Starting phenix.real_space_refine on Wed Jun 11 11:14:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t50_41041/06_2025/8t50_41041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t50_41041/06_2025/8t50_41041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t50_41041/06_2025/8t50_41041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t50_41041/06_2025/8t50_41041.map" model { file = "/net/cci-nas-00/data/ceres_data/8t50_41041/06_2025/8t50_41041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t50_41041/06_2025/8t50_41041.cif" } resolution = 3.6 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= 0.001 sd= 0.018 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 4 5.49 5 S 56 5.16 5 C 8016 2.51 5 N 2280 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12720 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "B" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "A" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "D" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 8.06, per 1000 atoms: 0.63 Number of scatterers: 12720 At special positions: 0 Unit cell: (105.342, 105.342, 115.116, 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 4 15.00 O 2364 8.00 N 2280 7.00 C 8016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 385 " distance=2.04 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 385 " distance=2.04 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 385 " distance=2.04 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 385 " distance=2.04 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: 3.46 Conformation dependent library (CDL) restraints added in 2.0 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 77.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'C' and resid 107 through 115 removed outlier: 4.131A pdb=" N LEU C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 141 through 165 Proline residue: C 161 - end of helix removed outlier: 3.766A pdb=" N THR C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 195 Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 263 through 285 removed outlier: 3.895A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 324 removed outlier: 3.622A pdb=" N ASN C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 341 through 358 Processing helix chain 'C' and resid 368 through 422 removed outlier: 3.573A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 452 Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 removed outlier: 3.713A pdb=" N MET C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.687A pdb=" N ALA C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 539 through 546 removed outlier: 3.618A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 Processing helix chain 'C' and resid 576 through 595 removed outlier: 4.005A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 606 Processing helix chain 'C' and resid 617 through 634 Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 116 through 130 Processing helix chain 'B' and resid 141 through 165 Proline residue: B 161 - end of helix removed outlier: 3.766A pdb=" N THR B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 195 Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 263 through 285 removed outlier: 3.902A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 324 removed outlier: 3.641A pdb=" N ASN B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 341 through 357 Processing helix chain 'B' and resid 368 through 422 removed outlier: 3.584A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 removed outlier: 3.761A pdb=" N MET B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.750A pdb=" N ALA B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.515A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 Processing helix chain 'B' and resid 576 through 595 removed outlier: 4.040A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 606 Processing helix chain 'B' and resid 617 through 634 Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 116 through 130 Processing helix chain 'A' and resid 141 through 165 Proline residue: A 161 - end of helix removed outlier: 3.766A pdb=" N THR A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 195 Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 263 through 285 removed outlier: 3.894A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 324 removed outlier: 3.635A pdb=" N ASN A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 341 through 