Starting phenix.real_space_refine on Sun Dec 10 02:54:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/12_2023/7uml_26603.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/12_2023/7uml_26603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/12_2023/7uml_26603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/12_2023/7uml_26603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/12_2023/7uml_26603.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/12_2023/7uml_26603.pdb" } resolution = 3.5 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= 0.053 sd= 1.358 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 S 37 5.16 5 C 4272 2.51 5 N 1126 2.21 5 O 1302 1.98 5 H 6477 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13227 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5980 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 361} Chain breaks: 1 Chain: "B" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2741 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "C" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 551 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain: "E" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 531 Classifications: {'peptide': 39} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 34} Chain: "F" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 263 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "R" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 391 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 11} Time building chain proxies: 6.17, per 1000 atoms: 0.47 Number of scatterers: 13227 At special positions: 0 Unit cell: (143.65, 100.3, 114.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 13 15.00 O 1302 8.00 N 1126 7.00 C 4272 6.00 H 6477 1.00 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: 9.28 Conformation dependent library (CDL) restraints added in 1.3 seconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 38.2% alpha, 13.5% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 5.31 Creating SS restraints... Processing helix chain 'A' and resid 28 through 33 removed outlier: 3.732A pdb=" N PHE A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 62 removed outlier: 3.636A pdb=" N LYS A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.539A pdb=" N VAL A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 149 through 169 removed outlier: 4.075A pdb=" N THR A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 189 through 205 Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.623A pdb=" N ILE A 218 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 220 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 221 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 323 through 341 removed outlier: 4.412A pdb=" N LEU A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 390 through 401 Processing helix chain 'A' and resid 411 through 420 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.718A pdb=" N ASN B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.755A pdb=" N LEU B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 201 through 208 removed outlier: 3.571A pdb=" N PHE B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.733A pdb=" N VAL C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.593A pdb=" N LEU C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.550A pdb=" N HIS C 192 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE C 193 " --> pdb=" O TRP C 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'D' and resid 27 through 35 removed outlier: 4.510A pdb=" N TYR D 31 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 removed outlier: 6.420A pdb=" N LEU A 40 " --> pdb=" O LYS A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90 Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 211 through 213 removed outlier: 6.959A pdb=" N ILE B 211 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 143 Processing sheet with id=AA6, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.578A pdb=" N ILE D 14 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 5 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS E 349 " --> pdb=" O LYS D 6 " (cutoff:3.500A) 247 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 6 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 9.