Starting phenix.real_space_refine on Wed Sep 17 23:38:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9go3_51489/09_2025/9go3_51489.cif Found real_map, /net/cci-nas-00/data/ceres_data/9go3_51489/09_2025/9go3_51489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9go3_51489/09_2025/9go3_51489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9go3_51489/09_2025/9go3_51489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9go3_51489/09_2025/9go3_51489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9go3_51489/09_2025/9go3_51489.map" } resolution = 3.15 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 7686 2.51 5 N 2149 2.21 5 O 2331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12187 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "C" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "F" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "G" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1741 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Time building chain proxies: 3.11, per 1000 atoms: 0.26 Number of scatterers: 12187 At special positions: 0 Unit cell: (101.38, 99.9, 113.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 2331 8.00 N 2149 7.00 C 7686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.07 Conformation dependent library (CDL) restraints added in 552.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 54.6% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 471 through 498 Processing helix chain 'A' and resid 506 through 532 Processing helix chain 'A' and resid 537 through 555 Processing helix chain 'A' and resid 555 through 571 Processing helix chain 'A' and resid 638 through 656 removed outlier: 3.632A pdb=" N ALA A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.506A pdb=" N VAL A 696 " --> pdb=" O LYS A 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 498 Processing helix chain 'B' and resid 506 through 532 Processing helix chain 'B' and resid 537 through 555 Processing helix chain 'B' and resid 555 through 571 Processing helix chain 'B' and resid 638 through 656 removed outlier: 3.598A pdb=" N ALA B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 656 " --> pdb=" O GLU B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 663 Processing helix chain 'B' and resid 692 through 712 removed outlier: 3.512A pdb=" N VAL B 696 " --> pdb=" O LYS B 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 498 Processing helix chain 'C' and resid 506 through 532 Processing helix chain 'C' and resid 537 through 555 Processing helix chain 'C' and resid 555 through 571 Processing helix chain 'C' and resid 638 through 656 removed outlier: 3.598A pdb=" N ALA C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 656 " --> pdb=" O GLU C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 663 Processing helix chain 'C' and resid 692 through 712 Processing helix chain 'D' and resid 472 through 498 Processing helix chain 'D' and resid 506 through 532 Processing helix chain 'D' and resid 537 through 555 Processing helix chain 'D' and resid 555 through 571 Processing helix chain 'D' and resid 638 through 656 removed outlier: 3.640A pdb=" N ALA D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D 656 " --> pdb=" O GLU D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 663 Processing helix chain 'D' and resid 692 through 712 removed outlier: 3.511A pdb=" N VAL D 696 " --> pdb=" O LYS D 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 498 Processing helix chain 'E' and resid 506 through 532 Processing helix chain 'E' and resid 537 through 555 Processing helix chain 'E' and resid 555 through 571 Processing helix chain 'E' and resid 638 through 656 removed outlier: 3.648A pdb=" N ALA E 642 " --> pdb=" O ASP E 638 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN E 656 " --> pdb=" O GLU E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 663 Processing helix chain 'E' and resid 692 through 712 Processing helix chain 'F' and resid 472 through 498 Processing helix chain 'F' and resid 506 through 532 Processing helix chain 'F' and resid 537 through 555 Processing helix chain 'F' and resid 555 through 571 Processing helix chain 'F' and resid 638 through 656 removed outlier: 3.583A pdb=" N ALA F 642 " --> pdb=" O ASP F 638 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN F 656 " --> pdb=" O GLU F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 663 Processing helix chain 'F' and resid 692 through 712 Processing helix chain 