Starting phenix.real_space_refine on Fri Dec 8 17:21:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2023/6pw9_20501_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2023/6pw9_20501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2023/6pw9_20501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2023/6pw9_20501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2023/6pw9_20501_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw9_20501/12_2023/6pw9_20501_updated.pdb" } resolution = 4.03 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 ------------------------------------------------------------------------------- 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= 0.005 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 P 9 5.49 5 S 56 5.16 5 C 5597 2.51 5 N 1508 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 513": "NH1" <-> "NH2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 740": "NH1" <-> "NH2" Residue "B ARG 757": "NH1" <-> "NH2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 825": "NH1" <-> "NH2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8836 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1260 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5470 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 27, 'TRANS': 637} Chain breaks: 1 Chain: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1287 Unusual residues: {'ACE': 1} Classifications: {'peptide': 160, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'ACE_C-N': 1, 'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 732 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 94} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'ACO': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.16, per 1000 atoms: 0.58 Number of scatterers: 8836 At special positions: 0 Unit cell: (114.562, 100.534, 106.379, 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 56 16.00 P 9 15.00 O 1666 8.00 N 1508 7.00 C 5597 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: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 3 sheets defined 57.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 165 through 175 removed outlier: 4.139A pdb=" N LYS B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.824A pdb=" N ILE B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 296 through 300 removed outlier: 4.066A pdb=" N PHE B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 319 removed outlier: 3.627A pdb=" N LYS B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 331 removed outlier: 4.043A pdb=" N PHE B 326 " --> pdb=" O PRO B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 356 removed outlier: 4.479A pdb=" N SER B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 390 through 403 removed outlier: 4.276A pdb=" N THR B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 420 removed outlier: 3.866A pdb=" N TYR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.806A pdb=" N GLU B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'B' and resid 502 through 524 removed outlier: 5.415A pdb=" N GLN B 522 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASP B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 536 through 546 Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 552 through 570 removed outlier: 4.124A pdb=" N ILE B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 647 No H-bonds generated for 'chain 'B' and resid 644 through 647' Processing helix chain 'B' and resid 654 through 667 Proline residue: B 663 - end of helix Processing helix chain 'B' and resid 672 through 682 Processing helix chain 'B' and resid 688 through 699 Processing helix chain 'B' and resid 706 through 721 Processing helix chain 'B' and resid 728 through 741 removed outlier: 3.732A pdb=" N THR B 732 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 733 " --> pdb=" O THR B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 757 Processing helix chain 'B' and resid 762 through 774 removed outlier: 3.797A pdb=" N MET B 771 " --> pdb=" O SER B 767 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 786 removed outlier: 3.529A pdb=" N GLN B 780 " --> pdb=" O PRO B 777 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 784 " --> pdb=" O LYS B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 810 Processing helix chain 'B' and resid 821 through 831 removed outlier: 3.824A pdb=" N LYS B 830 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 831 " --> pdb=" O ASN B 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 removed outlier: 