Starting phenix.real_space_refine on Thu Aug 6 01:22:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t50_41041/08_2026/8t50_41041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t50_41041/08_2026/8t50_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_41041/08_2026/8t50_41041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t50_41041/08_2026/8t50_41041.map" model { file = "/net/cci-nas-00/data/ceres_data/8t50_41041/08_2026/8t50_41041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t50_41041/08_2026/8t50_41041.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'ASN:plan1': 9, 'PHE:plan': 14, 'ARG:plan': 16, 'GLN:plan1': 13, 'GLU:plan': 11, 'ASP:plan': 13, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'ASN:plan1': 9, 'PHE:plan': 14, 'ARG:plan': 16, 'GLN:plan1': 13, 'GLU:plan': 11, 'ASP:plan': 13, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'ASN:plan1': 9, 'PHE:plan': 14, 'ARG:plan': 16, 'GLN:plan1': 13, 'GLU:plan': 11, 'ASP:plan': 13, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'ASN:plan1': 9, 'PHE:plan': 14, 'ARG:plan': 16, 'GLN:plan1': 13, 'GLU:plan': 11, 'ASP:plan': 13, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 361 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 2.75, per 1000 atoms: 0.22 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: 1.02 Conformation dependent library (CDL) restraints added in 679.4 milliseconds 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: 0.38 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: 2.14 Time building geometry restraints manager: 1.31 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=" C4' CMP D 901 " pdb=" C5' CMP D 901 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C4' CMP A 901 " pdb=" C5' CMP A 901 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C4' CMP B 901 " pdb=" C5' CMP B 901 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C4' CMP C 901 " pdb=" C5' CMP C 901 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C3' CMP D 901 " pdb=" C4' CMP D 901 " ideal model delta sigma weight residual 1.524 1.499 0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 12967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 17432 2.10 - 4.21: 260 4.21 - 6.31: 54 6.31 - 8.42: 17 8.42 - 10.52: 13 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=" C1' CMP B 901 " pdb=" C2' CMP B 901 " pdb=" C3' CMP B 901 " ideal model delta sigma weight residual 111.00 100.48 10.52 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C1' CMP A 901 " pdb=" C2' CMP A 901 " pdb=" C3' CMP A 901 " ideal model delta sigma weight residual 111.00 100.48 10.52 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C1' CMP D 901 " pdb=" C2' CMP D 901 " pdb=" C3' CMP D 901 " ideal model delta sigma weight residual 111.00 100.49 10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C1' CMP C 901 " pdb=" C2' CMP C 901 " pdb=" C3' CMP C 901 " ideal model delta sigma weight residual 111.00 100.53 10.47 3.00e+00 1.11e-01 1.22e+01 ... (remaining 17771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 6813 15.96 - 31.91: 530 31.91 - 47.87: 194 47.87 - 63.82: 23 63.82 - 79.78: 8 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 - 0.055: 1719 0.055 - 0.111: 315 0.111 - 0.166: 22 0.166 - 0.221: 0 0.221 - 0.276: 8 Chirality restraints: 2064 Sorted by residual: chirality pdb=" C2' CMP A 901 " pdb=" C1' CMP A 901 " pdb=" C3' CMP A 901 " pdb=" O2' CMP A 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C2' CMP C 901 " pdb=" C1' CMP C 901 " pdb=" C3' CMP C 901 " pdb=" O2' CMP C 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' CMP B 901 " pdb=" C1' CMP B 901 " pdb=" C3' CMP B 901 " pdb=" O2' CMP B 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.27 2.00e-01 2.50e+01 1.89e+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: 1.160 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.350 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 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= 0.157 Angle : 0.720 10.519 17784 Z= 0.375 Chirality : 0.042 0.276 2064 Planarity : 0.003 0.031 2344 Dihedral : 13.942 79.780 3932 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.001 ARG A 581 TYR 0.014 0.001 TYR B 411 PHE 0.026 0.001 PHE D 420 TRP 0.027 0.002 TRP C 175 HIS 0.005 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (12972) covalent geometry : angle 0.71989 / 0.37 (17776) SS BOND : bond 0.00613 / 0.31 ( 4) SS BOND : angle 1.35853 / 0.71 ( 8) hydrogen bonds : bond 0.09013 / 6.46 ( 1119) hydrogen bonds : angle 5.02287 / 3.76 ( 3309) *********************** 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 : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.7954 (mm110) cc_final: 0.7316 (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: 0.9482 (t) cc_final: 0.9266 (p) REVERT: B 562 TYR cc_start: 0.8398 (m-80) cc_final: 0.7041 (m-80) REVERT: A 562 TYR cc_start: 0.8236 (m-80) cc_final: 0.7010 (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: 0.0884 time to fit residues: 40.9838 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 : 0.441 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN C 463 ASN C 478 ASN B 286 HIS B 413 GLN B 463 ASN B 478 ASN A 286 HIS A 413 GLN A 463 ASN A 478 ASN D 286 HIS D 413 GLN D 463 ASN D 478 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.223271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.155033 restraints weight = 16817.