Starting phenix.real_space_refine on Sun Mar 10 22:41:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/03_2024/7wsi_32759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/03_2024/7wsi_32759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/03_2024/7wsi_32759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/03_2024/7wsi_32759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/03_2024/7wsi_32759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/03_2024/7wsi_32759.pdb" } resolution = 3.32 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 3678 2.51 5 N 913 2.21 5 O 1067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5701 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2348 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1669 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 15, 'TRANS': 205} Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Time building chain proxies: 3.67, per 1000 atoms: 0.64 Number of scatterers: 5701 At special positions: 0 Unit cell: (87.15, 72.21, 141.93, 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 43 16.00 O 1067 8.00 N 913 7.00 C 3678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 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: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 38.0% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.758A pdb=" N GLY A 19 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.565A pdb=" N ILE A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.888A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.568A pdb=" N ALA A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 243 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.587A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 309 removed outlier: 3.675A pdb=" N LYS A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.520A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY H 66 " --> pdb=" O LYS H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 66' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.104A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 199 removed outlier: 4.367A pdb=" N SER H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.547A pdb=" N LEU L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.610A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.599A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.599A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.324A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER H 187 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET H 185 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 161 removed outlier: 3.868A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.009A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 69 through 73 Processing sheet with id=AA8, first strand: chain 'L' and resid 122 through 123 removed outlier: 4.016A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 158 through 159 removed outlier: 6.077A pdb=" N HIS L 203 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N SER L 208 " --> pdb=" O HIS L 203 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 753 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: 1.45 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1736 1.35 - 1.46: 1445 1.46 - 1.58: 2593 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 5839 Sorted by residual: bond pdb=" CA GLY L 70 " pdb=" C GLY L 70 " ideal model delta sigma weight residual 1.520 1.513 0.008 7.30e-03 1.88e+04 1.06e+00 bond pdb=" N SER L 25 " pdb=" CA SER L 25 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.06e+00 bond pdb=" CA THR L 20 " pdb=" CB THR L 20 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.61e-02 3.86e+03 7.89e-01 bond pdb=" CA ALA H 16 " pdb=" CB ALA H 16 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.69e-02 3.50e+03 7.72e-01 bond pdb=" SD MET A 122 " pdb=" CE MET A 122 " ideal model delta sigma weight residual 1.791 1.770 0.021 2.50e-02 1.60e+03 7.33e-01 ... (remaining 5834 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.08: 169 106.08 - 113.07: 3191 113.07 - 120.06: 1965 120.06 - 127.05: 2541 127.05 - 134.04: 68 Bond angle restraints: 7934 Sorted by residual: angle pdb=" N ILE A 214 " pdb=" CA ILE A 214 " pdb=" C ILE A 214 " ideal model delta sigma weight residual 111.77 108.04 3.73 1.04e+00 9.25e-01 1.29e+01 angle pdb=" C PRO L 8 " pdb=" N SER L 9 " pdb=" CA SER L 9 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 6.98e+00 angle pdb=" CA CYS L 94 " pdb=" CB CYS L 94 " pdb=" SG CYS L 94 " ideal model delta sigma weight residual 114.40 120.23 -5.83 2.30e+00 1.89e-01 6.43e+00 angle pdb=" C ASP A 149 " pdb=" N LEU A 150 " pdb=" CA LEU A 150 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.82e+00 angle pdb=" N THR L 169 " pdb=" CA THR L 169 " pdb=" C THR L 169 " ideal model delta sigma weight residual 110.53 107.76 2.77 1.29e+00 6.01e-01 4.61e+00 ... (remaining 7929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 3061 13.97 - 27.94: 325 27.94 - 41.91: 84 41.91 - 55.87: 12 55.87 - 69.84: 2 Dihedral angle restraints: 3484 sinusoidal: 1332 harmonic: 2152 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 158.44 -65.44 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS H 148 " pdb=" SG CYS H 148 " pdb=" SG CYS H 203 " pdb=" CB CYS H 203 " ideal model delta sinusoidal sigma weight residual -86.00 -118.30 32.30 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CA TYR L 92 " pdb=" C TYR L 92 " pdb=" N TYR L 93 " pdb=" CA TYR L 93 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 559 0.032 - 0.064: 241 0.064 - 0.096: 77 0.096 - 0.127: 37 0.127 - 0.159: 4 