Starting phenix.real_space_refine on Sat Dec 28 10:02:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2x_27153/12_2024/8d2x_27153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2x_27153/12_2024/8d2x_27153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2x_27153/12_2024/8d2x_27153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2x_27153/12_2024/8d2x_27153.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2x_27153/12_2024/8d2x_27153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2x_27153/12_2024/8d2x_27153.cif" } resolution = 3.4 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= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1611 atoms to isotropic. 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 33 5.16 5 C 4465 2.51 5 N 1027 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6813 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3404 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 Conformer: "B" Number of residues, atoms: 460, 3404 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 bond proxies already assigned to first conformer: 3449 Chain: "B" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1401 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 1416 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1405 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 203, 1405 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1433 Chain: "A" Number of atoms: 551 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 481 Unusual residues: {'LMT': 13, 'ZGS': 1} Classifications: {'undetermined': 14, 'water': 4} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 18, 481 Unusual residues: {'LMT': 13, 'ZGS': 1} Classifications: {'undetermined': 14, 'water': 4} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 417 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AARG A 84 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 84 " occ=0.50 residue: pdb=" N AMET A 181 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 181 " occ=0.50 residue: pdb=" N APHE A 396 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 396 " occ=0.50 residue: pdb=" N APHE A 449 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 449 " occ=0.50 residue: pdb=" N AARG C 13 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 13 " occ=0.50 residue: pdb=" C1 ALMT A 604 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 604 " occ=0.50 residue: pdb=" C1 ALMT A 613 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 613 " occ=0.50 Time building chain proxies: 7.93, per 1000 atoms: 1.16 Number of scatterers: 6813 At special positions: 0 Unit cell: (70.896, 72.584, 141.792, 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 33 16.00 O 1288 8.00 N 1027 7.00 C 4465 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.02 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.11 Conformation dependent library (CDL) restraints added in 1.4 seconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 11 sheets defined 46.8% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.658A pdb=" N GLY A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.997A pdb=" N GLN A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 72 through 100 removed outlier: 3.654A pdb=" N ASP A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 88 " --> pdb=" O AARG A 84 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 109 through 128 Proline residue: A 118 - end of helix removed outlier: 3.519A pdb=" N LEU A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 167 removed outlier: 3.699A pdb=" N TRP A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Proline residue: A 158 - end of helix removed outlier: 3.527A pdb=" N ALA A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 202 removed outlier: 3.904A pdb=" N ALA A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 232 through 262 Processing helix chain 'A' and resid 277 through 288 removed outlier: 3.521A pdb=" N HIS A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 311 Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.537A pdb=" N VAL A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.089A pdb=" N THR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 removed outlier: 4.333A pdb=" N PHE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 414 Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 419 through 451 Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.663A pdb=" N LEU A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.594A pdb=" N SER A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.939A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'C' and resid 28 through 31 Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 12 removed outlier: 5.942A pdb=" N LYS B 11 " --> pdb=" O ASN B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 22 Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.419A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR B 48 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 32 " --> pdb=" O TYR B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.896A pdb=" N ALA B 127 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE B 174 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL B 129 