'G' and resid 472 through 498 Processing helix chain 'G' and resid 506 through 532 Processing helix chain 'G' and resid 537 through 555 Processing helix chain 'G' and resid 555 through 571 Processing helix chain 'G' and resid 638 through 656 removed outlier: 3.638A pdb=" N ALA G 642 " --> pdb=" O ASP G 638 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 656 " --> pdb=" O GLU G 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 663 Processing helix chain 'G' and resid 692 through 712 removed outlier: 3.512A pdb=" N VAL G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 579 through 582 removed outlier: 5.856A pdb=" N VAL A 589 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG A 600 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 591 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE G 617 " --> pdb=" O ILE A 608 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL G 589 " --> pdb=" O ARG G 600 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG G 600 " --> pdb=" O VAL G 589 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG G 591 " --> pdb=" O GLY G 598 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE F 617 " --> pdb=" O ILE G 608 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL F 589 " --> pdb=" O ARG F 600 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG F 600 " --> pdb=" O VAL F 589 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 591 " --> pdb=" O GLY F 598 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE E 617 " --> pdb=" O ILE F 608 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL E 589 " --> pdb=" O ARG E 600 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG E 600 " --> pdb=" O VAL E 589 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG E 591 " --> pdb=" O GLY E 598 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE D 617 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL D 589 " --> pdb=" O ARG D 600 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG D 600 " --> pdb=" O VAL D 589 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 591 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 617 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL C 589 " --> pdb=" O ARG C 600 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG C 600 " --> pdb=" O VAL C 589 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 591 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 617 " --> pdb=" O ILE C 608 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 589 " --> pdb=" O ARG B 600 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG B 600 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 591 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 617 " --> pdb=" O ILE B 608 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 634 removed outlier: 3.598A pdb=" N VAL A 627 " --> pdb=" O PHE A 686 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA A 679 " --> pdb=" O GLY A 674 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY A 674 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 681 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 672 " --> pdb=" O THR A 681 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ARG A 683 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AA4, first strand: chain 'B' and resid 625 through 634 removed outlier: 3.623A pdb=" N VAL B 627 " --> pdb=" O PHE B 686 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA B 679 " --> pdb=" O GLY B 674 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY B 674 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR B 681 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE B 672 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG B 683 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 625 through 634 removed outlier: 3.557A pdb=" N VAL C 627 " --> pdb=" O PHE C 686 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA C 679 " --> pdb=" O GLY C 674 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLY C 674 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C 681 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE C 672 " --> pdb=" O THR C 681 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG C 683 " --> pdb=" O ALA C 670 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 625 through 634 removed outlier: 3.585A pdb=" N VAL D 627 " --> pdb=" O PHE D 686 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA D 679 " --> pdb=" O GLY D 674 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLY D 