Starting phenix.real_space_refine on Thu Jan 18 00:45:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/01_2024/6v4u_21048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/01_2024/6v4u_21048.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/6v4u_21048/01_2024/6v4u_21048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/01_2024/6v4u_21048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/01_2024/6v4u_21048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4u_21048/01_2024/6v4u_21048.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= 0.002 sd= 0.039 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 23 5.16 5 C 4443 2.51 5 N 1262 2.21 5 O 1346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7074 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2475 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 324} Chain breaks: 7 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2075 Classifications: {'peptide': 356} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 221} Link IDs: {'PTRANS': 14, 'TRANS': 341} Chain breaks: 7 Unresolved non-hydrogen bonds: 785 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 630 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 20, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 12, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 401 Chain: "B" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 2524 Classifications: {'peptide': 421} Incomplete info: {'backbone_only': 13, 'truncation_to_alanine': 231} Link IDs: {'PTRANS': 12, 'TRANS': 408} Chain breaks: 11 Unresolved non-hydrogen bonds: 944 Unresolved non-hydrogen angles: 1200 Unresolved non-hydrogen dihedrals: 776 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 19, 'PHE:plan': 14, 'GLU:plan': 24, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 541 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG C 347 " occ=0.81 ... (9 atoms not shown) pdb=" NH2 ARG C 347 " occ=0.71 Time building chain proxies: 4.54, per 1000 atoms: 0.64 Number of scatterers: 7074 At special positions: 0 Unit cell: (74.698, 122.964, 155.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1346 8.00 N 1262 7.00 C 4443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.5 seconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 40.5% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'C' and resid 444 through 451 Processing helix chain 'A' and resid 55 through 69 removed outlier: 4.008A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.511A pdb=" N LEU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 141 removed outlier: 3.631A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 removed outlier: 3.632A pdb=" N THR A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 removed outlier: 4.180A pdb=" N ILE A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.779A pdb=" N TYR A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 388 removed outlier: 3.953A pdb=" N LEU A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.702A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 439 removed outlier: 3.862A pdb=" N LYS A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 4.472A pdb=" N MET A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Proline residue: A 457 - end of helix Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'B' and resid 83 through 98 removed outlier: 5.647A pdb=" N TYR B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 217 removed outlier: 3.738A pdb=" N ALA B 174 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 253 Processing helix chain 'B' and resid 321 through 340 removed outlier: 3.543A pdb=" N THR B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 359 Processing helix chain 'B' and resid 366 through 382 Processing helix chain 'B' and resid 707 through 716 Processing helix chain 'B' and resid 719 through 730 removed outlier: 3.955A pdb=" N ALA B 723 " --> pdb=" O PHE B 719 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 746 removed outlier: 3.592A pdb=" N LEU B 746 " --> pdb=" O ILE B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.507A pdb=" N LEU B 750 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 751 " --> pdb=" O THR B 748 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE B 752 " --> pdb=" O ALA B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 747 through 752' Processing helix chain 'B' and resid 771 through 779 removed outlier: 3.936A pdb=" N MET B 775 " --> pdb=" O PRO B 771 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 777 " --> pdb=" O HIS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 832 Processing helix chain 'B' and resid 842 through 868 Processing helix chain 'B' and resid 880 through 892 Processing helix chain 'B' and resid 900 through 914 Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.638A