358 Processing helix chain 'A' and resid 368 through 422 removed outlier: 3.625A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 removed outlier: 3.676A pdb=" N MET A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.704A pdb=" N ALA A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.519A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 576 through 595 removed outlier: 4.025A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 617 through 634 Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 116 through 130 Processing helix chain 'D' and resid 141 through 165 Proline residue: D 161 - end of helix removed outlier: 3.766A pdb=" N THR D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 195 Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.892A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 324 removed outlier: 3.641A pdb=" N ASN D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 341 through 358 Processing helix chain 'D' and resid 368 through 422 removed outlier: 4.417A pdb=" N ARG D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 removed outlier: 3.551A pdb=" N MET D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.668A pdb=" N ALA D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 Processing helix chain 'D' and resid 539 through 546 removed outlier: 3.553A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 Processing helix chain 'D' and resid 576 through 595 removed outlier: 4.023A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 606 Processing helix chain 'D' and resid 617 through 634 Processing sheet with id=AA1, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.395A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C 536 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.147A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 503 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.391A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER B 536 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.217A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 503 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.390A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 536 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.197A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 503 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.324A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 536 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.189A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 503 " --> pdb=" O VAL D 553 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4362 1.35 - 1.46: 3221 1.46 - 1.58: 5293 1.58 - 1.70: 8 1.70 - 1.82: 88 Bond restraints: 12972 Sorted by residual: bond pdb=" C3' CMP D 901 " pdb=" C4' CMP D 901 " ideal model delta sigma weight residual 1.521 1.499 0.022 1.50e-02 4.44e+03 2.15e+00 bond pdb=" C3' CMP B 901 " pdb=" C4' CMP B 901 " ideal model delta sigma weight residual 1.521 1.499 0.022 1.50e-02 4.44e+03 2.15e+00 bond pdb=" C3' CMP C 901 " pdb=" C4' CMP C 901 " ideal model delta sigma weight residual 1.521 1.499 0.022 1.50e-02 4.44e+03 2.11e+00 bond pdb=" C3' CMP A 901 " pdb=" C4' CMP A 901 " ideal model delta sigma weight residual 1.521 1.499 0.022 1.50e-02 4.44e+03 2.06e+00 bond pdb=" C4 CMP D 901 " pdb=" C5 CMP D 901 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.20e+00 ... (remaining 12967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 17338 1.78 - 3.56: 340 3.56 - 5.34: 76 5.34 - 7.13: 13 7.13 - 8.91: 9 Bond angle restraints: 17776 Sorted by residual: angle pdb=" CA LYS C 422 " pdb=" CB LYS C 422 " pdb=" CG LYS C 422 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CA LYS D 422 " pdb=" CB LYS D 422 " pdb=" CG LYS D 422 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CA LYS B 422 " pdb=" CB LYS B 422 " pdb=" CG LYS B 422 " ideal model delta sigma weight residual 114.10 120.74 -6.64 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA LYS A 422 " pdb=" CB LYS A 422 " pdb=" CG LYS A 422 " ideal model delta sigma weight residual 114.10 120.73 -6.63 2.00e+00 2.50e-01 1.10e+01 angle pdb=" C THR D 472 " pdb=" N MET D 473 " pdb=" CA MET D 473 " ideal model delta sigma weight residual 120.69 111.79 8.90 2.95e+00 1.15e-01 9.11e+00 ... (remaining 17771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 7206 25.61 - 51.22: 339 51.22 - 76.82: 18 76.82 - 102.43: 1 102.43 - 128.04: 4 Dihedral angle restraints: 7568 sinusoidal: 2000 harmonic: 5568 Sorted