674 " --> pdb=" O ALA D 679 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR D 681 " --> pdb=" O ILE D 672 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE D 672 " --> pdb=" O THR D 681 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG D 683 " --> pdb=" O ALA D 670 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 625 through 634 removed outlier: 3.610A pdb=" N VAL E 627 " --> pdb=" O PHE E 686 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ALA E 679 " --> pdb=" O GLY E 674 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLY E 674 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR E 681 " --> pdb=" O ILE E 672 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE E 672 " --> pdb=" O THR E 681 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG E 683 " --> pdb=" O ALA E 670 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 625 through 634 removed outlier: 3.599A pdb=" N VAL F 627 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA F 679 " --> pdb=" O GLY F 674 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY F 674 " --> pdb=" O ALA F 679 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR F 681 " --> pdb=" O ILE F 672 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE F 672 " --> pdb=" O THR F 681 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG F 683 " --> pdb=" O ALA F 670 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 625 through 634 removed outlier: 3.635A pdb=" N VAL G 627 " --> pdb=" O PHE G 686 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA G 679 " --> pdb=" O GLY G 674 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLY G 674 " --> pdb=" O ALA G 679 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR G 681 " --> pdb=" O ILE G 672 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE G 672 " --> pdb=" O THR G 681 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG G 683 " --> pdb=" O ALA G 670 " (cutoff:3.500A) 956 hydrogen bonds defined for protein. 2763 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: 2.21 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4214 1.34 - 1.46: 1510 1.46 - 1.57: 6596 1.57 - 1.69: 0 1.69 - 1.80: 42 Bond restraints: 12362 Sorted by residual: bond pdb=" CB GLU F 652 " pdb=" CG GLU F 652 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" C ALA A 538 " pdb=" N PRO A 539 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.30e-02 5.92e+03 9.48e-01 bond pdb=" N PRO A 502 " pdb=" CA PRO A 502 " ideal model delta sigma weight residual 1.468 1.475 -0.008 7.90e-03 1.60e+04 9.40e-01 bond pdb=" C ALA F 538 " pdb=" N PRO F 539 " ideal model delta sigma weight residual 1.335 1.348 -0.012 1.30e-02 5.92e+03 9.19e-01 bond pdb=" N PRO C 502 " pdb=" CA PRO C 502 " ideal model delta sigma weight residual 1.468 1.475 -0.008 7.90e-03 1.60e+04 9.05e-01 ... (remaining 12357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 16274 1.27 - 2.54: 501 2.54 - 3.81: 87 3.81 - 5.08: 27 5.08 - 6.35: 2 Bond angle restraints: 16891 Sorted by residual: angle pdb=" N VAL G 673 " pdb=" CA VAL G 673 " pdb=" C VAL G 673 " ideal model delta sigma weight residual 113.10 109.80 3.30 9.70e-01 1.06e+00 1.16e+01 angle pdb=" N VAL D 673 " pdb=" CA VAL D 673 " pdb=" C VAL D 673 " ideal model delta sigma weight residual 113.10 109.83 3.27 9.70e-01 1.06e+00 1.14e+01 angle pdb=" N VAL C 673 " pdb=" CA VAL C 673 " pdb=" C VAL C 673 " ideal model delta sigma weight residual 113.10 109.88 3.22 9.70e-01 1.06e+00 1.10e+01 angle pdb=" N VAL A 673 " pdb=" CA VAL A 673 " pdb=" C VAL A 673 " ideal model delta sigma weight residual 113.20 110.05 3.15 9.60e-01 1.09e+00 1.07e+01 angle pdb=" N VAL B 673 " pdb=" CA VAL B 673 " pdb=" C VAL B 673 " ideal model delta sigma weight residual 113.10 109.96 3.14 9.70e-01 1.06e+00 1.05e+01 ... (remaining 16886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6561 17.81 - 35.62: 531 35.62 - 53.43: 134 53.43 - 71.24: 19 71.24 - 89.05: 14 Dihedral angle restraints: 7259 sinusoidal: 2226 harmonic: 5033 Sorted by residual: dihedral pdb=" CA ASN G 656 " pdb=" C ASN G 656 " pdb=" N GLU G 657 " pdb=" CA GLU G 657 " ideal model delta harmonic sigma weight residual -180.00 -163.05 -16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU F 571 " pdb=" CG GLU F 571 " pdb=" CD GLU F 571 " pdb=" OE1 GLU F 571 " ideal model delta sinusoidal sigma weight residual 0.00 -89.05 89.05 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU G 571 " pdb=" CG GLU G 571 " pdb=" CD GLU G 571 " pdb=" OE1 GLU G 