pdb=" N LEU C 37 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 39 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 428 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 429 " --> pdb=" O THR C 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 50 removed outlier: 6.835A pdb=" N ALA C 60 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 49 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA C 58 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'C' and resid 105 through 109 removed outlier: 4.084A pdb=" N VAL C 117 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN C 127 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AA6, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 332 Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 43 removed outlier: 3.631A pdb=" N ARG A 40 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 27 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR A 109 " --> pdb=" O TRP A 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AB1, first strand: chain 'B' and resid 784 through 786 removed outlier: 8.209A pdb=" N LEU B 785 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL B 735 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR B 732 " --> pdb=" O SER B 808 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 810 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 734 " --> pdb=" O LEU B 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 322 hydrogen bonds defined for protein. 945 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: 1.86 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2456 1.34 - 1.46: 1512 1.46 - 1.58: 3169 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 7167 Sorted by residual: bond pdb=" N GLU A 442 " pdb=" CA GLU A 442 " ideal model delta sigma weight residual 1.456 1.469 -0.013 1.25e-02 6.40e+03 1.12e+00 bond pdb=" CA ASP C 163 " pdb=" CB ASP C 163 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 7.14e-01 bond pdb=" C LYS B 762 " pdb=" N PRO B 763 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.56e-01 bond pdb=" CA THR C 123 " pdb=" CB THR C 123 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.55e-01 bond pdb=" CA SER A 23 " pdb=" C SER A 23 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.10e-02 2.27e+03 5.11e-01 ... (remaining 7162 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 219 107.46 - 114.10: 4141 114.10 - 120.73: 2836 120.73 - 127.36: 2556 127.36 - 134.00: 65 Bond angle restraints: 9817 Sorted by residual: angle pdb=" N ILE A 224 " pdb=" CA ILE A 224 " pdb=" C ILE A 224 " ideal model delta sigma weight residual 111.91 109.33 2.58 8.90e-01 1.26e+00 8.43e+00 angle pdb=" C GLU A 442 " pdb=" CA GLU A 442 " pdb=" CB GLU A 442 " ideal model delta sigma weight residual 109.62 114.66 -5.04 1.79e+00 3.12e-01 7.92e+00 angle pdb=" C LEU C 162 " pdb=" N ASP C 163 " pdb=" CA ASP C 163 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.90e+00 angle pdb=" C THR C 122 " pdb=" N THR C 123 " pdb=" CA THR C 123 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.97e+00 angle pdb=" C MET C 255 " pdb=" N GLN C 256 " pdb=" CA GLN C 256 " ideal model delta sigma weight residual 121.54 125.61 -4.07 1.91e+00 2.74e-01 4.54e+00 ... (remaining 9812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.74: 3825 11.74 - 23.48: 238 23.48 - 35.22: 79 35.22 - 46.96: 22 46.96 - 58.70: 2 Dihedral angle restraints: 4166 sinusoidal: 999 harmonic: 3167 Sorted by residual: dihedral pdb=" CA GLN B 365 " pdb=" C GLN B 365 " pdb=" N HIS B 366 " pdb=" CA HIS B 366 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE B 85 " pdb=" C PHE B 85 " pdb=" N ASP B 86 " pdb=" CA ASP B 86 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA LEU B 711 " pdb=" CB LEU B 711 " pdb=" CG LEU B 711 " pdb=" CD1 LEU B 711 " ideal model delta sinusoidal sigma weight residual 180.00 135.03 44.97 3 1.50e+01 4.44e-03 8.09e+00 ... (remaining 4163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 712 0.028 - 0.056: 330 0.056 - 0.084: 95 0.084 - 0.112: 79 0.112 - 0.140: 10 Chirality restraints: 1226 Sorted by residual: chirality pdb=" CA ASP C 163 " pdb=" N ASP C 163 " pdb=" C ASP C 163 " pdb=" CB ASP C 163 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA VAL C 231 " pdb=" N VAL C 231 " pdb=" C VAL C 231 " pdb=" CB VAL C 231 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE C 402 " pdb=" N ILE C 402 " pdb=" C ILE C 402 " pdb=" CB ILE C 402 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1223 not shown) Planarity restraints: 1294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 466 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 467 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 332 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO C 333 