by residual: dihedral pdb=" CA PHE B 285 " pdb=" C PHE B 285 " pdb=" N HIS B 286 " pdb=" CA HIS B 286 " ideal model delta harmonic sigma weight residual 180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LEU C 561 " pdb=" C LEU C 561 " pdb=" N TYR C 562 " pdb=" CA TYR C 562 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LEU D 561 " pdb=" C LEU D 561 " pdb=" N TYR D 562 " pdb=" CA TYR D 562 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 7565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1695 0.053 - 0.106: 333 0.106 - 0.159: 32 0.159 - 0.212: 0 0.212 - 0.265: 4 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CG LEU A 377 " pdb=" CB LEU A 377 " pdb=" CD1 LEU A 377 " pdb=" CD2 LEU A 377 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU B 377 " pdb=" CB LEU B 377 " pdb=" CD1 LEU B 377 " pdb=" CD2 LEU B 377 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CG LEU D 377 " pdb=" CB LEU D 377 " pdb=" CD1 LEU D 377 " pdb=" CD2 LEU D 377 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2061 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 422 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C LYS C 422 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS C 422 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 423 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 175 " -0.009 2.00e-02 2.50e+03 9.93e-03 2.47e+00 pdb=" CG TRP C 175 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP C 175 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 175 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 175 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 175 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 175 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 175 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 175 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 175 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 175 " 0.009 2.00e-02 2.50e+03 9.93e-03 2.47e+00 pdb=" CG TRP B 175 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 175 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 175 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 175 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 175 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 175 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 175 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 175 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 175 " -0.000 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 779 2.74 - 3.28: 13663 3.28 - 3.82: 22225 3.82 - 4.36: 21370 4.36 - 4.90: 38295 Nonbonded interactions: 96332 Sorted by model distance: nonbonded pdb=" N GLU C 540 " pdb=" OE1 GLU C 540 " model vdw 2.194 3.120 nonbonded pdb=" OH TYR C 435 " pdb=" OE2 GLU D 452 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU B 452 " pdb=" OH TYR A 435 " model vdw 2.229 3.040 nonbonded pdb=" OE2 GLU A 452 " pdb=" OH TYR D 435 " model vdw 2.251 3.040 nonbonded pdb=" OE1 GLU B 540 " pdb=" O2' CMP B 901 " model vdw 2.252 3.040 ... (remaining 96327 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.190 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.590 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12976 Z= 0.155 Angle : 0.671 8.908 17784 Z= 0.371 Chirality : 0.040 0.265 2064 Planarity : 0.003 0.031 2344 Dihedral : 14.504 128.040 3932 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.47 % Allowed : 20.19 % Favored : 79.34 % 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: 2.00 (0.19), residues: 1848 helix: 2.20 (0.14), residues: 1360 sheet: 1.23 (0.48), residues: 84 loop : -1.84 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 175 HIS 0.005 0.001 HIS A 517 PHE 0.026 0.001 PHE D 420 TYR 0.014 0.001 TYR B 411 ARG 0.006 0.001 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.09013 ( 1119) hydrogen bonds : angle 5.02287 ( 3309) SS BOND : bond 0.00613 ( 4) SS BOND : angle 1.35853 ( 8) covalent geometry : bond 0.00303 (12972) covalent geometry : angle 0.67070 (17776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 311 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.7954 (mm110) cc_final: 0.7317 (tp40) REVERT: C 419 SER cc_start: 0.9406 (t) cc_final: 0.9023 (p) REVERT: C 562 TYR cc_start: 0.8333 (m-80) cc_final: 0.6822 (m-80) REVERT: B 408 GLN cc_start: 0.7872 (mm110) cc_final: 0.7228 (tp40) REVERT: B 419 SER cc_start: 0.9481 (t) cc_final: 0.9266 (p) REVERT: B 562 TYR cc_start: 0.8399 (m-80) cc_final: 