571 " ideal model delta sinusoidal sigma weight residual 0.00 89.02 -89.02 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1320 0.030 - 0.061: 450 0.061 - 0.091: 177 0.091 - 0.122: 118 0.122 - 0.152: 14 Chirality restraints: 2079 Sorted by residual: chirality pdb=" CA GLU B 657 " pdb=" N GLU B 657 " pdb=" C GLU B 657 " pdb=" CB GLU B 657 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE F 624 " pdb=" N ILE F 624 " pdb=" C ILE F 624 " pdb=" CB ILE F 624 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE B 624 " pdb=" N ILE B 624 " pdb=" C ILE B 624 " pdb=" CB ILE B 624 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 2076 not shown) Planarity restraints: 2226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 652 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" CD GLU F 652 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU F 652 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU F 652 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 652 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" CD GLU B 652 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU B 652 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 652 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 652 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" CD GLU G 652 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU G 652 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU G 652 " 0.011 2.00e-02 2.50e+03 ... (remaining 2223 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1662 2.75 - 3.29: 12316 3.29 - 3.83: 20961 3.83 - 4.36: 22390 4.36 - 4.90: 40124 Nonbonded interactions: 97453 Sorted by model distance: nonbonded pdb=" OD1 ASP C 561 " pdb=" OG SER C 612 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASP F 561 " pdb=" OG SER F 612 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP G 561 " pdb=" OG SER G 612 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP E 561 " pdb=" OG SER E 612 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP D 561 " pdb=" OG SER D 612 " model vdw 2.226 3.040 ... (remaining 97448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.990 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 0.041 12362 Z= 0.134 Angle : 0.537 6.351 16891 Z= 0.340 Chirality : 0.042 0.152 2079 Planarity : 0.003 0.031 2226 Dihedral : 15.181 89.048 4011 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.48 % Favored : 98.18 % Rotamer: Outliers : 0.38 % Allowed : 22.67 % Favored : 76.95 % 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 aren not related in a simple way. whole: 2.64 (0.20), residues: 1757 helix: 3.66 (0.16), residues: 924 sheet: 0.76 (0.31), residues: 259 loop : -1.18 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 600 TYR 0.014 0.002 TYR G 720 PHE 0.007 0.001 PHE D 680 TRP 0.011 0.001 TRP C 694 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00251 (12362) covalent geometry : angle 0.53657 (16891) hydrogen bonds : bond 0.16405 ( 956) hydrogen bonds : angle 5.54331 ( 2763) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 677 ASN cc_start: 0.7765 (m-40) cc_final: 0.7211 (t0) REVERT: B 720 TYR cc_start: 0.5056 (p90) cc_final: 0.4573 (p90) REVERT: C 677 ASN cc_start: 0.7674 (m-40) cc_final: 0.7126 (m-40) REVERT: D 677 ASN cc_start: 0.7839 (m-40) cc_final: 0.7409 (t0) REVERT: E 677 ASN cc_start: 0.7807 (m-40) cc_final: 0.7541 (t0) REVERT: G 592 MET cc_start: 0.6966 (mtt) cc_final: 0.6551 (mtt) outliers start: 4 outliers final: 2 residues processed: 158 average time/residue: 0.1081 time to fit residues: 25.0520 Evaluate side-chains 97 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain E residue 561 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0010 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 9.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.038348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.028627 restraints weight = 101227.206| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.89 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12362 Z= 0.143 Angle : 0.565 5.100 16891 Z= 0.322 Chirality : 0.043 0.155 2079 Planarity : 0.004 0.046 2226 Dihedral : 3.909 16.448 1845 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.40 % Allowed : 1.42 % Favored : 98.18 % Rotamer: Outliers : 1.43 % Allowed : 22.95 % Favored : 75.62 % 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 aren not related in a simple way. whole: 2.61 (0.20), residues: 1757 helix: 3.40 (0.15), residues: 952 sheet: 