Starting phenix.real_space_refine on Sun Dec 10 01:29:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/12_2023/6tdw_10469.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/12_2023/6tdw_10469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/12_2023/6tdw_10469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/12_2023/6tdw_10469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/12_2023/6tdw_10469.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdw_10469/12_2023/6tdw_10469.pdb" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 4087 2.51 5 N 1105 2.21 5 O 1234 1.98 5 H 6561 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 465": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 464": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 223": "OD1" <-> "OD2" Residue "M ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12997 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 398 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 3, 'TRANS': 21} Chain: "H" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4014 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 22, 'TRANS': 226} Chain breaks: 2 Chain: "B" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 4830 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "C" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2463 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "M" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 639 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 6, 'TRANS': 36} Chain: "N" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 509 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "T" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 6.26, per 1000 atoms: 0.48 Number of scatterers: 12997 At special positions: 0 Unit cell: (113.4, 72.45, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 1234 8.00 N 1105 7.00 C 4087 6.00 H 6561 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: 11.77 Conformation dependent library (CDL) restraints added in 1.6 seconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1614 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 2 sheets defined 67.9% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 474 through 487 removed outlier: 5.596A pdb=" N LYS A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 58 removed outlier: 4.020A pdb=" N LYS H 56 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR H 57 " --> pdb=" O ALA H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 79 Processing helix chain 'H' and resid 81 through 103 Proline residue: H 100 - end of helix Processing helix chain 'H' and resid 111 through 125 removed outlier: 4.378A pdb=" N GLU H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 279 removed outlier: 3.950A pdb=" N MET H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS H 274 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 277 " --> pdb=" O GLU H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 291 removed outlier: 3.782A pdb=" N LYS H 284 " --> pdb=" O ASN H 280 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU H 291 " --> pdb=" O PHE H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 297 removed outlier: 3.679A pdb=" N LYS H 296 " --> pdb=" O GLN H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 307 Processing helix chain 'H' and resid 309 through 330 removed outlier: 4.382A pdb=" N VAL H 313 " --> pdb=" O ASP H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 358 removed outlier: 3.694A pdb=" N GLU H 345 " --> pdb=" O GLN H 341 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE H 354 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP H 355 " --> pdb=" O GLY H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 455 removed outlier: 4.838A pdb=" N GLN H 450 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA H 453 " --> pdb=" O ALA H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 476 removed outlier: 3.860A pdb=" N SER H 460 " --> pdb=" O PRO H 456 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H 464 " --> pdb=" O SER H 460 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 471 " --> pdb=" O THR H 467 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 472 " --> pdb=" O GLU H 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 56 through 68 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 