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6470 1.03 - 1.23: 22 1.23 - 1.42: 3001 1.42 - 1.62: 3863 1.62 - 1.81: 67 Bond restraints: 13423 Sorted by residual: bond pdb=" CA PHE B 198 " pdb=" CB PHE B 198 " ideal model delta sigma weight residual 1.530 1.551 -0.020 1.69e-02 3.50e+03 1.46e+00 bond pdb=" N GLY C 146 " pdb=" CA GLY C 146 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.88e-01 bond pdb=" CA PHE A 182 " pdb=" CB PHE A 182 " ideal model delta sigma weight residual 1.533 1.547 -0.014 1.66e-02 3.63e+03 6.66e-01 bond pdb=" C ASN B 75 " pdb=" N ARG B 76 " ideal model delta sigma weight residual 1.331 1.348 -0.017 2.07e-02 2.33e+03 6.56e-01 bond pdb=" CB PHE B 78 " pdb=" CG PHE B 78 " ideal model delta sigma weight residual 1.502 1.484 0.018 2.30e-02 1.89e+03 6.44e-01 ... (remaining 13418 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.69: 322 106.69 - 113.51: 15450 113.51 - 120.33: 4505 120.33 - 127.15: 3839 127.15 - 133.97: 89 Bond angle restraints: 24205 Sorted by residual: angle pdb=" C SER C 224 " pdb=" N ILE C 225 " pdb=" CA ILE C 225 " ideal model delta sigma weight residual 121.97 129.52 -7.55 1.80e+00 3.09e-01 1.76e+01 angle pdb=" N ILE C 225 " pdb=" CA ILE C 225 " pdb=" C ILE C 225 " ideal model delta sigma weight residual 109.34 102.84 6.50 2.08e+00 2.31e-01 9.78e+00 angle pdb=" C ASP A 85 " pdb=" N LYS A 86 " pdb=" CA LYS A 86 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.91e+00 angle pdb=" C LYS B 197 " pdb=" N PHE B 198 " pdb=" CA PHE B 198 " ideal model delta sigma weight residual 121.54 127.06 -5.52 1.91e+00 2.74e-01 8.37e+00 angle pdb=" N PHE B 198 " pdb=" CA PHE B 198 " pdb=" CB PHE B 198 " ideal model delta sigma weight residual 110.49 115.35 -4.86 1.69e+00 3.50e-01 8.27e+00 ... (remaining 24200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 6064 34.69 - 69.38: 132 69.38 - 104.07: 6 104.07 - 138.76: 1 138.76 - 173.45: 1 Dihedral angle restraints: 6204 sinusoidal: 3312 harmonic: 2892 Sorted by residual: dihedral pdb=" CA ILE C 225 " pdb=" C ILE C 225 " pdb=" N SER C 226 " pdb=" CA SER C 226 " ideal model delta harmonic sigma weight residual -180.00 -133.49 -46.51 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" O4' U R 36 " pdb=" C1' U R 36 " pdb=" N1 U R 36 " pdb=" C2 U R 36 " ideal model delta sinusoidal sigma weight residual -160.00 13.45 -173.45 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U R 27 " pdb=" C1' U R 27 " pdb=" N1 U R 27 " pdb=" C2 U R 27 " ideal model delta sinusoidal sigma weight residual -160.00 -26.98 -133.02 1 1.50e+01 4.44e-03 7.18e+01 ... (remaining 6201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 703 0.034 - 0.068: 223 0.068 - 0.102: 57 0.102 - 0.135: 26 0.135 - 0.169: 6 Chirality restraints: 1015 Sorted by residual: chirality pdb=" C1' U R 36 " pdb=" O4' U R 36 " pdb=" C2' U R 36 " pdb=" N1 U R 36 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ILE C 225 " pdb=" N ILE C 225 " pdb=" C ILE C 225 " pdb=" CB ILE C 225 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA VAL B 68 " pdb=" N VAL B 68 " pdb=" C VAL B 68 " pdb=" CB VAL B 68 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1012 not shown) Planarity restraints: 1933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 197 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C LYS B 197 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS B 197 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE B 198 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 128 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO C 129 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 160 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO B 161 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " -0.026 5.00e-02 4.00e+02 ... (remaining 1930 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1020 2.21 - 2.81: 26688 2.81 - 3.41: 33005 3.41 - 4.00: 42734 4.00 - 4.60: 65211 Nonbonded interactions: 168658 Sorted by model distance: nonbonded pdb=" HE1 TRP B 190 " pdb=" O TRP B 220 " model vdw 1.616 1.850 nonbonded pdb=" HH TYR A 152 " pdb=" OP2 U R 35 " model vdw 1.618 1.850 nonbonded pdb=" H SER A 291 " pdb=" OP2 U R 31 " model vdw 1.644 1.850 nonbonded pdb=" O ARG D 7 " pdb=" H ASN D 11 " model vdw 1.659 1.850 nonbonded pdb=" OE1 GLN E 346 " pdb=" H TYR E 355 " model vdw 1.682 1.850 ... (remaining 168653 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 'B' and ((resid 58 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 59 through 227)) selection = (chain 'C' and resid 58 through 227) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.900 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: 0.180 Extract box with map and model: 4.120 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 45.150 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 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 0.024 6946 Z= 0.166 Angle : 0.579 7.548 9448 Z= 0.314 Chirality : 0.040 0.169 1015 Planarity : 0.005 0.051 1173 Dihedral : 15.494 173.453 2609 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.63 % Allowed : 2.01 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 2.22 % Twisted General : 0.26 % 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: -2.75 (0.27), residues: 798 helix: -0.80 (0.30), residues: 273 sheet: -0.74 (0.49), residues: 99 loop : -2.91 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 88 HIS 0.003 0.001 HIS A 298 PHE 0.013 0.001 PHE C 208 TYR 0.014 0.001 TYR B 178 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4449 time to fit residues: 102.6994 Evaluate side-chains 132 