0.68 (0.30), residues: 245 loop : -0.89 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 635 TYR 0.027 0.003 TYR A 720 PHE 0.008 0.001 PHE F 567 TRP 0.011 0.001 TRP C 694 HIS 0.001 0.000 HIS G 636 Details of bonding type rmsd covalent geometry : bond 0.00285 (12362) covalent geometry : angle 0.56539 (16891) hydrogen bonds : bond 0.04533 ( 956) hydrogen bonds : angle 4.43730 ( 2763) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8491 (p0) cc_final: 0.8273 (p0) REVERT: B 701 ASP cc_start: 0.9062 (m-30) cc_final: 0.8826 (m-30) REVERT: D 561 ASP cc_start: 0.9050 (m-30) cc_final: 0.8832 (m-30) REVERT: G 632 ASP cc_start: 0.8473 (p0) cc_final: 0.7927 (p0) outliers start: 15 outliers final: 11 residues processed: 113 average time/residue: 0.0744 time to fit residues: 13.9321 Evaluate side-chains 103 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 592 MET Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 644 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.036576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.027077 restraints weight = 107656.088| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 4.70 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12362 Z= 0.176 Angle : 0.519 5.657 16891 Z= 0.298 Chirality : 0.042 0.156 2079 Planarity : 0.003 0.040 2226 Dihedral : 3.768 15.224 1841 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.05 % Favored : 97.55 % Rotamer: Outliers : 3.90 % Allowed : 21.14 % Favored : 74.95 % 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 aren not related in a simple way. whole: 2.82 (0.20), residues: 1757 helix: 3.71 (0.15), residues: 952 sheet: 0.41 (0.29), residues: 245 loop : -0.87 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 635 TYR 0.030 0.003 TYR G 720 PHE 0.007 0.001 PHE D 567 TRP 0.014 0.002 TRP F 694 HIS 0.002 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00345 (12362) covalent geometry : angle 0.51883 (16891) hydrogen bonds : bond 0.03951 ( 956) hydrogen bonds : angle 4.19950 ( 2763) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8551 (p0) cc_final: 0.8227 (p0) REVERT: D 632 ASP cc_start: 0.8500 (p0) cc_final: 0.8206 (p0) REVERT: F 632 ASP cc_start: 0.8519 (p0) cc_final: 0.8266 (p0) REVERT: G 632 ASP cc_start: 0.8443 (p0) cc_final: 0.8014 (p0) REVERT: G 654 MET cc_start: 0.9019 (mmm) cc_final: 0.8787 (mmm) outliers start: 41 outliers final: 27 residues processed: 118 average time/residue: 0.0798 time to fit residues: 15.6929 Evaluate side-chains 107 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 592 MET Chi-restraints excluded: chain F residue 597 VAL Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 97 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.035329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.026155 restraints weight = 108551.892| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.56 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12362 Z= 0.220 Angle : 0.537 5.616 16891 Z= 0.306 Chirality : 0.043 0.146 2079 Planarity : 0.003 0.041 2226 Dihedral : 3.817 15.249 1841 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.28 % Favored : 97.38 % Rotamer: Outliers : 4.10 % Allowed : 21.90 % Favored : 74.00 % 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 aren not related in a simple way. whole: 2.84 (0.20), residues: 1757 helix: 3.81 (0.15), residues: 952 sheet: 0.23 (0.29), residues: 245 loop : -0.93 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 635 TYR 0.028 0.003 TYR G 720 PHE 0.015 0.001 PHE C 567 TRP 0.014 0.002 TRP F 694 HIS 0.002 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00435 (12362) covalent geometry : angle 0.53696 (16891) hydrogen bonds : bond 0.03802 ( 956) hydrogen bonds : angle 4.30531 ( 2763) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8571 (p0) cc_final: 0.8221 (p0) REVERT: D 632 ASP cc_start: 0.8488 (p0) cc_final: 0.8251 (p0) REVERT: E 632 ASP cc_start: 0.8396 (p0) cc_final: 0.8169 (p0) REVERT: F 632 ASP cc_start: 0.8610 (p0) cc_final: 0.8279 (p0) REVERT: G 632 ASP cc_start: 0.8432 (p0) cc_final: 0.7972 (p0) REVERT: G 654 MET cc_start: 0.9073 (mmm) cc_final: 0.8835 (mmm) outliers start: 43 outliers final: 37 residues processed: 110 average time/residue: 0.0773 time to fit residues: 14.6962 Evaluate side-chains 107 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 709 ASP Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 709 ASP Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 687 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 709 ASP Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 597 VAL Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 709 ASP Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 709 ASP Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 131 optimal weight: 0.0040 chunk 153 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 50.0000 chunk 86 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 overall best weight: 3.