104 through 107 removed outlier: 4.364A pdb=" N SER B 107 " --> pdb=" O PRO B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 107' Processing helix chain 'B' and resid 121 through 164 Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'B' and resid 235 through 249 Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 293 through 310 Processing helix chain 'B' and resid 324 through 337 Processing helix chain 'C' and resid 13 through 25 Processing helix chain 'C' and resid 36 through 42 Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 65 through 87 Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 105 through 130 Processing helix chain 'C' and resid 131 through 150 Processing helix chain 'C' and resid 153 through 168 Processing helix chain 'M' and resid 239 through 246 Processing helix chain 'M' and resid 249 through 263 Processing helix chain 'N' and resid 84 through 112 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 9 removed outlier: 5.916A pdb=" N LYS B 4 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B 36 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 6 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR B 38 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 8 " --> pdb=" O THR B 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 6.822A pdb=" N LEU B 50 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N SER B 268 " --> pdb=" O LEU B 50 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1260 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: 4.32 Time building geometry restraints manager: 12.03 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: 6556 1.03 - 1.23: 9 1.23 - 1.42: 2561 1.42 - 1.62: 3969 1.62 - 1.81: 15 Bond restraints: 13110 Sorted by residual: bond pdb=" C LYS C 36 " pdb=" N ASP C 37 " ideal model delta sigma weight residual 1.334 1.175 0.159 1.27e-02 6.20e+03 1.58e+02 bond pdb=" C ASP C 57 " pdb=" N SER C 58 " ideal model delta sigma weight residual 1.333 1.231 0.102 1.26e-02 6.30e+03 6.56e+01 bond pdb=" N VAL H 313 " pdb=" CA VAL H 313 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.24e+00 bond pdb=" N VAL H 302 " pdb=" CA VAL H 302 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.22e+00 bond pdb=" N VAL H 312 " pdb=" CA VAL H 312 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.85e+00 ... (remaining 13105 not shown) Histogram of bond angle deviations from ideal: 81.80 - 92.24: 6 92.24 - 102.68: 22 102.68 - 113.12: 16376 113.12 - 123.56: 6439 123.56 - 134.00: 1046 Bond angle restraints: 23889 Sorted by residual: angle pdb=" CG2 VAL B 119 " pdb=" CB VAL B 119 " pdb=" HB VAL B 119 " ideal model delta sigma weight residual 108.00 81.80 26.20 3.00e+00 1.11e-01 7.63e+01 angle pdb=" CG1 VAL B 119 " pdb=" CB VAL B 119 " pdb=" HB VAL B 119 " ideal model delta sigma weight residual 108.00 82.86 25.14 3.00e+00 1.11e-01 7.02e+01 angle pdb=" CD2 LEU M 246 " pdb=" CG LEU M 246 " pdb=" HG LEU M 246 " ideal model delta sigma weight residual 108.00 83.69 24.31 3.00e+00 1.11e-01 6.56e+01 angle pdb=" CD1 LEU M 246 " pdb=" CG LEU M 246 " pdb=" HG LEU M 246 " ideal model delta sigma weight residual 108.00 84.44 23.56 3.00e+00 1.11e-01 6.17e+01 angle pdb=" CA VAL B 119 " pdb=" CB VAL B 119 " pdb=" HB VAL B 119 " ideal model delta sigma weight residual 109.00 85.48 23.52 3.00e+00 1.11e-01 6.15e+01 ... (remaining 23884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.27: 5119 14.27 - 28.55: 693 28.55 - 42.82: 174 42.82 - 57.10: 41 57.10 - 71.37: 7 Dihedral angle restraints: 6034 sinusoidal: 3293 harmonic: 2741 Sorted by residual: dihedral pdb=" CA LEU C 29 " pdb=" C LEU C 29 " pdb=" N LYS C 30 " pdb=" CA LYS C 30 " ideal model delta harmonic sigma weight residual 180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA SER C 58 " pdb=" C SER C 58 " pdb=" N GLU C 59 " pdb=" CA GLU C 59 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLY B 179 " pdb=" C GLY B 179 " pdb=" N ASP B 180 " pdb=" CA ASP B 180 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 1048 0.343 - 0.685: 0 0.685 - 1.028: 0 1.028 - 1.370: 0 1.370 - 1.713: 2 Chirality restraints: 1050 Sorted by residual: chirality pdb=" CG LEU M 246 " pdb=" CB LEU M 246 " pdb=" CD1 LEU M 246 " pdb=" CD2 LEU M 246 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 chirality pdb=" CB VAL B 119 " pdb=" CA VAL B 119 " pdb=" CG1 VAL B 119 " pdb=" CG2 VAL B 119 " both_signs ideal model delta sigma weight residual False -2.63 -1.10 -1.53 2.00e-01 2.50e+01 5.82e+01 chirality pdb=" CA VAL B 73 " pdb=" N VAL B 73 " pdb=" C VAL B 73 " pdb=" CB VAL B 73 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 1047 not shown) Planarity restraints: 1929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 217 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.47e+00 pdb=" N PRO B 218 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 57 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ASP C 57 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP C 57 " -0.013 2.00e-02 2.50e+03 pdb=" N SER C 58 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 314 " -0.012 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" N ALA H 315 " 0.037 2.00e-02 2.50e+03 pdb=" CA ALA H 315 " -0.010 2.00e-02 2.50e+03 pdb=" H ALA H 315 " -0.016 2.00e-02 2.50e+03 ... (remaining 1926 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1812 2.26 - 2.85: 29645 2.85 - 3.43: 32052 3.43 - 4.02: 41178 4.02 - 4.60: 65451 Nonbonded interactions: 170138 Sorted by model distance: nonbonded pdb=" HG2 GLU H 311 " pdb="HG23 THR C 89 " model vdw 1.678 2.440 nonbonded pdb=" O PRO B 44 " pdb=" HH TYR B 67 " model vdw 1.725 1.850 nonbonded pdb="HH21 ARG H 319 " pdb=" OD1 ASP M 257 " model vdw 1.726 1.850 nonbonded pdb=" O ALA B 305 " pdb=" HG1 THR B 309 " model vdw 1.736 1.850 nonbonded pdb=" OE1 GLN B 240 " pdb="HH11 ARG C 90 " model vdw 1.748 1.850 ... (remaining 170133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 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: 0.200 Extract box with map and model: 18.850 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 46.220 Find NCS groups from input model: 0.250 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.007 0.159 6549 Z= 0.497 Angle : 0.839 11.010 8899 Z= 0.465 Chirality : 0.083 1.713 1050 Planarity : 0.005 0.058 1150 Dihedral : 13.713 71.372 2442 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.64 % 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: -1.91 (0.27), residues: 821 helix: -0.17 (0.20), residues: 523 sheet: -3.60 (0.56), residues: 59 loop : -2.97 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 152 HIS 0.006 0.001 HIS A 467 PHE 0.016 0.002 PHE B 223 TYR 0.011 0.002 TYR H 25 ARG 0.006 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.035 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 revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.4909 time to fit residues: 114.1849 Evaluate side-chains 95 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2316 time to fit residues: 1.5416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.0170 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6549 Z= 0.212 Angle : 0.619 10.905 8899 Z= 0.310 Chirality : 0.078 1.689 1050 Planarity : 0.005 0.045 1150 Dihedral : 4.328 18.972 885 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.16 % Allowed : 12.79 % Favored : 86.05 % 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: -0.35 (0.30), residues: 821 helix: 1.21 (0.22), residues: 528 sheet: -3.50 (0.56), residues: 61 loop : -2.69 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 217 HIS 0.004 0.001 HIS H 308 PHE 0.018 0.001 PHE B 19 TYR 0.012 0.001 TYR H 25 ARG 0.003 0.000 ARG H 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.990 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 outliers start: 8 outliers final: 5 residues processed: 110 average time/residue: 0.4820 time to fit residues: 68.5074 Evaluate side-chains 99 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1526 time to fit residues: 2.7196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 0.0040 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.0870 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4770 ------------------------------------------------------------------------------- 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: 0.7732 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6549 Z= 0.192 Angle : 0.571 10.971 8899 Z= 0.282 Chirality : 0.077 1.698 1050 Planarity : 0.004 0.045 1150 Dihedral : 4.006 17.863 885 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.16 % Allowed : 13.37 % Favored : 85.47 % 