4.068A pdb=" N MET C 12 " --> pdb=" O PRO C 8 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N HIS C 16 " --> pdb=" O MET C 12 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 34 Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'D' and resid 61 through 84 removed outlier: 3.961A pdb=" N VAL D 66 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'D' and resid 121 through 128 Processing sheet with id= A, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.222A pdb=" N PHE A 51 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG A 62 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE A 74 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP A 64 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU A 72 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N SER A 66 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LYS A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASN A 108 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE A 74 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR A 110 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR A 76 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N HIS A 112 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N GLY A 78 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 15.201A pdb=" N GLN A 114 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 133 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN A 151 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE A 131 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.362A pdb=" N LYS C 59 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE C 72 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU C 61 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLY C 70 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 106 through 112 removed outlier: 3.685A pdb=" N GLU C 132 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS C 148 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE C 130 " --> pdb=" O LYS C 148 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1191 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: 2.72 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1481 1.30 - 1.43: 2253 1.43 - 1.56: 5168 1.56 - 1.69: 15 1.69 - 1.82: 91 Bond restraints: 9008 Sorted by residual: bond pdb=" C1B ACO C 902 " pdb=" O4B ACO C 902 " ideal model delta sigma weight residual 1.416 1.660 -0.244 1.40e-02 5.10e+03 3.05e+02 bond pdb=" C1B ACO C 902 " pdb=" C2B ACO C 902 " ideal model delta sigma weight residual 1.531 1.345 0.186 1.20e-02 6.94e+03 2.39e+02 bond pdb=" C5P ACO C 902 " pdb=" N4P ACO C 902 " ideal model delta sigma weight residual 1.331 1.498 -0.167 1.20e-02 6.94e+03 1.93e+02 bond pdb=" C6A ACO C 902 " pdb=" N6A ACO C 902 " ideal model delta sigma weight residual 1.337 1.463 -0.126 1.00e-02 1.00e+04 1.58e+02 bond pdb=" O3A ACO C 902 " pdb=" P2A ACO C 902 " ideal model delta sigma weight residual 1.592 1.723 -0.131 1.10e-02 8.26e+03 1.43e+02 ... (remaining 9003 not shown) Histogram of bond angle deviations from ideal: 98.77 - 106.01: 176 106.01 - 113.25: 4703 113.25 - 120.49: 4160 120.49 - 127.73: 3058 127.73 - 134.97: 63 Bond angle restraints: 12160 Sorted by residual: angle pdb=" P1A ACO C 902 " pdb=" O3A ACO C 902 " pdb=" P2A ACO C 902 " ideal model delta sigma weight residual 136.83 121.67 15.16 1.00e+00 1.00e+00 2.30e+02 angle pdb=" N1A ACO C 902 " pdb=" C6A ACO C 902 " pdb=" N6A ACO C 902 " ideal model delta sigma weight residual 118.11 104.50 13.61 1.23e+00 6.64e-01 1.23e+02 angle pdb=" C5A ACO C 902 " pdb=" C6A ACO C 902 " pdb=" N6A ACO C 902 " ideal model delta sigma weight residual 123.59 134.97 -11.38 1.08e+00 8.64e-01 1.12e+02 angle pdb=" N1A ACO C 902 " pdb=" C2A ACO C 902 " pdb=" N3A ACO C 902 " ideal model delta sigma weight residual 128.69 119.33 9.36 1.00e+00 1.00e+00 8.76e+01 angle pdb=" C5A ACO C 902 " pdb=" C4A ACO C 902 " pdb=" N3A ACO C 902 " ideal model delta sigma weight residual 126.80 118.30 8.50 1.00e+00 1.00e+00 7.22e+01 ... (remaining 12155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.35: 5284 26.35 - 52.71: 272 52.71 - 79.06: 21 79.06 - 105.41: 3 105.41 - 131.77: 7 Dihedral angle restraints: 5587 sinusoidal: 2384 harmonic: 3203 Sorted by residual: dihedral pdb=" CA LYS B 500 " pdb=" C LYS B 500 " pdb=" N PHE B 501 " pdb=" CA PHE B 501 " ideal model delta harmonic sigma weight residual -180.00 -150.02 -29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL B 185 " pdb=" C VAL B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual -180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA PHE C 102 " pdb=" C PHE C 102 " pdb=" N ASN C 103 " pdb=" CA ASN C 103 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.011: 1324 1.011 - 2.022: 0 2.022 - 3.034: 0 3.034 - 4.045: 0 4.045 - 5.056: 3 Chirality restraints: 1327 Sorted by residual: chirality pdb=" C4 IHP C 901 " pdb=" C3 IHP C 901 " pdb=" C5 IHP C 901 " pdb=" O14 IHP C 901 " both_signs ideal model delta sigma weight residual False 2.48 -2.58 5.06 2.00e-01 2.50e+01 6.39e+02 chirality pdb=" C2 IHP C 901 " pdb=" C1 IHP C 901 " pdb=" C3 IHP C 901 " pdb=" O12 IHP C 901 " both_signs ideal model delta sigma weight residual False -2.52 2.50 -5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C1 IHP C 901 " pdb=" C2 IHP C 901 " pdb=" C6 IHP C 901 " pdb=" O11 IHP C 901 " both_signs ideal model delta sigma weight residual False 2.32 -2.48 4.80 2.00e-01 2.50e+01 5.75e+02 ... (remaining 1324 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 143 " -0.100 5.00e-02 4.00e+02 1.49e-01 3.56e+01 pdb=" N PRO A 144 " 0.258 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 707 " -0.020 2.00e-02 2.50e+03 1.73e-02 7.45e+00 pdb=" CG TRP B 707 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 707 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 707 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 707 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 707 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 707 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 565 " 0.015 2.00e-02 2.50e+03 1.74e-02 6.08e+00 pdb=" CG TYR B 565 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR B 565 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 565 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 565 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 565 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 565 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 565 " 0.001 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 15 2.40 - 3.03: 4199 3.03 - 3.65: 13982 3.65 - 4.28: 19123 4.28 - 4.90: 30446 Nonbonded interactions: 67765 Sorted by model distance: nonbonded pdb=" O PRO A 13 " pdb=" CD1 ILE A 16 " model vdw 1.781 3.460 nonbonded pdb=" OE2 GLU B 191 " pdb=" O ILE B 533 " model vdw 1.914 3.040 nonbonded pdb=" O GLU A 143 " pdb=" OE1 GLU A 143 " model vdw 1.918 3.040 nonbonded pdb=" CE2 TYR B 528 " pdb=" CE LYS B 532 " model vdw 2.180 3.740 nonbonded pdb=" O ILE B 784 " pdb=" OG1 THR B 788 " model vdw 2.260 2.440 ... (remaining 67760 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: 0.640 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: 2.300 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.300 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 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 0.244 9008 Z= 0.520 Angle : 1.225 15.157 12160 Z= 0.667 Chirality : 0.244 5.056 1327 Planarity : 0.008 0.149 1549 Dihedral : 15.091 131.767 3509 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.81 % Allowed : 8.18 % Favored : 90.01 % 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: -4.47 (0.20), residues: 1065 helix: -2.86 (0.15), residues: 637 sheet: -2.24 (0.57), residues: 71 loop : -2.92 (0.27), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 707 HIS 0.007 0.002 HIS A 148 PHE 0.030 0.003 PHE B 716 TYR 0.042 0.003 TYR B 565 ARG 0.007 0.001 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 302 time to evaluate : 1.072 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: 17 outliers final: 5 residues processed: 316 average time/residue: 0.2581 time to fit residues: 106.4045 Evaluate side-chains 186 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 181 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1521 time to fit residues: 2.5468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 65 HIS A 114 GLN A 148 HIS A 151 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 197 ASN B 212 HIS B 383 HIS ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS C 120 HIS D 116 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9008 Z= 0.176 Angle : 0.730 9.534 12160 Z= 0.361 Chirality : 0.046 0.315 1327 Planarity : 0.005 0.064 1549 Dihedral : 10.322 61.630 1281 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.74 % Allowed : 5.74 % Favored : 93.52 % 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: -2.80 (0.23), residues: 1065 helix: -1.45 (0.19), residues: 642 sheet: -2.08 (0.58), residues: 62 loop : -2.29 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 707 HIS 0.008 0.001 HIS B 526 PHE 0.017 