Starting phenix.real_space_refine on Fri Jul 19 02:06:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/07_2024/8u4r_41892.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/07_2024/8u4r_41892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/07_2024/8u4r_41892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/07_2024/8u4r_41892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/07_2024/8u4r_41892.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/07_2024/8u4r_41892.cif" } resolution = 3.1 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= 0.049 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 2008 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 23 5.16 5 C 2680 2.51 5 N 676 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4107 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 864 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "R" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2239 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.23, per 1000 atoms: 0.79 Number of scatterers: 4107 At special positions: 0 Unit cell: (55.25, 65.45, 110.5, 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 23 16.00 O 728 8.00 N 676 7.00 C 2680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " 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: 1.47 Conformation dependent library (CDL) restraints added in 691.7 milliseconds 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 7 sheets defined 46.0% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.539A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 65 Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 71 through 100 removed outlier: 3.709A pdb=" N LYS R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU R 86 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 106 through 140 removed outlier: 4.133A pdb=" N SER R 123 " --> pdb=" O SER R 119 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU R 125 " --> pdb=" O TYR R 121 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE R 126 " --> pdb=" O SER R 122 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 160 removed outlier: 3.880A pdb=" N VAL R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR R 157 " --> pdb=" O GLU R 153 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL R 158 " --> pdb=" O LYS R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 167 Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 192 through 209 removed outlier: 4.494A pdb=" N VAL R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 226 Processing helix chain 'R' and resid 235 through 252 removed outlier: 3.819A pdb=" N THR R 240 " --> pdb=" O LYS R 236 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP R 252 " --> pdb=" O PHE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 267 Processing helix chain 'R' and resid 274 through 292 Processing helix chain 'R' and resid 293 through 295 No H-bonds generated for 'chain 'R' and resid 293 through 295' Processing helix chain 'R' and resid 296 through 304 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.624A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.624A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.506A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 8.327A pdb=" N TYR H 32 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.944A pdb=" N CYS H 96 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL H 115 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG H 98 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR H 111 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N THR H 102 " --> pdb=" O TYR H 109 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N TYR H 109 " --> pdb=" O THR H 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 175 through 180 243 hydrogen bonds defined for protein. 