0.7041 (m-80) REVERT: A 562 TYR cc_start: 0.8236 (m-80) cc_final: 0.7009 (m-80) REVERT: D 418 MET cc_start: 0.7942 (mtm) cc_final: 0.7636 (mtp) REVERT: D 419 SER cc_start: 0.9452 (t) cc_final: 0.9054 (p) outliers start: 4 outliers final: 1 residues processed: 312 average time/residue: 0.2310 time to fit residues: 104.4315 Evaluate side-chains 288 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 0.0170 chunk 48 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN C 478 ASN B 286 HIS B 413 GLN B 478 ASN A 286 HIS A 413 GLN A 478 ASN D 286 HIS D 413 GLN D 478 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.223144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.151638 restraints weight = 16735.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.155387 restraints weight = 10875.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.158072 restraints weight = 8215.166| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12976 Z= 0.195 Angle : 0.625 10.958 17784 Z= 0.323 Chirality : 0.043 0.246 2064 Planarity : 0.004 0.037 2344 Dihedral : 7.371 130.063 2042 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.40 % Allowed : 18.90 % Favored : 75.70 % 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: 2.12 (0.19), residues: 1848 helix: 2.31 (0.14), residues: 1372 sheet: 1.04 (0.50), residues: 84 loop : -1.95 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 175 HIS 0.006 0.001 HIS D 517 PHE 0.017 0.002 PHE C 166 TYR 0.015 0.001 TYR C 411 ARG 0.007 0.001 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1119) hydrogen bonds : angle 4.41185 ( 3309) SS BOND : bond 0.00336 ( 4) SS BOND : angle 0.60883 ( 8) covalent geometry : bond 0.00438 (12972) covalent geometry : angle 0.62454 (17776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.8258 (mm110) cc_final: 0.7637 (tp40) REVERT: B 408 GLN cc_start: 0.8172 (mm110) cc_final: 0.7771 (tp40) REVERT: B 562 TYR cc_start: 0.8222 (m-80) cc_final: 0.7951 (m-80) REVERT: D 540 GLU cc_start: 0.7173 (pm20) cc_final: 0.6863 (pm20) outliers start: 46 outliers final: 44 residues processed: 311 average time/residue: 0.2278 time to fit residues: 105.4407 Evaluate side-chains 321 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 11 optimal weight: 60.0000 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 182 optimal weight: 0.0970 chunk 129 optimal weight: 0.0170 chunk 155 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 50.0000 chunk 57 optimal weight: 5.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN C 416 GLN C 478 ASN B 413 GLN B 478 ASN A 413 GLN D 413 GLN D 416 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.226633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.159627 restraints weight = 16741.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.163245 restraints weight = 11988.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.163034 restraints weight = 7617.219| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12976 Z= 0.128 Angle : 0.564 8.767 17784 Z= 0.292 Chirality : 0.040 0.229 2064 Planarity : 0.003 0.035 2344 Dihedral : 7.385 132.030 2042 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.81 % Allowed : 19.72 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 1848 helix: 2.35 (0.14), residues: 1376 sheet: 0.98 (0.48), residues: 84 loop : -2.07 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 175 HIS 0.004 0.000 HIS A 517 PHE 0.013 0.001 PHE B 166 TYR 0.022 0.001 TYR D 439 ARG 0.008 0.000 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 1119) hydrogen bonds : angle 4.18171 ( 3309) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.65168 ( 8) covalent geometry : bond 0.00257 (12972) covalent geometry : angle 0.56402 (17776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9195 (t80) cc_final: 0.8867 (t80) REVERT: C 408 GLN cc_start: 0.8220 (mm110) cc_final: 0.7548 (tp40) REVERT: C 562 TYR cc_start: 0.8238 (m-80) cc_final: 0.7399 (m-80) REVERT: C 581 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7677 (mtm110) REVERT: B 408 GLN cc_start: 0.8186 (mm110) cc_final: 0.7594 (tp40) REVERT: A 540 GLU cc_start: 0.6955 (pm20) cc_final: 0.6731 (pm20) REVERT: A 562 TYR cc_start: 0.8453 (m-80) cc_final: 0.7625 (m-80) REVERT: D 562 TYR cc_start: 0.8395 (m-80) cc_final: 0.7595 (m-80) outliers start: 41 outliers final: 37 residues processed: 311 average time/residue: 0.2167 time to fit residues: 99.6694 Evaluate side-chains 310 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 6 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 94 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 185 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 chunk 152 optimal weight: 50.