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE L 54 " pdb=" N ILE L 54 " pdb=" C ILE L 54 " pdb=" CB ILE L 54 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ILE H 104 " pdb=" N ILE H 104 " pdb=" C ILE H 104 " pdb=" CB ILE H 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE A 145 " pdb=" N ILE A 145 " pdb=" C ILE A 145 " pdb=" CB ILE A 145 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 915 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 64 " 0.041 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO L 65 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 65 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 65 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 180 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 181 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 49 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO L 50 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO L 50 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 50 " -0.020 5.00e-02 4.00e+02 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 82 2.68 - 3.23: 5605 3.23 - 3.79: 8449 3.79 - 4.34: 11132 4.34 - 4.90: 18947 Nonbonded interactions: 44215 Sorted by model distance: nonbonded pdb=" OD1 ASP H 102 " pdb=" N GLY H 103 " model vdw 2.122 2.520 nonbonded pdb=" OG SER A 105 " pdb=" OE1 GLU A 257 " model vdw 2.229 2.440 nonbonded pdb=" NE2 GLN L 96 " pdb=" OG1 THR L 102 " model vdw 2.328 2.520 nonbonded pdb=" NH1 ARG L 160 " pdb=" O ASN L 162 " model vdw 2.340 2.520 nonbonded pdb=" O TYR L 55 " pdb=" OG1 THR L 59 " model vdw 2.354 2.440 ... (remaining 44210 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.040 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.350 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 0.027 5839 Z= 0.199 Angle : 0.668 6.068 7934 Z= 0.349 Chirality : 0.043 0.159 918 Planarity : 0.005 0.063 981 Dihedral : 12.247 69.843 2099 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -0.23 (0.32), residues: 737 helix: 0.97 (0.34), residues: 241 sheet: 0.43 (0.39), residues: 195 loop : -1.50 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 41 HIS 0.002 0.001 HIS H 106 PHE 0.018 0.001 PHE A 292 TYR 0.017 0.002 TYR A 69 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TRP cc_start: 0.5403 (m-10) cc_final: 0.5077 (m-10) REVERT: H 3 GLN cc_start: 0.7813 (pp30) cc_final: 0.7395 (pp30) REVERT: H 117 LEU cc_start: 0.8462 (tt) cc_final: 0.8099 (tp) REVERT: L 42 TYR cc_start: 0.8120 (m-80) cc_final: 0.7786 (m-80) REVERT: L 44 GLN cc_start: 0.8043 (tt0) cc_final: 0.7616 (tt0) REVERT: L 128 GLU cc_start: 0.7847 (pm20) cc_final: 0.7550 (pm20) REVERT: L 143 ASN cc_start: 0.8175 (m-40) cc_final: 0.7957 (m-40) REVERT: L 160 ARG cc_start: 0.8007 (ptm-80) cc_final: 0.7635 (ptp90) REVERT: L 168 TRP cc_start: 0.8956 (m-90) cc_final: 0.8650 (m-90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1698 time to fit residues: 64.9577 Evaluate side-chains 234 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 59.4302 > 50: distance: 81 - 85: 16.144 distance: 85 - 86: 10.130 distance: 86 - 87: 6.863 distance: 86 - 89: 14.153 distance: 87 - 88: 6.052 distance: 87 - 96: 16.345 distance: 89 - 90: 6.918 distance: 90 - 91: 17.593 distance: 90 - 92: 11.959 distance: 91 - 93: 13.716 distance: 92 - 94: 17.394 distance: 93 - 95: 19.682 distance: 94 - 95: 17.175 distance: 96 - 97: 18.749 distance: 96 - 218: 18.150 distance: 97 - 98: 13.802 distance: 97 - 100: 19.836 distance: 98 - 99: 6.941 distance: 98 - 104: 8.281 distance: 99 - 215: 17.634 distance: 100 - 101: 10.479 distance: 101 - 102: 20.106 distance: 101 - 103: 14.369 distance: 104 - 105: 10.962 distance: 105 - 106: 9.571 distance: 105 - 108: 5.791 distance: 106 - 107: 26.698 distance: 106 - 112: 14.671 distance: 108 - 109: 14.724 distance: 109 - 110: 12.394 distance: 109 - 111: 30.829 distance: 113 - 114: 8.702 distance: 113 - 116: 4.554 distance: 114 - 115: 21.237 distance: 114 - 120: 21.506 distance: 116 - 117: 3.197 distance: 117 - 118: 12.897 distance: 117 - 119: 13.558 distance: 120 - 121: 25.255 distance: 121 - 122: 32.900 distance: 121 - 124: 16.283 distance: 122 - 123: 8.323 distance: 122 - 131: 13.583 distance: 124 - 125: 10.240 distance: 125 - 126: 9.292 distance: 125 - 127: 16.971 distance: 126 - 128: 13.356 distance: 127 - 129: 6.368 distance: 128 - 130: 4.127 distance: 129 - 130: 5.332 distance: 131 - 132: 29.102 distance: 132 - 133: 32.115 distance: 132 - 135: 23.697 distance: 133 - 134: 14.473 distance: 133 - 143: 15.536 distance: 135 - 136: 12.614 distance: 136 - 137: 24.594 distance: 136 - 138: 22.806 distance: 137 - 139: 14.480 distance: 138 - 140: 25.335 distance: 139 - 141: 36.250 distance: 140 - 141: 15.876 distance: 141 - 142: 7.627 distance: 143 - 144: 37.807 distance: 143 - 149: 12.671 distance: 144 - 145: 20.527 distance: 144 - 147: 16.847 distance: 145 - 146: 7.226 distance: 145 - 150: 20.828 distance: 147 - 148: 16.434 distance: 148 - 149: 51.753 distance: 150 - 151: 8.599 distance: 151 - 152: 9.310 distance: 151 - 154: 9.135 distance: 152 - 153: 21.693 distance: 152 - 159: 3.631 distance: 154 - 155: 11.683 distance: 155 - 156: 15.941 distance: 156 - 157: 17.585 distance: 157 - 158: 31.047 distance: 159 - 160: 30.978 distance: 160 - 161: 7.083 distance: 160 - 163: 21.367 distance: 161 - 162: 5.458 distance: 161 - 167: 25.069 distance: 163 - 164: 22.865 distance: 164 - 165: 24.504 distance: 164 - 166: 14.283 distance: 167 - 168: 16.985 distance: 168 - 169: 22.742 distance: 168 - 171: 10.268 distance: 169 - 170: 13.163 distance: 169 - 175: 6.845 distance: 171 - 172: 13.321 distance: 171 - 173: 13.345 distance: 172 - 174: 17.665 distance: 175 - 232: 3.275