0.002 PHE B 716 TYR 0.015 0.002 TYR B 528 ARG 0.005 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 252 time to evaluate : 1.184 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: 7 outliers final: 2 residues processed: 257 average time/residue: 0.2375 time to fit residues: 82.2326 Evaluate side-chains 185 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0864 time to fit residues: 1.6647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 509 HIS B 736 GLN ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9008 Z= 0.200 Angle : 0.705 8.804 12160 Z= 0.353 Chirality : 0.046 0.224 1327 Planarity : 0.004 0.040 1549 Dihedral : 9.561 58.862 1281 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.21 % Allowed : 5.10 % Favored : 94.69 % 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: -2.19 (0.24), residues: 1065 helix: -0.94 (0.20), residues: 643 sheet: -1.76 (0.62), residues: 67 loop : -2.11 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 707 HIS 0.006 0.001 HIS B 526 PHE 0.026 0.002 PHE B 515 TYR 0.021 0.002 TYR B 154 ARG 0.006 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 1.177 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 outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 0.2224 time to fit residues: 73.8339 Evaluate side-chains 187 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0832 time to fit residues: 1.6219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 114 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 9008 Z= 0.447 Angle : 0.954 11.086 12160 Z= 0.497 Chirality : 0.056 0.310 1327 Planarity : 0.006 0.059 1549 Dihedral : 9.993 56.100 1281 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.32 % Allowed : 6.27 % Favored : 93.41 % 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: -2.42 (0.23), residues: 1065 helix: -1.19 (0.19), residues: 640 sheet: -1.02 (0.85), residues: 36 loop : -2.20 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 707 HIS 0.007 0.002 HIS B 212 PHE 0.034 0.004 PHE B 838 TYR 0.019 0.003 TYR B 379 ARG 0.009 0.001 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 227 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 229 average time/residue: 0.2299 time to fit residues: 71.1949 Evaluate side-chains 170 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9008 Z= 0.190 Angle : 0.732 9.306 12160 Z= 0.363 Chirality : 0.046 0.232 1327 Planarity : 0.004 0.056 1549 Dihedral : 9.356 60.285 1281 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % 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: -1.81 (0.25), residues: 1065 helix: -0.65 (0.20), residues: 642 sheet: -1.22 (0.77), residues: 48 loop : -2.02 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 486 HIS 0.013 0.001 HIS B 551 PHE 0.027 0.002 PHE B 716 TYR 0.026 0.002 TYR C 122 ARG 0.008 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.067 Fit side-chains 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: 237 average time/residue: 0.2200 time to fit residues: 71.3063 Evaluate side-chains 180 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 71 HIS C 110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9008 Z= 0.325 Angle : 0.819 8.703 12160 Z= 0.420 Chirality : 0.051 0.278 1327 Planarity : 0.005 0.039 1549 Dihedral : 9.529 59.716 1281 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: -1.81 (0.25), residues: 1065 helix: -0.66 (0.20), residues: 642 sheet: -1.72 (0.69), residues: 58 loop : -1.89 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP B 151 HIS 0.009 0.002 HIS B 551 PHE 0.043 0.003 PHE B 174 TYR 0.021 0.002 TYR B 495 ARG 0.009 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.018 Fit side-chains 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: 231 average time/residue: 0.2346 time to fit residues: 73.3244 Evaluate side-chains 173 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.0570 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9008 Z= 0.186 Angle : 0.731 8.503 12160 Z= 0.365 Chirality : 0.046 0.230 1327 Planarity : 0.004 0.042 1549 Dihedral : 9.065 62.422 1281 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: -1.38 (0.25), residues: 1065 helix: -0.31 (0.20), residues: 637 sheet: -1.23 (0.77), residues: 48 loop : -1.79 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 486 HIS 0.008 0.001 HIS B 551 PHE 0.031 0.002 PHE B 174 TYR 0.018 0.001 TYR B 158 ARG 0.009 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2316 time to fit residues: 73.5841 Evaluate side-chains 179 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 64 