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU B 172 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N PHE B 131 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 170 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N MET B 168 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 140 through 144 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.544A pdb=" N ALA C 77 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 5.203A pdb=" N TRP C 46 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE C 38 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP C 33 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.867A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.867A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 184 through 187 removed outlier: 4.726A pdb=" N ALA C 184 " --> pdb=" O VAL C 200 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1087 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: 2.02 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 990 1.31 - 1.44: 1961 1.44 - 1.56: 3948 1.56 - 1.69: 55 1.69 - 1.81: 46 Bond restraints: 7000 Sorted by residual: bond pdb=" C1B LMT A 612 " pdb=" O5B LMT A 612 " ideal model delta sigma weight residual 1.393 1.523 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C1B LMT A 610 " pdb=" O5B LMT A 610 " ideal model delta sigma weight residual 1.393 1.521 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C1B LMT A 608 " pdb=" O5B LMT A 608 " ideal model delta sigma weight residual 1.393 1.520 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C1BALMT A 613 " pdb=" O5BALMT A 613 " ideal model delta sigma weight residual 1.393 1.518 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C1B LMT A 609 " pdb=" O5B LMT A 609 " ideal model delta sigma weight residual 1.393 1.517 -0.124 2.00e-02 2.50e+03 3.83e+01 ... (remaining 6995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.99: 9337 4.99 - 9.98: 204 9.98 - 14.96: 0 14.96 - 19.95: 4 19.95 - 24.94: 3 Bond angle restraints: 9548 Sorted by residual: angle pdb=" C09 ZGS A 601 " pdb=" C10 ZGS A 601 " pdb=" C11 ZGS A 601 " ideal model delta sigma weight residual 127.16 152.10 -24.94 3.00e+00 1.11e-01 6.91e+01 angle pdb=" C06 ZGS A 601 " pdb=" C07 ZGS A 601 " pdb=" C08 ZGS A 601 " ideal model delta sigma weight residual 127.52 152.20 -24.68 3.00e+00 1.11e-01 6.77e+01 angle pdb=" C03 ZGS A 601 " pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " ideal model delta sigma weight residual 127.34 151.48 -24.14 3.00e+00 1.11e-01 6.47e+01 angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 110.70 130.46 -19.76 3.00e+00 1.11e-01 4.34e+01 angle pdb=" C02 ZGS A 601 " pdb=" C03 ZGS A 601 " pdb=" C04 ZGS A 601 " ideal model delta sigma weight residual 127.67 110.53 17.14 3.00e+00 1.11e-01 3.26e+01 ... (remaining 9543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.22: 4009 23.22 - 46.44: 286 46.44 - 69.66: 111 69.66 - 92.88: 72 92.88 - 116.10: 135 Dihedral angle restraints: 4613 sinusoidal: 2141 harmonic: 2472 Sorted by residual: dihedral pdb=" C1' LMT A 608 " pdb=" C2' LMT A 608 " pdb=" C3' LMT A 608 " pdb=" O3' LMT A 608 " ideal model delta sinusoidal sigma weight residual -176.68 -60.58 -116.10 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C2B LMT A 611 " pdb=" C1B LMT A 611 " pdb=" O5B LMT A 611 " pdb=" C5B LMT A 611 " ideal model delta sinusoidal sigma weight residual -57.12 58.43 -115.55 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C5B LMT A 611 " pdb=" C1B LMT A 611 " pdb=" O5B LMT A 611 " pdb=" O1B LMT A 611 " ideal model delta sinusoidal sigma weight residual -64.39 -179.76 115.37 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 4610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 837 0.053 - 0.107: 230 0.107 - 0.160: 73 0.160 - 0.213: 7 0.213 - 0.266: 8 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C1B LMT A 605 " pdb=" C2B LMT A 605 " pdb=" O1B LMT A 605 " pdb=" O5B LMT A 605 " both_signs ideal model delta sigma weight residual False -2.20 -2.47 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C4' LMT A 614 " pdb=" C3' LMT A 614 " pdb=" C5' LMT A 614 " pdb=" O1B LMT A 614 " both_signs ideal model delta sigma weight residual False -2.55 -2.29 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1B LMT A 607 " pdb=" C2B LMT A 607 " pdb=" O1B LMT A 607 " pdb=" O5B LMT A 607 " both_signs ideal model delta sigma weight residual False -2.20 -2.45 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1152 not shown) Planarity restraints: 1135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 204 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C ALA A 204 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA A 204 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO A 205 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO C 47 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 75 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO B 76 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.029 5.00e-02 4.00e+02 ... (remaining 1132 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1540 2.79 - 3.32: 5980 3.32 - 3.84: 11561 3.84 - 4.37: 12568 4.37 - 4.90: 22716 Nonbonded interactions: 54365 Sorted by model distance: nonbonded