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.034832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.025814 restraints weight = 107620.580| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 4.50 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12362 Z= 0.196 Angle : 0.515 9.870 16891 Z= 0.287 Chirality : 0.043 0.164 2079 Planarity : 0.003 0.041 2226 Dihedral : 3.758 13.322 1841 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.88 % Favored : 97.89 % Rotamer: Outliers : 2.57 % Allowed : 24.95 % Favored : 72.48 % 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 aren not related in a simple way. whole: 2.91 (0.20), residues: 1757 helix: 3.91 (0.15), residues: 945 sheet: 0.14 (0.29), residues: 245 loop : -0.86 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 635 TYR 0.027 0.003 TYR G 720 PHE 0.010 0.001 PHE G 617 TRP 0.013 0.002 TRP E 694 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00389 (12362) covalent geometry : angle 0.51456 (16891) hydrogen bonds : bond 0.03612 ( 956) hydrogen bonds : angle 4.25799 ( 2763) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8502 (p0) cc_final: 0.8165 (p0) REVERT: D 632 ASP cc_start: 0.8626 (p0) cc_final: 0.8229 (p0) REVERT: E 632 ASP cc_start: 0.8464 (p0) cc_final: 0.8103 (p0) REVERT: F 632 ASP cc_start: 0.8550 (p0) cc_final: 0.8196 (p0) REVERT: G 632 ASP cc_start: 0.8466 (p0) cc_final: 0.8010 (p0) REVERT: G 654 MET cc_start: 0.9046 (mmm) cc_final: 0.8825 (mmm) outliers start: 27 outliers final: 24 residues processed: 99 average time/residue: 0.0791 time to fit residues: 13.6171 Evaluate side-chains 91 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 687 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 597 VAL Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 66 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 0.0050 chunk 103 optimal weight: 0.0670 chunk 126 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.035610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.026351 restraints weight = 106611.852| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.54 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12362 Z= 0.106 Angle : 0.476 8.191 16891 Z= 0.263 Chirality : 0.042 0.140 2079 Planarity : 0.003 0.037 2226 Dihedral : 3.625 13.902 1841 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Rotamer: Outliers : 1.52 % Allowed : 27.05 % Favored : 71.43 % 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 aren not related in a simple way. whole: 3.02 (0.20), residues: 1757 helix: 3.93 (0.15), residues: 945 sheet: 0.25 (0.29), residues: 245 loop : -0.70 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 635 TYR 0.026 0.002 TYR G 720 PHE 0.007 0.001 PHE F 567 TRP 0.009 0.001 TRP C 694 HIS 0.001 0.001 HIS G 636 Details of bonding type rmsd covalent geometry : bond 0.00209 (12362) covalent geometry : angle 0.47623 (16891) hydrogen bonds : bond 0.03362 ( 956) hydrogen bonds : angle 4.01217 ( 2763) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8508 (p0) cc_final: 0.8152 (p0) REVERT: D 632 ASP cc_start: 0.8590 (p0) cc_final: 0.8177 (p0) REVERT: E 632 ASP cc_start: 0.8463 (p0) cc_final: 0.8110 (p0) REVERT: F 632 ASP cc_start: 0.8559 (p0) cc_final: 0.8221 (p0) REVERT: G 632 ASP cc_start: 0.8510 (p0) cc_final: 0.8054 (p0) REVERT: G 654 MET cc_start: 0.9017 (mmm) cc_final: 0.8767 (mmm) outliers start: 16 outliers final: 13 residues processed: 87 average time/residue: 0.0866 time to fit residues: 12.4384 Evaluate side-chains 81 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 119 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 50 optimal weight: 80.0000 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 102 optimal weight: 50.0000 chunk 154 optimal weight: 6.