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.157848 restraints weight = 12288.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.158026 restraints weight = 9021.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158457 restraints weight = 8224.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.158684 restraints weight = 7676.852| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12976 Z= 0.189 Angle : 0.664 10.944 17784 Z= 0.324 Chirality : 0.043 0.250 2064 Planarity : 0.004 0.037 2344 Dihedral : 4.493 38.739 2042 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.87 % Allowed : 18.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.19), residues: 1848 helix: 2.31 (0.14), residues: 1372 sheet: 1.06 (0.50), residues: 84 loop : -1.95 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 581 TYR 0.015 0.001 TYR C 411 PHE 0.017 0.002 PHE B 166 TRP 0.016 0.001 TRP A 175 HIS 0.006 0.001 HIS D 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (12972) covalent geometry : angle 0.66427 / 0.32 (17776) SS BOND : bond 0.00335 / 0.17 ( 4) SS BOND : angle 0.64345 / 0.34 ( 8) hydrogen bonds : bond 0.04040 / 3.01 ( 1119) hydrogen bonds : angle 4.40412 / 3.28 ( 3309) *********************** 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 340 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.8239 (mm110) cc_final: 0.7643 (tp40) REVERT: B 408 GLN cc_start: 0.8149 (mm110) cc_final: 0.7777 (tp40) REVERT: B 562 TYR cc_start: 0.8166 (m-80) cc_final: 0.7870 (m-80) REVERT: D 540 GLU cc_start: 0.7121 (pm20) cc_final: 0.6810 (pm20) outliers start: 50 outliers final: 45 residues processed: 316 average time/residue: 0.0847 time to fit residues: 40.5210 Evaluate side-chains 322 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 418 MET 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 110 optimal weight: 7.9990 chunk 141 optimal weight: 50.0000 chunk 186 optimal weight: 40.0000 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 32 optimal weight: 0.0570 chunk 39 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 162 optimal weight: 0.4980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN C 416 GLN C 478 ASN B 413 GLN B 478 ASN A 413 GLN D 413 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.226134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158135 restraints weight = 16948.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.161101 restraints weight = 11941.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.161218 restraints weight = 8394.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.161405 restraints weight = 7873.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.161778 restraints weight = 7503.664| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12976 Z= 0.128 Angle : 0.608 9.610 17784 Z= 0.294 Chirality : 0.041 0.228 2064 Planarity : 0.003 0.036 2344 Dihedral : 4.348 40.331 2042 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.05 % Allowed : 19.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.19), residues: 1848 helix: 2.34 (0.14), residues: 1376 sheet: 0.95 (0.48), residues: 84 loop : -2.07 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 581 TYR 0.022 0.001 TYR D 439 PHE 0.014 0.001 PHE B 166 TRP 0.013 0.001 TRP C 175 HIS 0.004 0.000 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (12972) covalent geometry : angle 0.60748 / 0.29 (17776) SS BOND : bond 0.00306 / 0.15 ( 4) SS BOND : angle 0.66226 / 0.35 ( 8) hydrogen bonds : bond 0.03690 / 2.74 ( 1119) hydrogen bonds : angle 4.17991 / 3.12 ( 3309) *********************** 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 335 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9141 (t80) cc_final: 0.8857 (t80) REVERT: C 408 GLN cc_start: 0.8209 (mm110) cc_final: 0.7543 (tp40) REVERT: C 581 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7676 (mtm110) REVERT: B 408 GLN cc_start: 0.8180 (mm110) cc_final: 0.7590 (tp40) REVERT: A 540 GLU cc_start: 0.6995 (pm20) cc_final: 0.6712 (pm20) REVERT: A 562 TYR cc_start: 0.8275 (m-80) cc_final: 0.7394 (m-80) REVERT: D 540 GLU cc_start: 0.7084 (pm20) cc_final: 0.6867 (pm20) REVERT: D 562 TYR cc_start: 0.8384 (m-80) cc_final: 0.7573 (m-80) outliers start: 43 outliers final: 38 residues processed: 313 average time/residue: 0.0836 time to fit residues: 39.6765 Evaluate side-chains 313 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 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 389 PHE 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 166 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 50.0000 chunk 142 optimal weight: 20.0000 chunk 125 optimal weight: 0.7980 chunk 50 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN C 478 ASN B 413 GLN A 413 GLN D 413 GLN D 463 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.219124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.149257 restraints weight = 17003.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.150889 restraints weight = 13775.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.151716 restraints weight = 9986.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.151818 restraints weight = 8830.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151826 restraints weight = 8965.386| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 12976 Z= 0.309 Angle : 0.743 10.995 17784 Z= 0.367 Chirality : 0.046 0.220 2064 Planarity : 0.004 0.037 2344 Dihedral : 4.663 44.975 2042 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 7.39 % Allowed : 20.19 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.20), residues: 1848 helix: 2.27 (0.14), residues: 1376 sheet: 0.91 (0.51), residues: 84 loop : -2.25 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 581 TYR 0.019 0.002 TYR C 411 PHE 0.024 0.003 PHE A 538 TRP 0.012 0.001 TRP D 175 HIS 0.010 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.31 (12972) covalent geometry : angle 0.74322 / 0.37 (17776) SS BOND : bond 0.00517 / 0.26 ( 4) SS BOND : angle 0.58624 / 0.32 ( 8) hydrogen bonds : bond 0.04314 / 3.23 ( 1119) hydrogen bonds : angle 4.42459 / 3.29 ( 3309) *********************** 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 340 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.8356 (mm110) cc_final: 0.7755 (tp40) REVERT: C 422 LYS cc_start: 0.8400 (tptt) cc_final: 0.8188 (tptt) REVERT: C 581 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7793 (mtm110) REVERT: B 408 GLN cc_start: 0.8257 (mm110) cc_final: 0.7860 (tp40) REVERT: A 540 GLU cc_start: 0.7280 (pm20) cc_final: 0.7026 (pm20) REVERT: D 540 GLU cc_start: 0.7311 (pm20) cc_final: 0.7105 (pm20) outliers start: 63 outliers final: 54 residues processed: 317 average time/residue: 0.0876 time to fit residues: 41.5124 Evaluate side-chains 318 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 264 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 519 VAL Chi-restraints excluded: chain C residue 541 ILE 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 396 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 414 VAL 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 557 THR 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 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 557 THR Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 129 optimal weight: 0.8980 chunk 105 optimal weight: 60.0000 chunk 104 optimal weight: 10.0000 chunk 182 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 172 optimal weight: 0.6980 chunk 165 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN B 413 GLN A 413 GLN D 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.222017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.150062 restraints weight = 16998.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.153703 restraints weight = 10945.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.156408 restraints weight = 8273.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.157699 restraints weight = 6949.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.158882 restraints weight = 6286.474| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12976 Z= 0.185 Angle : 0.657 10.140 17784 Z= 0.321 Chirality : 0.042 0.209 2064 Planarity : 0.003 0.035 2344 Dihedral : 4.526 46.982 2042 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 7.16 % Allowed : 22.54 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.20), residues: 1848 helix: 2.33 (0.14), residues: 1376 sheet: 0.99 (0.46), residues: 84 loop : -2.24 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 581 TYR 0.018 0.001 TYR C 411 PHE 0.016 0.002 PHE A 317 TRP 0.011 0.001 TRP B 175 HIS 0.005 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (12972) covalent geometry : angle 0.65677 / 0.32 (17776) SS BOND : bond 0.00395 / 0.20 ( 4) SS BOND : angle 0.59938 / 0.32 ( 8) hydrogen bonds : bond 0.03911 / 2.92 ( 1119) hydrogen bonds : angle 4.23920 / 3.16 ( 3309) *********************** REFINEMENT MACRO_CYCLE 5 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 348 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 287 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9283 (t80) cc_final: 0.8986 (t80) REVERT: C 408 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7539 (tp40) REVERT: C 579 MET cc_start: 0.7223 (mmp) cc_final: 0.6882 (mmt) REVERT: B 408 GLN cc_start: 0.8235 (mm110) cc_final: 0.7587 (tp40) REVERT: B 540 GLU cc_start: 0.7087 (pm20) cc_final: 0.6805 (pm20) REVERT: B 562 TYR cc_start: 0.8422 (m-80) cc_final: 0.8092 (m-80) REVERT: D 284 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.7120 (tp) REVERT: D 540 GLU cc_start: 0.7139 (pm20) cc_final: 0.6888 (pm20) outliers start: 61 outliers final: 58 residues processed: 323 average time/residue: 0.0885 time to fit residues: 43.3808 Evaluate side-chains 328 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 268 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 408 GLN Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 419 SER 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 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG 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 384 THR 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 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 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 286 HIS 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 413 GLN Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 554 ARG Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 23 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 41 optimal weight: 0.0370 chunk 179 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN B 413 GLN A 413 GLN D 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.223525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.152542 restraints weight = 16815.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.156411 restraints weight = 10593.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.159243 restraints weight = 7964.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.161090 restraints weight = 6612.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161768 restraints weight = 5908.620| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12976 Z= 0.153 Angle : 0.642 9.824 17784 Z= 0.312 Chirality : 0.042 0.192 2064 Planarity : 0.003 0.033 2344 Dihedral : 4.446 48.546 2042 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 7.63 % Allowed : 23.00 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.20), residues: 1848 helix: 2.39 (0.14), residues: 1376 sheet: 1.01 (0.44), residues: 84 loop : -2.23 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 590 TYR 0.018 0.001 TYR C 411 PHE 0.013 0.002 PHE B 166 TRP 0.011 0.001 TRP B 175 HIS 0.005 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (12972) covalent geometry : angle 0.64238 / 0.31 (17776) SS BOND : bond 0.00361 / 0.18 ( 4) SS BOND : angle 0.66597 / 0.36 ( 8) hydrogen bonds : bond 0.03744 / 2.79 ( 1119) hydrogen bonds : angle 4.14501 / 3.09 ( 3309) *********************** REFINEMENT MACRO_CYCLE 6 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: 65 poor density : 274 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9291 (t80) cc_final: 0.8982 (t80) REVERT: C 408 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7583 (tp40) REVERT: B 408 GLN cc_start: 0.8201 (mm110) cc_final: 0.7512 (tp40) REVERT: B 540 GLU cc_start: 0.6998 (pm20) cc_final: 0.6796 (pm20) REVERT: B 562 TYR cc_start: 0.8379 (m-80) cc_final: 0.8011 (m-80) REVERT: D 280 GLN cc_start: 0.8137 (tp40) cc_final: 0.7922 (tp40) REVERT: D 284 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7142 (tp) outliers start: 65 outliers final: 59 residues processed: 312 average time/residue: 0.0851 time to fit residues: 40.3146 Evaluate side-chains 328 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 267 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 408 GLN Chi-restraints excluded: chain C residue 457 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 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 512 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 564 LEU 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 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 512 MET 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 284 ILE Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 286 HIS 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 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 512 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 554 ARG Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 19 optimal weight: 30.0000 chunk 37 optimal weight: 0.0020 chunk 102 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 156 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 82 optimal weight: 0.0000 chunk 13 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN B 413 GLN A 413 GLN D 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.226093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.156569 restraints weight = 16954.