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 182 " -0.016 5.00e-02 4.00e+02 2.44e-02 9.54e-01 pdb=" N PRO C 183 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " -0.014 5.00e-02 4.00e+02 ... (remaining 1291 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1966 2.80 - 3.32: 6433 3.32 - 3.85: 11052 3.85 - 4.37: 11027 4.37 - 4.90: 19623 Nonbonded interactions: 50101 Sorted by model distance: nonbonded pdb=" O LEU B 750 " pdb=" OH TYR B 760 " model vdw 2.273 2.440 nonbonded pdb=" OD1 ASP C 233 " pdb=" OG SER C 235 " model vdw 2.329 2.440 nonbonded pdb=" OD1 ASN C 232 " pdb=" OG1 THR C 290 " model vdw 2.329 2.440 nonbonded pdb=" N GLU C 409 " pdb=" O CYS C 422 " model vdw 2.345 2.520 nonbonded pdb=" O ALA B 706 " pdb=" OG1 THR B 748 " model vdw 2.356 2.440 ... (remaining 50096 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=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: 1.730 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: 0.010 Extract box with map and model: 3.230 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.610 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 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 : 0.002 0.021 7167 Z= 0.106 Angle : 0.471 8.209 9817 Z= 0.237 Chirality : 0.041 0.140 1226 Planarity : 0.003 0.029 1294 Dihedral : 9.643 58.703 2096 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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: -3.58 (0.23), residues: 1050 helix: 0.19 (0.23), residues: 411 sheet: -4.40 (0.39), residues: 76 loop : -4.35 (0.19), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 148 HIS 0.002 0.000 HIS C 404 PHE 0.008 0.001 PHE B 372 TYR 0.004 0.000 TYR B 99 ARG 0.001 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 LYS cc_start: 0.6796 (tppt) cc_final: 0.6446 (tppt) REVERT: C 211 ASP cc_start: 0.4780 (m-30) cc_final: 0.3466 (m-30) REVERT: A 385 PHE cc_start: 0.4738 (m-10) cc_final: 0.4289 (m-80) REVERT: A 417 GLU cc_start: 0.5917 (mm-30) cc_final: 0.5697 (mm-30) REVERT: A 479 MET cc_start: 0.8090 (mmt) cc_final: 0.7830 (mpp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1816 time to fit residues: 36.2848 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.0770 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN C 328 HIS B 337 GLN B 356 GLN B 708 GLN B 721 HIS B 848 GLN B 903 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7167 Z= 0.178 Angle : 0.536 8.371 9817 Z= 0.268 Chirality : 0.043 0.145 1226 Planarity : 0.004 0.068 1294 Dihedral : 2.936 14.943 1110 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.65 % Allowed : 17.31 % Favored : 80.04 % 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: -2.47 (0.25), residues: 1050 helix: 1.61 (0.26), residues: 411 sheet: -3.89 (0.37), residues: 98 loop : -4.10 (0.21), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 148 HIS 0.008 0.001 HIS C 417 PHE 0.024 0.002 PHE B 345 TYR 0.024 0.002 TYR C 413 ARG 0.007 0.001 ARG B 926 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: C 40 LYS cc_start: 0.7216 (tppt) cc_final: 0.6670 (tppt) REVERT: A 385 PHE cc_start: 0.4570 (m-10) cc_final: 0.4308 (m-80) REVERT: A 417 GLU cc_start: 0.6268 (mm-30) cc_final: 0.5960 (mm-30) outliers start: 13 outliers final: 8 residues processed: 109 average time/residue: 0.1847 time to fit residues: 27.3288 Evaluate side-chains 91 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 380 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.0000 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 2.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS B 343 HIS B 868 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7167 Z= 0.351 Angle : 0.721 7.026 9817 Z= 0.381 Chirality : 0.047 0.167 1226 Planarity : 0.006 0.083 1294 Dihedral : 5.062 24.972 1110 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 5.91 % Allowed : 18.94 % Favored : 75.15 % 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: -2.63 (0.26), residues: 1050 helix: 1.26 (0.26), residues: 411 sheet: -3.80 (0.37), residues: 123 loop : -3.98 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 431 HIS 0.010 0.002 HIS B 846 PHE 0.028 0.003 PHE B 345 TYR 0.030 0.003 TYR A 124 ARG 0.005 0.001 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: C 292 ASP cc_start: 0.7328 (p0) cc_final: 0.7126 (p0) REVERT: C 322 HIS cc_start: 0.4466 (OUTLIER) cc_final: 0.3433 (m90) REVERT: A 61 PHE cc_start: 0.8829 (t80) cc_final: 0.8516 (t80) REVERT: A 417 GLU cc_start: 0.6320 (mm-30) cc_final: 0.6043 (mm-30) REVERT: B 911 LEU cc_start: 0.9282 (mt) cc_final: 0.8860 (mt) outliers start: 29 outliers final: 17 residues processed: 122 average time/residue: 0.1729 time to fit residues: 28.8719 Evaluate side-chains 98 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 901 