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 89 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9008 Z= 0.179 Angle : 0.727 8.822 12160 Z= 0.361 Chirality : 0.046 0.226 1327 Planarity : 0.004 0.046 1549 Dihedral : 8.737 60.855 1281 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.13 (0.25), residues: 1065 helix: -0.09 (0.20), residues: 639 sheet: -1.09 (0.79), residues: 48 loop : -1.72 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 486 HIS 0.007 0.001 HIS B 551 PHE 0.031 0.002 PHE B 174 TYR 0.025 0.002 TYR B 154 ARG 0.008 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2185 time to fit residues: 68.7832 Evaluate side-chains 182 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 52 ASN B 124 GLN ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9008 Z= 0.213 Angle : 0.752 9.111 12160 Z= 0.375 Chirality : 0.047 0.232 1327 Planarity : 0.004 0.043 1549 Dihedral : 8.565 60.496 1281 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.04 (0.25), residues: 1065 helix: -0.01 (0.20), residues: 631 sheet: -1.51 (0.68), residues: 58 loop : -1.60 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 486 HIS 0.008 0.001 HIS B 551 PHE 0.028 0.002 PHE B 174 TYR 0.018 0.002 TYR B 154 ARG 0.008 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2109 time to fit residues: 65.5503 Evaluate side-chains 174 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0370 chunk 47 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 89 optimal weight: 0.0170 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN B 159 HIS B 478 ASN B 526 HIS ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN C 71 HIS C 81 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9008 Z= 0.174 Angle : 0.741 10.139 12160 Z= 0.365 Chirality : 0.046 0.237 1327 Planarity : 0.004 0.046 1549 Dihedral : 8.319 62.980 1281 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.88 (0.26), residues: 1065 helix: 0.06 (0.21), residues: 634 sheet: -0.98 (0.78), residues: 48 loop : -1.52 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 38 HIS 0.015 0.001 HIS D 116 PHE 0.027 0.001 PHE B 174 TYR 0.022 0.001 TYR B 154 ARG 0.012 0.001 ARG D 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2120 time to fit residues: 69.1488 Evaluate side-chains 187 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 60.4189 > 50: distance: 36 - 56: 5.046 distance: 40 - 62: 6.127 distance: 46 - 71: 5.981 distance: 51 - 80: 18.932 distance: 57 - 58: 4.753 distance: 57 - 60: 13.275 distance: 58 - 59: 14.704 distance: 58 - 62: 7.176 distance: 60 - 61: 10.542 distance: 62 - 63: 7.237 distance: 63 - 64: 5.144 distance: 63 - 66: 8.197 distance: 64 - 65: 23.924 distance: 66 - 67: 19.681 distance: 67 - 68: 30.999 distance: 68 - 69: 6.450 distance: 68 - 70: 8.268 distance: 71 - 72: 3.615 distance: 72 - 73: 6.774 distance: 72 - 75: 8.722 distance: 73 - 74: 6.656 distance: 73 - 80: 16.854 distance: 75 - 76: 14.832 distance: 76 - 77: 13.650 distance: 77 - 78: 20.581 distance: 78 - 79: 21.107 distance: 80 - 81: 16.861 distance: 81 - 82: 15.223 distance: 81 - 84: 29.098 distance: 82 - 83: 14.518 distance: 82 - 88: 16.252 distance: 84 - 85: 19.718 distance: 85 - 86: 9.255 distance: 85 - 87: 10.521 distance: 88 - 89: 7.232 distance: 89 - 90: 20.655 distance: 90 - 91: 21.252 distance: 90 - 92: 24.303 distance: 92 - 93: 30.631 distance: 93 - 94: 10.185 distance: 93 - 96: 13.291 distance: 94 - 95: 14.931 distance: 94 - 99: 35.810 distance: 96 - 97: 14.507 distance: 96 - 98: 20.012 distance: 99 - 100: 21.595 distance: 100 - 101: 7.512 distance: 100 - 103: 25.162 distance: 101 - 102: 25.661 distance: 101 - 110: 35.413 distance: 103 - 104: 5.015 distance: 104 - 105: 29.503 distance: 104 - 106: 10.200 distance: 105 - 107: 12.314 distance: 106 - 108: 10.194 distance: 107 - 109: 10.888 distance: 108 - 109: 23.982 distance: 110 - 111: 36.076 distance: 111 - 112: 45.587 distance: 111 - 114: 20.818 distance: 112 - 113: 27.279 distance: 112 - 118: 8.678 distance: 114 - 115: 13.316 distance: 115 - 116: 37.612 distance: 115 - 117: 12.001 distance: 118 - 119: 37.332 distance: 119 - 120: 24.006 distance: 119 - 122: 15.476 distance: 120 - 121: 29.170 distance: 120 - 126: 32.981 distance: 122 - 123: 23.149 distance: 123 - 124: 24.657 distance: 123 - 125: 3.584 distance: 126 - 127: 24.893 distance: 126 - 160: 13.374 distance: 127 - 128: 18.784 distance: 127 - 130: 14.045 distance: 128 - 129: 9.825 distance: 128 - 134: 25.197 distance: 129 - 157: 20.237 distance: 130 - 131: 11.891 distance: 130 - 132: 5.195 distance: 131 - 133: 5.637