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.160696 restraints weight = 10424.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.163526 restraints weight = 7659.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.165509 restraints weight = 6334.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.165777 restraints weight = 5620.835| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12976 Z= 0.123 Angle : 0.620 9.291 17784 Z= 0.300 Chirality : 0.041 0.183 2064 Planarity : 0.003 0.030 2344 Dihedral : 4.311 49.358 2042 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.34 % Allowed : 24.53 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.20), residues: 1848 helix: 2.47 (0.14), residues: 1368 sheet: 1.09 (0.44), residues: 84 loop : -2.00 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 581 TYR 0.016 0.001 TYR A 411 PHE 0.013 0.001 PHE B 166 TRP 0.012 0.001 TRP B 175 HIS 0.005 0.000 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (12972) covalent geometry : angle 0.61982 / 0.30 (17776) SS BOND : bond 0.00271 / 0.14 ( 4) SS BOND : angle 0.78790 / 0.42 ( 8) hydrogen bonds : bond 0.03469 / 2.58 ( 1119) hydrogen bonds : angle 4.03031 / 3.01 ( 3309) *********************** REFINEMENT MACRO_CYCLE 7 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 333 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 279 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9296 (t80) cc_final: 0.9057 (t80) REVERT: C 408 GLN cc_start: 0.8158 (mm110) cc_final: 0.7597 (tp40) REVERT: C 562 TYR cc_start: 0.8202 (m-80) cc_final: 0.7397 (m-80) REVERT: B 408 GLN cc_start: 0.8100 (mm110) cc_final: 0.7525 (tp40) REVERT: B 463 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8308 (t0) REVERT: B 562 TYR cc_start: 0.8306 (m-80) cc_final: 0.7897 (m-80) REVERT: A 562 TYR cc_start: 0.8262 (m-80) cc_final: 0.7376 (m-80) REVERT: D 280 GLN cc_start: 0.8113 (tp40) cc_final: 0.7882 (tp40) REVERT: D 284 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7035 (tp) REVERT: D 562 TYR cc_start: 0.8284 (m-80) cc_final: 0.7434 (m-80) outliers start: 54 outliers final: 49 residues processed: 310 average time/residue: 0.0892 time to fit residues: 41.5037 Evaluate side-chains 312 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 261 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 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 463 ASN Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 564 LEU 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 413 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 286 HIS 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 396 LEU 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 512 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 554 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 10 optimal weight: 20.0000 chunk 127 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 187 optimal weight: 50.0000 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN B 413 GLN A 413 GLN D 568 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.223355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.158540 restraints weight = 16896.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.157539 restraints weight = 13046.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.158485 restraints weight = 9309.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.158490 restraints weight = 7974.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.158970 restraints weight = 7794.837| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12976 Z= 0.182 Angle : 0.663 9.979 17784 Z= 0.322 Chirality : 0.042 0.176 2064 Planarity : 0.003 0.032 2344 Dihedral : 4.397 51.025 2042 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 7.86 % Allowed : 23.71 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.20), residues: 1848 helix: 2.47 (0.14), residues: 1368 sheet: 1.08 (0.43), residues: 84 loop : -2.09 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 581 TYR 0.016 0.001 TYR B 411 PHE 0.016 0.002 PHE C 538 TRP 0.013 0.001 TRP C 175 HIS 0.005 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (12972) covalent geometry : angle 0.66272 / 0.32 (17776) SS BOND : bond 0.00372 / 0.19 ( 4) SS BOND : angle 0.70427 / 0.38 ( 8) hydrogen bonds : bond 0.03705 / 2.76 ( 1119) hydrogen bonds : angle 4.07967 / 3.05 ( 3309) *********************** REFINEMENT MACRO_CYCLE 8 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 333 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9274 (t80) cc_final: 0.8963 (t80) REVERT: C 408 GLN cc_start: 0.8180 (mm110) cc_final: 0.7587 (tp40) REVERT: B 408 GLN cc_start: 0.8110 (mm110) cc_final: 0.7544 (tp40) REVERT: B 554 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7027 (ptt90) REVERT: B 562 TYR cc_start: 0.8387 (m-80) cc_final: 0.7953 (m-80) REVERT: D 280 GLN cc_start: 0.8088 (tp40) cc_final: 0.7848 (tp40) REVERT: D 284 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6773 (tp) REVERT: D 554 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7111 (ptt90) outliers start: 67 outliers final: 60 residues processed: 310 average time/residue: 0.0840 time to fit residues: 39.4824 Evaluate side-chains 320 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 257 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 385 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 457 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 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 385 CYS 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 512 MET Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 564 LEU 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 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 512 MET 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 284 ILE Chi-restraints excluded: chain D residue 286 HIS 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 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 554 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 139 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 176 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 140 optimal weight: 50.0000 chunk 11 optimal weight: 70.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN B 413 GLN A 413 GLN D 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.223515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.162664 restraints weight = 16922.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.158961 restraints weight = 11553.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.157617 restraints weight = 10236.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.158779 restraints weight = 9636.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.158929 restraints weight = 8610.744| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12976 Z= 0.172 Angle : 0.662 9.845 17784 Z= 0.322 Chirality : 0.042 0.173 2064 Planarity : 0.003 0.033 2344 Dihedral : 4.394 52.227 2042 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 7.75 % Allowed : 23.59 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.20), residues: 1848 helix: 2.47 (0.14), residues: 1368 sheet: 1.16 (0.42), residues: 84 loop : -2.10 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 581 TYR 0.016 0.001 TYR A 411 PHE 0.016 0.002 PHE A 538 TRP 0.012 0.001 TRP C 175 HIS 0.004 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (12972) covalent geometry : angle 0.66235 / 0.32 (17776) SS BOND : bond 0.00345 / 0.17 ( 4) SS BOND : angle 0.72806 / 0.39 ( 8) hydrogen bonds : bond 0.03665 / 2.73 ( 1119) hydrogen bonds : angle 4.06054 / 3.03 ( 3309) *********************** REFINEMENT MACRO_CYCLE 9 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 326 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 260 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9264 (t80) cc_final: 0.9023 (t80) REVERT: C 408 GLN cc_start: 0.8152 (mm110) cc_final: 0.7591 (tp40) REVERT: B 408 GLN cc_start: 0.8090 (mm110) cc_final: 0.7527 (tp40) REVERT: B 554 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.7043 (ptt90) REVERT: B 562 TYR cc_start: 0.8419 (m-80) cc_final: 0.7968 (m-80) REVERT: D 280 GLN cc_start: 0.8063 (tp40) cc_final: 0.7820 (tp40) REVERT: D 554 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6983 (ptt90) outliers start: 66 outliers final: 61 residues processed: 303 average time/residue: 0.0754 time to fit residues: 35.2330 Evaluate side-chains 322 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 259 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 396 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 457 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 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 385 CYS 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 512 MET Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 564 LEU 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 385 CYS 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 512 MET 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 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 554 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.4980 chunk 121 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 75 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN C 463 ASN D 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.224195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.162872 restraints weight = 17045.