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: 0.56 (0.31), residues: 821 helix: 1.88 (0.22), residues: 535 sheet: -3.02 (0.61), residues: 57 loop : -2.48 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 152 HIS 0.005 0.001 HIS A 467 PHE 0.017 0.001 PHE B 19 TYR 0.008 0.001 TYR B 99 ARG 0.002 0.000 ARG H 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.077 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 outliers start: 8 outliers final: 5 residues processed: 105 average time/residue: 0.4838 time to fit residues: 65.0327 Evaluate side-chains 95 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1568 time to fit residues: 2.8059 ------------------------------------------------------------------------------- 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: 56.068 > 50: distance: 156 - 163: 18.643 distance: 157 - 160: 4.214 distance: 158 - 159: 12.352 distance: 158 - 172: 9.833 distance: 160 - 161: 6.213 distance: 160 - 162: 5.979 distance: 160 - 165: 6.884 distance: 161 - 166: 6.728 distance: 161 - 167: 5.687 distance: 161 - 168: 10.412 distance: 162 - 169: 7.889 distance: 162 - 170: 8.795 distance: 172 - 173: 6.839 distance: 172 - 180: 12.949 distance: 173 - 174: 14.589 distance: 173 - 176: 5.063 distance: 173 - 181: 5.770 distance: 174 - 175: 16.114 distance: 174 - 184: 26.916 distance: 176 - 177: 6.057 distance: 176 - 182: 14.874 distance: 176 - 183: 8.217 distance: 177 - 178: 5.424 distance: 177 - 179: 9.144 distance: 184 - 185: 3.951 distance: 184 - 198: 14.965 distance: 185 - 186: 17.305 distance: 185 - 188: 20.467 distance: 185 - 199: 13.048 distance: 186 - 187: 25.416 distance: 186 - 208: 27.428 distance: 188 - 189: 8.012 distance: 188 - 200: 20.633 distance: 188 - 201: 21.960 distance: 189 - 190: 9.466 distance: 189 - 191: 3.966 distance: 190 - 192: 15.040 distance: 190 - 202: 17.650 distance: 191 - 193: 14.423 distance: 191 - 194: 12.743 distance: 192 - 193: 13.062 distance: 192 - 203: 8.223 distance: 193 - 195: 14.586 distance: 194 - 196: 3.764 distance: 194 - 204: 4.662 distance: 195 - 197: 17.090 distance: 195 - 205: 5.751 distance: 196 - 197: 19.812 distance: 196 - 206: 3.472 distance: 197 - 207: 4.449 distance: 208 - 209: 21.508 distance: 208 - 215: 12.326 distance: 209 - 210: 20.621 distance: 209 - 212: 15.724 distance: 209 - 216: 10.505 distance: 210 - 211: 13.803 distance: 210 - 222: 7.656 distance: 212 - 213: 11.681 distance: 212 - 214: 14.120 distance: 212 - 217: 22.618 distance: 213 - 218: 21.494 distance: 214 - 219: 4.289 distance: 214 - 220: 3.242 distance: 214 - 221: 11.190 distance: 222 - 223: 5.688 distance: 222 - 228: 15.008 distance: 223 - 224: 16.167 distance: 223 - 226: 22.086 distance: 223 - 229: 21.281 distance: 224 - 225: 25.770 distance: 224 - 233: 11.090 distance: 226 - 227: 3.560 distance: 226 - 230: 7.726 distance: 226 - 231: 8.249 distance: 227 - 232: 9.565 distance: 233 - 234: 9.549 distance: 233 - 241: 6.300 distance: 234 - 235: 44.198 distance: 234 - 237: 43.038 distance: 234 - 242: 8.177 distance: 235 - 236: 12.345 distance: 235 - 252: 9.018 distance: 237 - 238: 14.217 distance: 237 - 243: 14.017 distance: 237 - 244: 21.368 distance: 238 - 239: 15.792 distance: 238 - 240: 19.000 distance: 238 - 245: 21.483 distance: 239 - 246: 15.768 distance: 239 - 247: 10.928 distance: 239 - 248: 10.797 distance: 240 - 249: 6.129 distance: 240 - 250: 8.375 distance: 240 - 251: 13.354 distance: 252 - 253: 7.217 distance: 253 - 254: 12.977 distance: 253 - 256: 9.291 distance: 253 - 259: 19.864 distance: 254 - 255: 20.176 distance: 254 - 266: 13.448 distance: 256 - 257: 3.199 distance: 256 - 260: 4.410 distance: 256 - 261: 13.300 distance: 257 - 258: 9.145 distance: 257 - 262: 4.667 distance: 257 - 263: 14.903 distance: 258 - 264: 15.044 distance: 258 - 265: 11.873 distance: 266 - 267: 10.158 distance: 266 - 271: 11.398 distance: 267 - 268: 18.381 distance: 267 - 270: 20.731 distance: 267 - 272: 12.735 distance: 268 - 269: 13.297 distance: 268 - 276: 25.242 distance: 270 - 273: 9.972 distance: 270 - 274: 3.870 distance: 270 - 275: 7.499 distance: 276 - 277: 6.995 distance: 276 - 281: 6.870 distance: 277 - 278: 16.636 distance: 277 - 280: 9.390 distance: 277 - 282: 8.914 distance: 278 - 279: 20.325 distance: 278 - 286: 18.320 distance: 280 - 283: 16.962 distance: 280 - 284: 12.548 distance: 280 - 285: 16.575