pdb=" O TYR A 43 " pdb=" OH TYR A 159 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR A 53 " pdb=" OE1 GLN A 152 " model vdw 2.297 3.040 nonbonded pdb=" OD1 ASP A 67 " pdb=" OH TYR A 452 " model vdw 2.308 3.040 nonbonded pdb=" O SER B 30 " pdb=" OG SER B 30 " model vdw 2.343 3.040 nonbonded pdb=" O THR A 381 " pdb=" OG SER A 385 " model vdw 2.344 3.040 ... (remaining 54360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 24.820 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.012 0.130 7000 Z= 0.794 Angle : 1.402 24.938 9548 Z= 0.568 Chirality : 0.057 0.266 1155 Planarity : 0.007 0.054 1135 Dihedral : 30.539 116.099 3027 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.66 % Favored : 93.22 % Rotamer: Outliers : 0.34 % Allowed : 6.42 % Favored : 93.24 % 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: -1.77 (0.26), residues: 871 helix: 0.18 (0.24), residues: 390 sheet: -0.79 (0.40), residues: 162 loop : -3.13 (0.28), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 106 HIS 0.002 0.001 HIS A 156 PHE 0.021 0.002 PHE B 89 TYR 0.016 0.001 TYR B 48 ARG 0.002 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.663 Fit side-chains REVERT: A 70 LEU cc_start: 0.8582 (mt) cc_final: 0.8381 (mt) REVERT: A 134 ASP cc_start: 0.7768 (m-30) cc_final: 0.7261 (p0) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1884 time to fit residues: 39.1966 Evaluate side-chains 117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 50.0000 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 23 ASN C 39 GLN C 57 GLN C 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7000 Z= 0.244 Angle : 0.912 9.635 9548 Z= 0.385 Chirality : 0.055 0.554 1155 Planarity : 0.005 0.055 1135 Dihedral : 17.883 70.014 1851 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.38 % Allowed : 13.18 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.28), residues: 871 helix: 1.34 (0.25), residues: 382 sheet: -0.63 (0.42), residues: 162 loop : -2.95 (0.29), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 103 HIS 0.008 0.002 HIS A 288 PHE 0.014 0.002 PHE A 367 TYR 0.014 0.001 TYR A 251 ARG 0.005 0.001 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8685 (mt) cc_final: 0.8453 (mt) REVERT: A 134 ASP cc_start: 0.7799 (m-30) cc_final: 0.7282 (p0) REVERT: A 291 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6177 (t80) REVERT: C 190 PHE cc_start: 0.7859 (t80) cc_final: 0.7349 (t80) outliers start: 19 outliers final: 10 residues processed: 135 average time/residue: 0.1879 time to fit residues: 34.2470 Evaluate side-chains 118 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7000 Z= 0.224 Angle : 0.771 9.200 9548 Z= 0.341 Chirality : 0.048 0.311 1155 Planarity : 0.005 0.053 1135 Dihedral : 12.614 58.551 1851 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.21 % Allowed : 16.72 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 871 helix: 1.79 (0.26), residues: 385 sheet: -0.77 (0.41), residues: 167 loop : -2.82 (0.30), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 346 HIS 0.002 0.001 HIS A 156 PHE 0.017 0.002 PHE A 427 TYR 0.014 0.001 TYR A 251 ARG 0.004 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.624 Fit side-chains REVERT: A 70 LEU cc_start: 0.8669 (mt) cc_final: 0.8432 (mt) REVERT: A 134 ASP cc_start: 0.7796 (m-30) cc_final: 0.7298 (p0) REVERT: A 170 GLN cc_start: 0.7192 (tp40) cc_final: 0.6972 (tp40) REVERT: A 291 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6326 (t80) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 0.1911 time to fit residues: 31.3796 Evaluate side-chains 119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.974 > 50: distance: 58 - 90: 6.015 distance: 61 - 87: 23.309 distance: 76 - 79: 3.334 distance: 79 - 80: 3.551 distance: 80 - 81: 3.247 distance: 80 - 83: 7.437 distance: 81 - 82: 6.553 distance: 81 - 87: 22.923 distance: 83 - 84: 7.839 distance: 84 - 85: 6.248 distance: 84 - 86: 4.932 distance: 87 - 88: 10.593 distance: 88 - 89: 22.845 distance: 88 - 91: 12.340 distance: 89 - 90: 14.061 distance: 89 - 94: 21.209 distance: 91 - 92: 16.534 distance: 91 - 93: 16.910 distance: 94 - 95: 13.555 distance: 95 - 96: 22.774 distance: 95 - 98: 20.908 distance: 96 - 97: 30.276 distance: 96 - 102: 18.216 distance: 98 - 99: 21.294 distance: 99 - 100: 20.819 distance: 99 - 101: 22.789 distance: 102 - 103: 4.501 distance: 103 - 104: 35.361 distance: 104 - 105: 17.108 distance: 104 - 106: 43.343 distance: 106 - 107: 19.069 distance: 107 - 108: 24.669 distance: 107 - 110: 25.670 distance: 108 - 109: 22.737 distance: 108 - 111: 17.114 distance: 111 - 112: 29.692 distance: 112 - 113: 24.626 distance: 112 - 115: 24.988 distance: 113 - 114: 24.956 distance: 113 - 116: 16.835 distance: 116 - 117: 7.104 distance: 117 - 118: 9.143 distance: 118 - 119: 24.292 distance: 118 - 120: 10.910 distance: 120 - 121: 18.004 distance: 121 - 122: 24.669 distance: 121 - 124: 16.867 distance: 122 - 123: 8.140 distance: 122 - 125: 14.896 distance: 125 - 126: 25.891 distance: 126 - 127: 28.738 distance: 126 - 129: 17.807 distance: 127 - 128: 29.377 distance: 127 - 130: 37.091 distance: 130 - 131: 12.425 distance: 131 - 132: 14.586 distance: 131 - 134: 28.177 distance: 132 - 133: 11.018 distance: 132 - 135: 18.843