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.161524 restraints weight = 11321.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.160021 restraints weight = 7962.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161020 restraints weight = 8818.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.161031 restraints weight = 8136.720| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12976 Z= 0.156 Angle : 0.649 9.701 17784 Z= 0.316 Chirality : 0.042 0.172 2064 Planarity : 0.003 0.032 2344 Dihedral : 4.378 52.817 2042 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 7.51 % Allowed : 23.83 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.20), residues: 1848 helix: 2.48 (0.14), residues: 1368 sheet: 1.15 (0.43), residues: 84 loop : -2.11 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 581 TYR 0.018 0.001 TYR B 411 PHE 0.014 0.002 PHE B 166 TRP 0.012 0.001 TRP C 175 HIS 0.004 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (12972) covalent geometry : angle 0.64917 / 0.32 (17776) SS BOND : bond 0.00326 / 0.16 ( 4) SS BOND : angle 0.76016 / 0.41 ( 8) hydrogen bonds : bond 0.03609 / 2.68 ( 1119) hydrogen bonds : angle 3.98511 / 2.98 ( 3309) ********************** REFINEMENT MACRO_CYCLE 10 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 326 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9282 (t80) cc_final: 0.8973 (t80) REVERT: C 408 GLN cc_start: 0.8137 (mm110) cc_final: 0.7588 (tp40) REVERT: B 408 GLN cc_start: 0.8070 (mm110) cc_final: 0.7547 (tp40) REVERT: B 540 GLU cc_start: 0.7039 (pm20) cc_final: 0.6739 (pm20) REVERT: B 562 TYR cc_start: 0.8550 (m-80) cc_final: 0.8117 (m-80) REVERT: D 280 GLN cc_start: 0.8100 (tp40) cc_final: 0.7864 (tp40) REVERT: D 554 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6970 (ptt90) outliers start: 64 outliers final: 62 residues processed: 307 average time/residue: 0.0768 time to fit residues: 36.3721 Evaluate side-chains 319 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 256 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 385 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 457 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 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 385 CYS Chi-restraints excluded: chain B residue 396 LEU 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 512 MET Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 564 LEU 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 385 CYS 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 512 MET 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 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 554 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 50.0000 chunk 48 optimal weight: 30.0000 chunk 185 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN B 413 GLN A 413 GLN A 463 ASN D 413 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.220219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.155903 restraints weight = 17034.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.152286 restraints weight = 13895.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.152546 restraints weight = 10317.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.152948 restraints weight = 9408.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153476 restraints weight = 8482.809| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12976 Z= 0.267 Angle : 0.728 12.249 17784 Z= 0.357 Chirality : 0.044 0.171 2064 Planarity : 0.004 0.036 2344 Dihedral : 4.610 54.058 2042 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 8.33 % Allowed : 23.83 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.20), residues: 1848 helix: 2.45 (0.14), residues: 1368 sheet: 1.03 (0.42), residues: 84 loop : -2.20 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 581 TYR 0.017 0.002 TYR B 434 PHE 0.021 0.002 PHE A 538 TRP 0.014 0.001 TRP C 175 HIS 0.008 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.27 (12972) covalent geometry : angle 0.72816 / 0.36 (17776) SS BOND : bond 0.00445 / 0.22 ( 4) SS BOND : angle 0.68002 / 0.37 ( 8) hydrogen bonds : bond 0.04017 / 3.00 ( 1119) hydrogen bonds : angle 4.14013 / 3.09 ( 3309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2058.86 seconds wall clock time: 36 minutes 5.08 seconds (2165.08 seconds total)