=" O SER C 524 " model vdw 2.339 2.440 nonbonded pdb=" O VAL B 163 " pdb=" ND1 HIS B 166 " model vdw 2.361 2.520 ... (remaining 28744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.090 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: 0.590 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.990 Find NCS groups from input model: 0.120 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5551 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 : 0.002 0.050 3954 Z= 0.163 Angle : 0.571 6.949 5429 Z= 0.339 Chirality : 0.039 0.136 618 Planarity : 0.004 0.047 639 Dihedral : 16.564 146.514 1510 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.94 % Allowed : 11.56 % Favored : 87.50 % Rotamer: Outliers : 5.70 % Allowed : 9.84 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -4.07 (0.31), residues: 424 helix: -3.47 (0.33), residues: 95 sheet: -1.85 (0.49), residues: 77 loop : -2.75 (0.30), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 533 HIS 0.002 0.000 HIS B 166 PHE 0.016 0.001 PHE C 467 TYR 0.010 0.001 TYR B 151 ARG 0.001 0.000 ARG C 591 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.6038 (OUTLIER) cc_final: 0.5038 (mp10) REVERT: A 53 MET cc_start: 0.6572 (mtm) cc_final: 0.6343 (mpp) REVERT: A 75 PHE cc_start: 0.7684 (t80) cc_final: 0.7453 (t80) REVERT: B 160 PHE cc_start: 0.6461 (p90) cc_final: 0.6220 (p90) REVERT: B 167 HIS cc_start: 0.8149 (m-70) cc_final: 0.7539 (t-170) REVERT: C 478 VAL cc_start: 0.4301 (OUTLIER) cc_final: 0.3902 (t) REVERT: C 479 ASP cc_start: 0.8308 (m-30) cc_final: 0.7717 (p0) REVERT: C 531 GLN cc_start: 0.7691 (pt0) cc_final: 0.7128 (tm-30) outliers start: 22 outliers final: 6 residues processed: 129 average time/residue: 0.1855 time to fit residues: 28.4827 Evaluate side-chains 54 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 0.0070 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3954 Z= 0.261 Angle : 0.783 8.185 5429 Z= 0.425 Chirality : 0.047 0.189 618 Planarity : 0.006 0.050 639 Dihedral : 19.525 147.066 657 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.31 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -3.07 (0.34), residues: 424 helix: -1.18 (0.47), residues: 90 sheet: -1.26 (0.54), residues: 80 loop : -2.77 (0.30), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 101 HIS 0.004 0.002 HIS B 167 PHE 0.020 0.003 PHE A 75 TYR 0.016 0.003 TYR C 610 ARG 0.003 0.001 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.4050 (mmm) cc_final: 0.3797 (mmm) REVERT: B 135 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8579 (mmtt) REVERT: B 154 ILE cc_start: 0.7202 (pt) cc_final: 0.6848 (pt) REVERT: B 160 PHE cc_start: 0.7017 (p90) cc_final: 0.6763 (p90) REVERT: C 536 LEU cc_start: 0.9222 (mp) cc_final: 0.9017 (mp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1827 time to fit residues: 13.8979 Evaluate side-chains 39 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 62.8251 > 50: distance: 95 - 101: 18.435 distance: 101 - 102: 23.156 distance: 102 - 103: 28.190 distance: 102 - 105: 44.380 distance: 103 - 104: 46.459 distance: 103 - 110: 10.181 distance: 105 - 106: 30.654 distance: 106 - 107: 20.491 distance: 107 - 108: 22.838 distance: 107 - 109: 11.951 distance: 110 - 111: 35.347 distance: 111 - 112: 18.538 distance: 111 - 114: 26.507 distance: 112 - 113: 43.377 distance: 112 - 122: 5.534 distance: 114 - 115: 41.067 distance: 115 - 116: 28.047 distance: 115 - 117: 29.922 distance: 116 - 118: 23.497 distance: 117 - 119: 20.680 distance: 118 - 120: 15.006 distance: 119 - 120: 3.680 distance: 120 - 121: 12.279 distance: 122 - 123: 40.960 distance: 123 - 124: 8.871 distance: 123 - 126: 16.929 distance: 124 - 125: 30.799 distance: 124 - 127: 27.461 distance: 127 - 128: 29.385 distance: 128 - 129: 18.109 distance: 128 - 131: 16.958 distance: 129 - 130: 41.302 distance: 129 - 134: 39.391 distance: 131 - 132: 33.580 distance: 131 - 133: 27.182 distance: 134 - 135: 22.569 distance: 135 - 136: 18.283 distance: 135 - 138: 10.275 distance: 136 - 137: 16.009 distance: 136 - 142: 26.145 distance: 138 - 139: 15.022 distance: 138 - 140: 26.285 distance: 139 - 141: 23.311 distance: 142 - 143: 26.464 distance: 143 - 144: 10.138 distance: 143 - 146: 18.843 distance: 144 - 145: 21.831 distance: 144 - 151: 23.246 distance: 146 - 147: 34.661 distance: 147 - 148: 18.077 distance: 148 - 149: 20.368 distance: 149 - 150: 22.879 distance: 151 - 152: 33.579 distance: 151 - 157: 14.539 distance: 152 - 153: 15.174 distance: 152 - 155: 26.234 distance: 153 - 154: 21.800 distance: 153 - 158: 19.846 distance: 155 - 156: 18.041 distance: 156 - 157: 29.424 distance: 158 - 159: 26.050 distance: 159 - 160: 33.782 distance: 159 - 162: 29.033 distance: 160 - 161: 25.326 distance: 160 - 166: 34.304 distance: 162 - 163: 22.030 distance: 162 - 164: 24.108 distance: 163 - 165: 49.285 distance: 167 - 168: 13.519 distance: 167 - 170: 25.982 distance: 168 - 169: 14.805 distance: 168 - 174: 26.470 distance: 170 - 171: 25.561 distance: 171 - 172: 25.626 distance: 171 - 173: 35.545 distance: 174 - 175: 32.511 distance: 175 - 176: 14.223 distance: 175 - 178: 35.789 distance: 176 - 177: 21.504 distance: 176 - 180: 19.878 distance: 178 - 179: 14.062