678 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: 1.12 Time building geometry restraints manager: 1.63 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: 1254 1.34 - 1.46: 1017 1.46 - 1.58: 1910 1.58 - 1.70: 1 1.70 - 1.82: 33 Bond restraints: 4215 Sorted by residual: bond pdb=" C6 CLR R 701 " pdb=" C7 CLR R 701 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C14 CLR R 701 " pdb=" C15 CLR R 701 " ideal model delta sigma weight residual 1.523 1.565 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C13 CLR R 701 " pdb=" C14 CLR R 701 " ideal model delta sigma weight residual 1.537 1.578 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C20 CLR R 701 " pdb=" C22 CLR R 701 " ideal model delta sigma weight residual 1.535 1.575 -0.040 2.00e-02 2.50e+03 4.01e+00 bond pdb=" C15 CLR R 701 " pdb=" C16 CLR R 701 " ideal model delta sigma weight residual 1.541 1.581 -0.040 2.00e-02 2.50e+03 3.97e+00 ... (remaining 4210 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.16: 92 106.16 - 113.17: 2269 113.17 - 120.18: 1536 120.18 - 127.18: 1788 127.18 - 134.19: 52 Bond angle restraints: 5737 Sorted by residual: angle pdb=" CA TRP H 116 " pdb=" CB TRP H 116 " pdb=" CG TRP H 116 " ideal model delta sigma weight residual 113.60 119.67 -6.07 1.90e+00 2.77e-01 1.02e+01 angle pdb=" C TYR H 111 " pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta sigma weight residual 123.46 116.30 7.16 2.42e+00 1.71e-01 8.74e+00 angle pdb=" C ASP R 181 " pdb=" CA ASP R 181 " pdb=" CB ASP R 181 " ideal model delta sigma weight residual 110.42 116.07 -5.65 1.99e+00 2.53e-01 8.07e+00 angle pdb=" N LEU L 52 " pdb=" CA LEU L 52 " pdb=" C LEU L 52 " ideal model delta sigma weight residual 112.12 108.44 3.68 1.34e+00 5.57e-01 7.53e+00 angle pdb=" C GLY H 112 " pdb=" N MET H 113 " pdb=" CA MET H 113 " ideal model delta sigma weight residual 123.93 128.07 -4.14 1.54e+00 4.22e-01 7.24e+00 ... (remaining 5732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2254 17.92 - 35.83: 205 35.83 - 53.75: 35 53.75 - 71.67: 4 71.67 - 89.58: 5 Dihedral angle restraints: 2503 sinusoidal: 1011 harmonic: 1492 Sorted by residual: dihedral pdb=" CB CYS R 28 " pdb=" SG CYS R 28 " pdb=" SG CYS R 274 " pdb=" CB CYS R 274 " ideal model delta sinusoidal sigma weight residual -86.00 -161.73 75.73 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 93 " pdb=" CB CYS L 93 " ideal model delta sinusoidal sigma weight residual 93.00 135.21 -42.21 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " pdb=" CD GLU L 86 " pdb=" OE1 GLU L 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.58 -89.58 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 588 0.074 - 0.148: 55 0.148 - 0.222: 3 0.222 - 0.296: 2 0.296 - 0.371: 2 Chirality restraints: 650 Sorted by residual: chirality pdb=" C17 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C16 CLR R 701 " pdb=" C20 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C20 CLR R 701 " pdb=" C17 CLR R 701 " pdb=" C21 CLR R 701 " pdb=" C22 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.59 2.90 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C13 CLR R 701 " pdb=" C12 CLR R 701 " pdb=" C14 CLR R 701 " pdb=" C17 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.93 -3.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 647 not shown) Planarity restraints: 704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 216 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.81e+00 pdb=" C LEU R 216 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU R 216 " -0.018 2.00e-02 2.50e+03 pdb=" N SER R 217 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 190 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO R 191 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 191 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 191 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 91 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO R 92 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO R 92 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 92 " 0.034 5.00e-02 4.00e+02 ... (remaining 701 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 103 2.71 - 3.26: 3861 3.26 - 3.81: 6317 3.81 - 4.35: 7782 4.35 - 4.90: 14107 Nonbonded interactions: 32170 Sorted by model distance: nonbonded pdb=" OG1 THR R 117 " pdb=" OD2 ASP R 171 " model vdw 2.165 2.440 nonbonded pdb=" NH1 ARG L 51 " pdb=" OD1 ASP H 114 " model vdw 2.221 2.520 nonbonded pdb=" OE1 GLN R 200 " pdb=" OG SER R 263 " model vdw 2.313 2.440 nonbonded pdb=" O ALA R 83 " pdb=" OG SER R 119 " model vdw 2.334 2.440 nonbonded pdb=" NH2 ARG H 105 " pdb=" OE1 GLU R 288 " model vdw 2.404 2.520 ... (remaining 32165 