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6946 Z= 0.349 Angle : 0.646 5.172 9448 Z= 0.349 Chirality : 0.042 0.169 1015 Planarity : 0.005 0.044 1173 Dihedral : 12.474 170.989 1044 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.77 % Favored : 89.60 % Rotamer: Outliers : 2.30 % Allowed : 9.93 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -2.54 (0.27), residues: 798 helix: -0.48 (0.30), residues: 284 sheet: -0.74 (0.45), residues: 119 loop : -3.02 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 248 HIS 0.004 0.001 HIS B 192 PHE 0.014 0.002 PHE B 78 TYR 0.014 0.002 TYR C 178 ARG 0.003 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 16 residues processed: 144 average time/residue: 0.4156 time to fit residues: 79.2445 Evaluate side-chains 145 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1534 time to fit residues: 5.7146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6946 Z= 0.243 Angle : 0.579 5.199 9448 Z= 0.310 Chirality : 0.040 0.189 1015 Planarity : 0.005 0.039 1173 Dihedral : 12.427 174.718 1044 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.89 % Favored : 91.73 % Rotamer: Outliers : 0.86 % Allowed : 13.81 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.30 (0.28), residues: 798 helix: -0.16 (0.31), residues: 279 sheet: -0.83 (0.44), residues: 119 loop : -2.86 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 88 HIS 0.003 0.001 HIS A 203 PHE 0.013 0.001 PHE B 110 TYR 0.012 0.001 TYR A 277 ARG 0.003 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 132 average time/residue: 0.4249 time to fit residues: 73.3381 Evaluate side-chains 130 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1431 time to fit residues: 2.2352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 70.3957 > 50: distance: 101 - 111: 21.271 distance: 111 - 112: 30.344 distance: 111 - 120: 14.517 distance: 112 - 113: 30.837 distance: 112 - 115: 19.984 distance: 112 - 121: 26.372 distance: 113 - 114: 3.574 distance: 115 - 116: 15.775 distance: 115 - 122: 42.620 distance: 115 - 123: 32.211 distance: 116 - 117: 27.300 distance: 116 - 124: 14.076 distance: 116 - 125: 16.141 distance: 117 - 118: 16.772 distance: 117 - 127: 37.351 distance: 118 - 119: 21.434 distance: 118 - 128: 17.718 distance: 118 - 129: 4.963 distance: 119 - 130: 4.517 distance: 119 - 131: 4.737 distance: 119 - 132: 7.042 distance: 133 - 134: 45.901 distance: 133 - 145: 50.367 distance: 134 - 135: 19.891 distance: 134 - 137: 34.932 distance: 134 - 146: 25.173 distance: 135 - 136: 46.085 distance: 135 - 154: 30.407 distance: 137 - 138: 22.262 distance: 138 - 139: 5.478 distance: 138 - 140: 19.071 distance: 139 - 141: 36.841 distance: 139 - 149: 33.534 distance: 140 - 142: 20.048 distance: 141 - 143: 44.710 distance: 141 - 151: 19.686 distance: 142 - 143: 20.564 distance: 142 - 152: 19.002 distance: 143 - 144: 39.327 distance: 144 - 153: 39.648 distance: 154 - 155: 49.692 distance: 154 - 161: 15.714 distance: 155 - 156: 31.176 distance: 155 - 158: 29.363 distance: 155 - 162: 49.710 distance: 156 - 157: 24.898 distance: 156 - 168: 39.016 distance: 158 - 159: 39.546 distance: 158 - 160: 40.156 distance: 159 - 164: 38.850 distance: 168 - 169: 40.768 distance: 169 - 170: 40.756 distance: 169 - 172: 56.336 distance: 169 - 175: 40.160 distance: 170 - 171: 20.651 distance: 170 - 182: 34.166 distance: 172 - 177: 8.095 distance: 173 - 174: 39.325 distance: 173 - 179: 56.253 distance: 174 - 180: 36.418 distance: 174 - 181: 33.559 distance: 182 - 183: 37.423 distance: 182 - 190: 31.638 distance: 183 - 184: 38.915 distance: 183 - 186: 16.085 distance: 183 - 191: 14.594 distance: 184 - 194: 22.002 distance: 186 - 187: 9.803 distance: 186 - 192: 49.321 distance: 186 - 193: 40.173 distance: 187 - 188: 18.008 distance: 187 - 189: 5.671 distance: 194 - 195: 42.381 distance: 194 - 202: 20.941 distance: 195 - 198: 42.147 distance: 198 - 199: 9.721 distance: 198 - 204: 36.898 distance: 198 - 205: 20.989 distance: 199 - 200: 35.356 distance: 199 - 201: 24.343 distance: 206 - 207: 33.632 distance: 207 - 208: 10.565 distance: 207 - 210: 54.713 distance: 207 - 213: 39.740 distance: 208 - 209: 32.523 distance: 208 - 217: 29.964 distance: 210 - 211: 40.090 distance: 210 - 214: 5.268 distance: 211 - 216: 33.228 distance: 217 - 218: 47.488 distance: 217 - 224: 28.473 distance: 218 - 219: 28.185 distance: 218 - 221: 9.041 distance: 218 - 225: 10.486 distance: 219 - 220: 9.648 distance: 219 - 231: 34.469 distance: 221 - 222: 13.621 distance: 221 - 223: 11.379 distance: 222 - 227: 14.762 distance: 223 - 228: 28.104 distance: 223 - 229: 14.399 distance: 223 - 230: 18.406 distance: 231 - 232: 22.065 distance: 231 - 235: 7.457 distance: 232 - 233: 16.114 distance: 232 - 236: 45.996 distance: 232 - 237: 18.995 distance: 233 - 234: 19.577 distance: 233 - 238: 4.901 distance: 238 - 239: 40.221 distance: 238 - 242: 29.548 distance: 239 - 240: 57.117 distance: 239 - 244: 39.683 distance: 240 - 241: 8.876 distance: 240 - 245: 29.833