Starting phenix.real_space_refine on Mon Dec 11 17:20:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/12_2023/6qoz_4610.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/12_2023/6qoz_4610.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/6qoz_4610/12_2023/6qoz_4610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/12_2023/6qoz_4610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/12_2023/6qoz_4610.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/12_2023/6qoz_4610.pdb" } 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= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 655 atoms to isotropic. 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 125 5.16 5 C 11466 2.51 5 N 3011 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17987 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "B" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "D" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "E" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "G" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "H" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "I" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "C" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 655 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Time building chain proxies: 11.79, per 1000 atoms: 0.66 Number of scatterers: 17987 At special positions: 0 Unit cell: (141.4, 152.6, 175, 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 125 16.00 O 3385 8.00 N 3011 7.00 C 11466 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: 6.54 Conformation dependent library (CDL) restraints added in 3.4 seconds 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4288 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 13.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.512A pdb=" N ASN B 52 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 103 through 109 removed outlier: 4.584A pdb=" N SER B 109 " --> pdb=" O TYR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 230 through 237 removed outlier: 3.500A pdb=" N SER B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'E' and resid 4 through 8 Processing helix chain 'E' and resid 48 through 52 removed outlier: 3.512A pdb=" N ASN E 52 " --> pdb=" O ASP E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 103 through 109 removed outlier: 4.586A pdb=" N SER E 109 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'G' and resid 4 through 8 Processing helix chain 'G' and resid 48 through 52 removed outlier: 3.512A pdb=" N ASN G 52 " --> pdb=" O ASP G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 65 Processing helix chain 'G' and resid 103 through 109 removed outlier: 4.586A pdb=" N SER G 109 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 144 Processing helix chain 'G' and resid 230 through 237 removed outlier: 3.500A pdb=" N SER G 237 " --> pdb=" O ASN G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 300 through 304 Processing helix chain 'H' and resid 54 through 62 Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 137 through 141 Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 48 through 52 removed outlier: 3.513A pdb=" N ASN I 52 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 65 Processing helix chain 'I' and resid 103 through 109 removed outlier: 4.585A pdb=" N SER I 109 " --> pdb=" O TYR I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 144 Processing helix chain 'I' and resid 230 through 237 Processing helix chain 'I' and resid 277 through 281 Processing helix chain 'I' and resid 300 through 304 Processing helix chain 'C' and resid 33 through 53 135 hydrogen bonds defined for protein. 273 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: 3.56 Time building geometry restraints manager: 7.06 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: 4973 1.33 - 1.46: 4187 1.46 - 1.58: 9102 1.58 - 1.70: 0 1.70 - 1.83: 194 Bond restraints: 18456 Sorted by residual: bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.531 -0.080 1.60e-02 3.91e+03 2.53e+01 bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.530 -0.079 1.60e-02 3.91e+03 2.46e+01 bond pdb=" N GLY D 1 " pdb=" CA GLY D 1 " ideal model delta sigma weight residual 1.451 1.530 -0.079 1.60e-02 3.91e+03 2.46e+01 bond pdb=" N GLY F 1 " pdb=" CA GLY F 1 " ideal model delta sigma