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 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.920 Find NCS groups from input model: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 0.050 4215 Z= 0.205 Angle : 0.672 7.746 5737 Z= 0.345 Chirality : 0.050 0.371 650 Planarity : 0.006 0.063 704 Dihedral : 14.014 89.582 1537 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.38 (0.40), residues: 503 helix: 1.07 (0.38), residues: 218 sheet: 0.04 (0.46), residues: 133 loop : -0.55 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 116 HIS 0.004 0.001 HIS R 294 PHE 0.012 0.001 PHE R 293 TYR 0.010 0.001 TYR H 107 ARG 0.004 0.001 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.504 Fit side-chains REVERT: R 24 MET cc_start: 0.6356 (tmm) cc_final: 0.6053 (tmm) REVERT: R 301 LEU cc_start: 0.8430 (mp) cc_final: 0.8173 (mp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2060 time to fit residues: 16.8784 Evaluate side-chains 59 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.0870 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 58 ASN R 203 HIS R 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4215 Z= 0.170 Angle : 0.534 5.275 5737 Z= 0.278 Chirality : 0.041 0.135 650 Planarity : 0.005 0.055 704 Dihedral : 4.345 21.853 627 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.90 % Allowed : 4.48 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.69 (0.39), residues: 503 helix: 1.44 (0.37), residues: 214 sheet: 0.26 (0.48), residues: 133 loop : -0.62 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS H 99 PHE 0.007 0.001 PHE L 41 TYR 0.007 0.001 TYR R 135 ARG 0.002 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: H 18 VAL cc_start: 0.8458 (t) cc_final: 0.8225 (t) REVERT: R 301 LEU cc_start: 0.8329 (mp) cc_final: 0.7933 (mp) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 0.1977 time to fit residues: 15.1467 Evaluate side-chains 58 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain R residue 33 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.692 > 50: distance: 60 - 65: 18.751 distance: 61 - 91: 22.359 distance: 65 - 66: 15.914 distance: 66 - 67: 10.166 distance: 66 - 69: 37.010 distance: 67 - 68: 18.188 distance: 67 - 72: 22.498 distance: 68 - 95: 16.144 distance: 69 - 70: 19.003 distance: 69 - 71: 22.171 distance: 72 - 73: 37.747 distance: 73 - 74: 12.024 distance: 73 - 76: 43.157 distance: 74 - 75: 29.414 distance: 74 - 84: 12.661 distance: 76 - 77: 26.714 distance: 77 - 78: 23.260 distance: 77 - 79: 26.464 distance: 78 - 80: 39.543 distance: 80 - 82: 12.135 distance: 81 - 82: 12.225 distance: 82 - 83: 15.204 distance: 84 - 85: 12.693 distance: 85 - 86: 18.360 distance: 85 - 88: 45.527 distance: 86 - 91: 14.788 distance: 88 - 89: 30.231 distance: 88 - 90: 28.274 distance: 91 - 92: 43.638 distance: 92 - 93: 36.368 distance: 93 - 94: 23.893 distance: 93 - 95: 33.675 distance: 95 - 96: 13.918 distance: 96 - 97: 14.475 distance: 96 - 99: 10.334 distance: 97 - 98: 23.792 distance: 97 - 102: 23.879 distance: 98 - 131: 47.265 distance: 99 - 100: 36.605 distance: 99 - 101: 22.574 distance: 102 - 103: 24.842 distance: 103 - 104: 37.875 distance: 103 - 106: 19.895 distance: 104 - 105: 26.093 distance: 104 - 116: 41.212 distance: 105 - 136: 23.064 distance: 106 - 107: 37.872 distance: 107 - 108: 12.385 distance: 107 - 109: 34.301 distance: 108 - 110: 23.015 distance: 109 - 111: 65.692 distance: 109 - 112: 39.299 distance: 110 - 111: 49.512 distance: 111 - 113: 39.574 distance: 112 - 114: 17.313 distance: 113 - 115: 18.117 distance: 114 - 115: 18.186 distance: 116 - 117: 15.694 distance: 117 - 118: 35.023 distance: 117 - 120: 17.918 distance: 118 - 119: 13.147 distance: 118 - 124: 22.240 distance: 119 - 144: 30.980 distance: 120 - 121: 31.756 distance: 120 - 122: 38.991 distance: 121 - 123: 38.254 distance: 124 - 125: 12.901 distance: 124 - 130: 15.792 distance: 125 - 128: 34.689 distance: 126 - 127: 43.272 distance: 126 - 131: 24.899 distance: 127 - 152: 37.264 distance: 128 - 129: 18.999 distance: 129 - 130: 47.890 distance: 132 - 133: 38.153 distance: 133 - 134: 3.191 distance: 133 - 136: 39.901 distance: 137 - 138: 12.549 distance: 138 - 139: 47.924 distance: 138 - 144: 29.614 distance: 141 - 142: 38.157 distance: 141 - 143: 3.609