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.034686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.025645 restraints weight = 109306.937| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 4.45 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12362 Z= 0.206 Angle : 0.522 7.059 16891 Z= 0.295 Chirality : 0.042 0.138 2079 Planarity : 0.003 0.039 2226 Dihedral : 3.676 12.985 1841 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.05 % Favored : 97.61 % Rotamer: Outliers : 2.86 % Allowed : 25.81 % Favored : 71.33 % 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 aren not related in a simple way. whole: 3.09 (0.21), residues: 1757 helix: 4.07 (0.15), residues: 945 sheet: 0.12 (0.29), residues: 245 loop : -0.77 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 595 TYR 0.025 0.003 TYR G 720 PHE 0.009 0.001 PHE F 567 TRP 0.011 0.001 TRP F 694 HIS 0.002 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00409 (12362) covalent geometry : angle 0.52189 (16891) hydrogen bonds : bond 0.03546 ( 956) hydrogen bonds : angle 4.16450 ( 2763) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8445 (p0) cc_final: 0.8123 (p0) REVERT: D 632 ASP cc_start: 0.8585 (p0) cc_final: 0.8184 (p0) REVERT: E 632 ASP cc_start: 0.8483 (p0) cc_final: 0.8157 (p0) REVERT: F 632 ASP cc_start: 0.8465 (p0) cc_final: 0.8160 (p0) REVERT: G 632 ASP cc_start: 0.8408 (p0) cc_final: 0.7982 (p0) REVERT: G 654 MET cc_start: 0.8994 (mmm) cc_final: 0.8772 (mmm) outliers start: 30 outliers final: 21 residues processed: 88 average time/residue: 0.0883 time to fit residues: 13.0548 Evaluate side-chains 86 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 627 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 687 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 709 ASP Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 592 MET Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 709 ASP Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 709 ASP Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 37 optimal weight: 0.0070 chunk 133 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.035117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.026030 restraints weight = 104249.544| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 4.48 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12362 Z= 0.120 Angle : 0.478 7.177 16891 Z= 0.267 Chirality : 0.042 0.138 2079 Planarity : 0.003 0.039 2226 Dihedral : 3.612 13.713 1841 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.22 % Favored : 97.55 % Rotamer: Outliers : 1.81 % Allowed : 26.86 % Favored : 71.33 % 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 aren not related in a simple way. whole: 3.11 (0.20), residues: 1757 helix: 4.01 (0.15), residues: 945 sheet: 0.24 (0.29), residues: 245 loop : -0.68 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 595 TYR 0.026 0.002 TYR G 720 PHE 0.007 0.001 PHE E 567 TRP 0.009 0.001 TRP E 694 HIS 0.002 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00242 (12362) covalent geometry : angle 0.47834 (16891) hydrogen bonds : bond 0.03360 ( 956) hydrogen bonds : angle 4.07854 ( 2763) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8457 (p0) cc_final: 0.8112 (p0) REVERT: D 632 ASP cc_start: 0.8519 (p0) cc_final: 0.8127 (p0) REVERT: E 632 ASP cc_start: 0.8488 (p0) cc_final: 0.8094 (p0) REVERT: F 632 ASP cc_start: 0.8466 (p0) cc_final: 0.8160 (p0) REVERT: G 632 ASP cc_start: 0.8434 (p0) cc_final: 0.7977 (p0) REVERT: G 654 MET cc_start: 0.8975 (mmm) cc_final: 0.8734 (mmm) outliers start: 19 outliers final: 19 residues processed: 86 average time/residue: 0.0784 time to fit residues: 11.7392 Evaluate side-chains 88 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 627 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 687 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 592 MET Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 132 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.034535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.025597 restraints weight = 106704.655| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.47 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12362 Z= 0.184 Angle : 0.502 6.762 16891 Z= 0.282 Chirality : 0.043 0.335 2079 Planarity : 0.003 0.040 2226 Dihedral : 3.638 13.228 1841 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.88 % Favored : 97.84 % Rotamer: Outliers : 2.38 % Allowed : 26.38 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.17 (0.21), residues: 1757 helix: 4.11 (0.15), residues: 945 sheet: 0.21 (0.29), residues: 245 loop : -0.71 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 595 TYR 0.024 0.002 TYR G 720 PHE 0.008 0.001 PHE A 567 TRP 0.010 0.001 TRP F 694 HIS 0.002 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00369 (12362) covalent geometry : angle 0.50248 (16891) hydrogen bonds : bond 0.03443 ( 956) hydrogen bonds : angle 4.16463 ( 2763) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8441 (p0) cc_final: 0.8111 (p0) REVERT: D 632 ASP cc_start: 0.8529 (p0) cc_final: 0.8158 (p0) REVERT: E 632 ASP cc_start: 0.8478 (p0) cc_final: 0.8141 (p0) REVERT: F 632 ASP cc_start: 0.8487 (p0) cc_final: 0.8184 (p0) REVERT: G 632 ASP cc_start: 0.8395 (p0) cc_final: 0.7932 (p0) REVERT: G 654 MET cc_start: 0.8967 (mmm) cc_final: 0.8732 (mmm) outliers start: 25 outliers final: 24 residues processed: 86 average time/residue: 0.0771 time to fit residues: 11.5602 Evaluate side-chains 90 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 627 VAL Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 687 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 592 MET Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain G residue 688 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 69 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 50 optimal weight: 80.0000 chunk 106 optimal weight: 0.0980 chunk 129 optimal weight: 30.0000 chunk 133 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.035367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.026255 restraints weight = 102913.322| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 4.51 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12362 Z= 0.096 Angle : 0.502 16.687 16891 Z= 0.268 Chirality : 0.043 0.138 2079 Planarity : 0.003 0.039 2226 Dihedral : 3.527 13.922 1841 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 1.33 % Allowed : 27.33 % Favored : 71.33 % 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 aren not related in a simple way. whole: 3.10 (0.20), residues: 1757 helix: 3.96 (0.15), residues: 945 sheet: 0.35 (0.29), residues: 245 loop : -0.65 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 595 TYR 0.026 0.002 TYR G 720 PHE 0.008 0.001 PHE C 686 TRP 0.009 0.001 TRP F 694 HIS 0.001 0.000 HIS G 636 Details of bonding type rmsd covalent geometry : bond 0.00185 (12362) covalent geometry : angle 0.50227 (16891) hydrogen bonds : bond 0.03229 ( 956) hydrogen bonds : angle 3.99293 ( 2763) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8491 (p0) cc_final: 0.8141 (p0) REVERT: D 632 ASP cc_start: 0.8498 (p0) cc_final: 0.8110 (p0) REVERT: E 632 ASP cc_start: 0.8525 (p0) cc_final: 0.8062 (p0) REVERT: F 632 ASP cc_start: 0.8508 (p0) cc_final: 0.8218 (p0) REVERT: G 632 ASP cc_start: 0.8492 (p0) cc_final: 0.8073 (p0) REVERT: G 654 MET cc_start: 0.8964 (mmm) cc_final: 0.8698 (mmm) outliers start: 14 outliers final: 13 residues processed: 82 average time/residue: 0.0774 time to fit residues: 11.2511 Evaluate side-chains 82 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 627 VAL Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 720 TYR Chi-restraints excluded: chain E residue 687 THR Chi-restraints excluded: chain E residue 720 TYR Chi-restraints excluded: chain F residue 592 MET Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 687 THR Chi-restraints excluded: chain G residue 720 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 110 optimal weight: 0.0980 chunk 163 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 0.0870 chunk 172 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 2 optimal weight: 50.0000 chunk 70 optimal weight: 9.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.035491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.026406 restraints weight = 102613.528| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 4.49 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12362 Z= 0.097 Angle : 0.488 15.467 16891 Z= 0.266 Chirality : 0.043 0.136 2079 Planarity : 0.003 0.038 2226 Dihedral : 3.419 13.035 1841 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.43 % Allowed : 27.33 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.07 (0.20), residues: 1757 helix: 3.90 (0.15), residues: 945 sheet: 0.46 (0.30), residues: 245 loop : -0.66 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 595 TYR 0.025 0.002 TYR G 720 PHE 0.007 0.001 PHE C 686 TRP 0.009 0.001 TRP F 694 HIS 0.001 0.000 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00191 (12362) covalent geometry : angle 0.48816 (16891) hydrogen bonds : bond 0.03194 ( 956) hydrogen bonds : angle 3.92885 ( 2763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.85 seconds wall clock time: 41 minutes 22.82 seconds (2482.82 seconds total)