weight residual 1.451 1.530 -0.079 1.60e-02 3.91e+03 2.46e+01 bond pdb=" CA PRO D 187 " pdb=" C PRO D 187 " ideal model delta sigma weight residual 1.517 1.545 -0.028 6.70e-03 2.23e+04 1.81e+01 ... (remaining 18451 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.13: 432 104.13 - 111.60: 7425 111.60 - 119.07: 7259 119.07 - 126.55: 9676 126.55 - 134.02: 349 Bond angle restraints: 25141 Sorted by residual: angle pdb=" N ARG I 367 " pdb=" CA ARG I 367 " pdb=" C ARG I 367 " ideal model delta sigma weight residual 110.55 118.98 -8.43 1.35e+00 5.49e-01 3.90e+01 angle pdb=" N ARG E 367 " pdb=" CA ARG E 367 " pdb=" C ARG E 367 " ideal model delta sigma weight residual 110.55 118.98 -8.43 1.35e+00 5.49e-01 3.90e+01 angle pdb=" N ARG G 367 " pdb=" CA ARG G 367 " pdb=" C ARG G 367 " ideal model delta sigma weight residual 110.55 118.94 -8.39 1.35e+00 5.49e-01 3.87e+01 angle pdb=" N ARG B 367 " pdb=" CA ARG B 367 " pdb=" C ARG B 367 " ideal model delta sigma weight residual 110.55 118.93 -8.38 1.35e+00 5.49e-01 3.85e+01 angle pdb=" N GLY C 71 " pdb=" CA GLY C 71 " pdb=" C GLY C 71 " ideal model delta sigma weight residual 112.52 104.58 7.94 1.37e+00 5.33e-01 3.36e+01 ... (remaining 25136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 9750 17.68 - 35.36: 846 35.36 - 53.04: 186 53.04 - 70.72: 69 70.72 - 88.40: 20 Dihedral angle restraints: 10871 sinusoidal: 4222 harmonic: 6649 Sorted by residual: dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N ASP D 9 " pdb=" CA ASP D 9 " ideal model delta harmonic sigma weight residual 180.00 -153.20 -26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA SER A 8 " pdb=" C SER A 8 " pdb=" N ASP A 9 " pdb=" CA ASP A 9 " ideal model delta harmonic sigma weight residual 180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA SER H 8 " pdb=" C SER H 8 " pdb=" N ASP H 9 " pdb=" CA ASP H 9 " ideal model delta harmonic sigma weight residual -180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 10868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2338 0.121 - 0.242: 424 0.242 - 0.362: 22 0.362 - 0.483: 4 0.483 - 0.604: 4 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CA ASN B 174 " pdb=" N ASN B 174 " pdb=" C ASN B 174 " pdb=" CB ASN B 174 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" CA ASN I 174 " pdb=" N ASN I 174 " pdb=" C ASN I 174 " pdb=" CB ASN I 174 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.11e+00 chirality pdb=" CA ASN G 174 " pdb=" N ASN G 174 " pdb=" C ASN G 174 " pdb=" CB ASN G 174 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.06e+00 ... (remaining 2789 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 255 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO G 256 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 256 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 256 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 255 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO I 256 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO I 256 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 256 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 255 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO E 256 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 256 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 256 " 0.029 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 23 1.97 - 2.71: 591 2.71 - 3.44: 24257 3.44 - 4.17: 46687 4.17 - 4.90: 80930 Nonbonded interactions: 152488 Sorted by model distance: nonbonded pdb=" CA GLY B 53 " pdb=" CD2 LEU C 35 " model vdw 1.243 3.860 nonbonded pdb=" O GLY B 53 " pdb=" CD1 LEU C 35 " model vdw 1.334 3.460 nonbonded pdb=" O GLY G 53 " pdb=" CD GLU C 32 " model vdw 1.352 3.270 nonbonded pdb=" OD2 ASP G 49 " pdb=" CG1 VAL C 68 " model vdw 1.422 3.460 nonbonded pdb=" N GLN G 54 " pdb=" N GLU C 32 " model vdw 1.450 3.200 ... (remaining 152483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 15.760 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 48.160 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 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 : 0.011 0.080 18456 Z= 0.746 Angle : 1.458 10.725 25141 Z= 0.897 Chirality : 0.092 0.604 2792 Planarity : 0.006 0.055 3245 Dihedral : 15.400 88.397 6583 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.92 % Allowed : 6.03 % Favored : 93.05 % Rotamer: Outliers : 5.13 % Allowed : 10.01 % Favored : 84.87 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -3.28 (0.15), residues: 2289 helix: -2.98 (0.27), residues: 224 sheet: -2.11 (0.16), residues: 829 loop : -2.02 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP F 144 HIS 0.004 0.002 HIS B 331 PHE 0.028 0.005 PHE E 62 TYR 0.024 0.005 TYR E 105 ARG 0.017 0.002 ARG I 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 526 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 7 residues processed: 591 average time/residue: 0.3328 time to fit residues: 285.1449 Evaluate side-chains 282 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 275 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2073 time to fit residues: 5.3380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 71 HIS A 112 GLN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN E 27 GLN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 GLN F 48 ASN F 112 GLN F 128 ASN F 158 GLN G 27 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN G 130 ASN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 48 ASN H 158 GLN I 27 GLN I 233 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18456 Z= 0.217 Angle : 0.654 7.415 25141 Z= 0.338 Chirality : 0.046 0.181 2792 Planarity : 0.005 0.048 3245 Dihedral : 5.648 21.648 2459 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.84 % Favored : 96.94 % Rotamer: Outliers : 3.92 % Allowed : 17.50 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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 (0.16), residues: 2289 helix: -1.89 (0.31), residues: 232 sheet: -1.41 (0.18), residues: 760 loop : -1.43 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 47 HIS 0.003 0.001 HIS A 71 PHE 0.014 0.002 PHE G 56 TYR 0.028 0.002 TYR C 75 ARG 0.010 0.001 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 313 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 32 residues processed: 370 average time/residue: 0.2745 time to fit residues: 161.3687 Evaluate side-chains 266 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 234 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1583 time to fit residues: 12.4813 ------------------------------------------------------------------------------- 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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 64.1378 > 50: distance: 30 - 35: 22.610 distance: 35 - 36: 21.463 distance: 36 - 37: 12.113 distance: 36 - 39: 30.234 distance: 37 - 38: 4.928 distance: 37 - 42: 31.004 distance: 39 - 40: 24.414 distance: 39 - 41: 26.113 distance: 42 - 43: 32.926 distance: 43 - 46: 15.934 distance: 44 - 45: 38.848 distance: 44 - 54: 42.222 distance: 46 - 47: 24.793 distance: 47 - 48: 13.826 distance: 47 - 49: 8.458 distance: 48 - 50: 15.612 distance: 49 - 51: 6.489 distance: 50 - 52: 15.909 distance: 51 - 52: 13.385 distance: 52 - 53: 24.705 distance: 54 - 55: 15.190 distance: 55 - 56: 23.246 distance: 55 - 58: 32.045 distance: 56 - 57: 25.709 distance: 56 - 60: 31.613 distance: 58 - 59: 16.861 distance: 60 - 61: 23.459 distance: 60 - 66: 21.081 distance: 61 - 62: 27.582 distance: 61 - 64: 30.210 distance: 62 - 63: 18.003 distance: 62 - 67: 24.501 distance: 64 - 65: 36.018 distance: 65 - 66: 36.769 distance: 67 - 68: 7.597 distance: 68 - 69: 15.265 distance: 68 - 71: 6.274 distance: 69 - 70: 34.989 distance: 69 - 73: 11.205 distance: 71 - 72: 9.434 distance: 73 - 74: 16.012 distance: 74 - 75: 5.855 distance: 74 - 77: 37.247 distance: 75 - 76: 7.870 distance: 75 - 81: 56.732 distance: 77 - 78: 56.020 distance: 78 - 79: 11.221 distance: 79 - 80: 21.765 distance: 81 - 82: 25.541 distance: 82 - 83: 13.116 distance: 82 - 85: 15.384 distance: 83 - 84: 12.538 distance: 83 - 89: 12.979 distance: 85 - 86: 18.240 distance: 85 - 87: 37.626 distance: 86 - 88: 29.727 distance: 89 - 90: 15.891 distance: 90 - 91: 30.736 distance: 90 - 93: 41.356 distance: 91 - 92: 13.288 distance: 91 - 94: 48.080 distance: 94 - 95: 15.870 distance: 95 - 96: 21.983 distance: 95 - 98: 10.896 distance: 96 - 97: 34.386 distance: 96 - 100: 34.705 distance: 98 - 99: 49.810 distance: 100 - 101: 32.095 distance: 101 - 102: 17.672 distance: 101 - 104: 24.098 distance: 102 - 103: 16.579 distance: 102 - 107: 21.100 distance: 104 - 105: 16.716 distance: 104 - 106: 17.153