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS B 848 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7167 Z= 0.301 Angle : 0.661 9.311 9817 Z= 0.348 Chirality : 0.045 0.165 1226 Planarity : 0.004 0.068 1294 Dihedral : 4.667 21.794 1110 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 6.11 % Allowed : 24.03 % Favored : 69.86 % 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: -2.47 (0.26), residues: 1050 helix: 1.42 (0.27), residues: 411 sheet: -3.64 (0.41), residues: 121 loop : -3.95 (0.23), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 148 HIS 0.022 0.002 HIS A 65 PHE 0.025 0.002 PHE B 345 TYR 0.014 0.002 TYR A 124 ARG 0.004 0.001 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: C 40 LYS cc_start: 0.7587 (tppp) cc_final: 0.7281 (tppt) REVERT: C 302 ARG cc_start: 0.5826 (tpt90) cc_final: 0.5598 (tpt90) REVERT: C 322 HIS cc_start: 0.5090 (OUTLIER) cc_final: 0.3707 (m90) REVERT: A 417 GLU cc_start: 0.6394 (mm-30) cc_final: 0.6093 (mm-30) REVERT: B 850 MET cc_start: 0.8035 (mpp) cc_final: 0.7610 (mpp) outliers start: 30 outliers final: 15 residues processed: 105 average time/residue: 0.1640 time to fit residues: 24.0699 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 901 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.0170 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 94 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7167 Z= 0.157 Angle : 0.581 9.569 9817 Z= 0.292 Chirality : 0.043 0.148 1226 Planarity : 0.004 0.070 1294 Dihedral : 3.847 16.205 1110 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 3.87 % Allowed : 27.70 % Favored : 68.43 % 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: -1.99 (0.27), residues: 1050 helix: 2.03 (0.27), residues: 415 sheet: -3.98 (0.38), residues: 110 loop : -3.77 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 148 HIS 0.003 0.001 HIS C 404 PHE 0.026 0.002 PHE B 345 TYR 0.011 0.001 TYR B 725 ARG 0.005 0.001 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: C 40 LYS cc_start: 0.7485 (tppp) cc_final: 0.7233 (tppt) REVERT: C 137 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7766 (mmtm) REVERT: A 97 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8566 (mp) REVERT: A 417 GLU cc_start: 0.6165 (mm-30) cc_final: 0.5872 (mm-30) REVERT: B 850 MET cc_start: 0.8057 (mpp) cc_final: 0.7676 (mpp) outliers start: 19 outliers final: 10 residues processed: 109 average time/residue: 0.1610 time to fit residues: 24.7917 Evaluate side-chains 92 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 735 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 57.4726 > 50: distance: 50 - 120: 24.768 distance: 53 - 117: 11.415 distance: 66 - 103: 14.375 distance: 68 - 74: 29.491 distance: 69 - 100: 25.876 distance: 74 - 75: 51.073 distance: 74 - 80: 6.427 distance: 75 - 78: 39.198 distance: 76 - 77: 9.126 distance: 76 - 81: 39.882 distance: 78 - 79: 3.756 distance: 79 - 80: 21.713 distance: 81 - 82: 31.313 distance: 82 - 83: 23.698 distance: 82 - 85: 16.783 distance: 83 - 84: 25.267 distance: 83 - 89: 20.455 distance: 85 - 86: 15.436 distance: 86 - 88: 22.235 distance: 89 - 90: 30.465 distance: 90 - 91: 11.374 distance: 90 - 93: 15.293 distance: 91 - 100: 7.644 distance: 93 - 94: 3.936 distance: 94 - 95: 15.612 distance: 95 - 96: 14.821 distance: 96 - 97: 17.911 distance: 97 - 98: 12.490 distance: 97 - 99: 17.200 distance: 100 - 101: 8.251 distance: 101 - 102: 10.659 distance: 101 - 104: 10.156 distance: 102 - 103: 12.016 distance: 104 - 105: 10.717 distance: 105 - 106: 8.663 distance: 106 - 107: 12.255 distance: 106 - 108: 19.416 distance: 109 - 110: 11.700 distance: 109 - 189: 11.802 distance: 110 - 111: 8.958 distance: 110 - 113: 13.188 distance: 111 - 112: 7.084 distance: 111 - 117: 9.116 distance: 112 - 186: 19.153 distance: 113 - 114: 10.920 distance: 114 - 115: 18.003 distance: 114 - 116: 13.626 distance: 117 - 118: 11.681 distance: 118 - 119: 5.978 distance: 118 - 121: 8.577 distance: 119 - 120: 18.207 distance: 119 - 125: 7.106 distance: 121 - 122: 18.328 distance: 121 - 123: 8.649 distance: 122 - 124: 17.592 distance: 126 - 127: 10.323 distance: 126 - 129: 6.281 distance: 127 - 128: 15.685 distance: 127 - 131: 8.456 distance: 129 - 130: 24.596 distance: 131 - 132: 8.501 distance: 132 - 133: 11.183 distance: 132 - 135: 4.595 distance: 133 - 134: 12.560 distance: 133 - 137: 20.491 distance: 135 - 136: 32.118 distance: 137 - 138: 13.538 distance: 138 - 139: 9.276 distance: 138 - 141: 6.060 distance: 139 - 140: 7.464 distance: 139 - 143: 21.497 distance: 141 - 142: 36.259 distance: 143 - 144: 3.519 distance: 144 - 145: 12.518 distance: 144 - 147: 20.497 distance: 145 - 146: 27.928 distance: 145 - 152: 9.682 distance: 147 - 148: 23.734 distance: 148 - 149: 17.977 distance: 149 - 150: 37.934 distance: 149 - 151: 28.473