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN C 463 ASN C 478 ASN B 413 GLN B 463 ASN A 413 GLN A 463 ASN D 413 GLN D 463 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.222863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.158394 restraints weight = 16861.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.158529 restraints weight = 11302.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.157034 restraints weight = 8813.625| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12976 Z= 0.204 Angle : 0.619 9.392 17784 Z= 0.321 Chirality : 0.043 0.220 2064 Planarity : 0.003 0.030 2344 Dihedral : 7.322 129.426 2042 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 7.39 % Allowed : 19.84 % Favored : 72.77 % 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: 2.15 (0.20), residues: 1848 helix: 2.37 (0.14), residues: 1376 sheet: 0.90 (0.48), residues: 84 loop : -2.15 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 175 HIS 0.006 0.001 HIS C 517 PHE 0.017 0.002 PHE C 538 TYR 0.018 0.002 TYR B 411 ARG 0.004 0.000 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 1119) hydrogen bonds : angle 4.22176 ( 3309) SS BOND : bond 0.00410 ( 4) SS BOND : angle 0.59576 ( 8) covalent geometry : bond 0.00466 (12972) covalent geometry : angle 0.61882 (17776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9207 (t80) cc_final: 0.8872 (t80) REVERT: C 408 GLN cc_start: 0.8281 (mm110) cc_final: 0.7619 (tp40) REVERT: C 581 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7759 (mtm110) REVERT: B 408 GLN cc_start: 0.8204 (mm110) cc_final: 0.7636 (tp40) REVERT: D 540 GLU cc_start: 0.7047 (pm20) cc_final: 0.6845 (pm20) outliers start: 63 outliers final: 51 residues processed: 316 average time/residue: 0.2616 time to fit residues: 121.6336 Evaluate side-chains 315 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 57.1123 > 50: distance: 31 - 51: 11.233 distance: 47 - 51: 7.873 distance: 51 - 52: 27.628 distance: 52 - 53: 38.902 distance: 52 - 55: 44.789 distance: 53 - 60: 36.350 distance: 55 - 56: 10.092 distance: 56 - 57: 15.029 distance: 57 - 58: 10.167 distance: 58 - 59: 14.158 distance: 60 - 61: 12.304 distance: 61 - 62: 30.889 distance: 61 - 64: 55.799 distance: 62 - 63: 29.626 distance: 62 - 68: 26.021 distance: 64 - 65: 42.179 distance: 65 - 66: 26.435 distance: 65 - 67: 21.738 distance: 68 - 69: 22.140 distance: 68 - 74: 7.656 distance: 69 - 70: 13.844 distance: 69 - 72: 17.820 distance: 70 - 71: 10.887 distance: 70 - 75: 32.234 distance: 71 - 96: 26.961 distance: 72 - 73: 33.744 distance: 73 - 74: 29.988 distance: 75 - 76: 38.915 distance: 76 - 77: 12.688 distance: 76 - 79: 43.103 distance: 77 - 78: 8.054 distance: 77 - 80: 21.178 distance: 78 - 107: 31.347 distance: 80 - 81: 11.988 distance: 81 - 82: 32.523 distance: 81 - 84: 27.973 distance: 82 - 83: 13.356 distance: 82 - 88: 25.751 distance: 83 - 116: 25.818 distance: 84 - 85: 10.495 distance: 85 - 87: 10.306 distance: 88 - 89: 6.587 distance: 89 - 90: 11.621 distance: 89 - 92: 28.399 distance: 90 - 91: 39.053 distance: 90 - 96: 18.997 distance: 91 - 125: 33.426 distance: 92 - 93: 4.024 distance: 93 - 94: 35.578 distance: 94 - 95: 29.121 distance: 96 - 97: 27.845 distance: 97 - 98: 35.812 distance: 97 - 100: 6.521 distance: 98 - 99: 37.896 distance: 98 - 107: 32.287 distance: 99 - 133: 27.609 distance: 100 - 101: 7.762 distance: 101 - 102: 13.483 distance: 102 - 103: 5.575 distance: 103 - 104: 10.425 distance: 104 - 105: 3.415 distance: 104 - 106: 4.565 distance: 107 - 108: 20.252 distance: 108 - 109: 12.083 distance: 108 - 111: 7.552 distance: 109 - 110: 9.500 distance: 109 - 116: 28.956 distance: 110 - 140: 19.593 distance: 111 - 112: 22.167 distance: 112 - 113: 17.146 distance: 113 - 114: 11.666 distance: 113 - 115: 23.288 distance: 116 - 117: 12.529 distance: 117 - 118: 10.709 distance: 117 - 120: 20.099 distance: 118 - 119: 9.729 distance: 118 - 125: 3.734 distance: 119 - 147: 14.575 distance: 120 - 121: 12.930 distance: 121 - 122: 13.390 distance: 122 - 123: 16.622 distance: 123 - 124: 9.561 distance: 125 - 126: 10.380 distance: 126 - 127: 6.013 distance: 126 - 129: 17.190 distance: 127 - 128: 13.034 distance: 127 - 133: 7.628 distance: 129 - 130: 17.614 distance: 129 - 131: 7.124 distance: 130 - 132: 24.500