Starting phenix.real_space_refine on Sat Aug 23 13:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vql_65259/08_2025/9vql_65259.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vql_65259/08_2025/9vql_65259.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/9vql_65259/08_2025/9vql_65259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vql_65259/08_2025/9vql_65259.map" model { file = "/net/cci-nas-00/data/ceres_data/9vql_65259/08_2025/9vql_65259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vql_65259/08_2025/9vql_65259.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= -0.002 sd= 0.057 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 122 5.16 5 C 7619 2.51 5 N 2021 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12122 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 5936 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 49, 'TRANS': 762} Chain breaks: 8 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 17, 'PHE:plan': 4, 'ASP:plan': 11, 'TYR:plan': 2, 'ARG:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 183 Chain: "B" Number of atoms: 5990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 5990 Classifications: {'peptide': 814} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 49, 'TRANS': 764} Chain breaks: 7 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 9, 'TYR:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 182 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.30, per 1000 atoms: 0.19 Number of scatterers: 12122 At special positions: 0 Unit cell: (155.441, 108.7, 164.137, 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 122 16.00 O 2360 8.00 N 2021 7.00 C 7619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 505 " - pdb=" SG CYS A 509 " distance=2.02 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 602 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS A 618 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 638 " distance=2.04 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 739 " distance=2.04 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 844 " distance=2.03 Simple disulfide: pdb=" SG CYS A 820 " - pdb=" SG CYS A 856 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 841 " distance=2.03 Simple disulfide: pdb=" SG CYS A 859 " - pdb=" SG CYS A 888 " distance=2.03 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 902 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 324 " distance=2.03 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 379 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 509 " distance=2.02 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 602 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS B 618 " distance=2.03 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 638 " distance=2.04 Simple disulfide: pdb=" SG CYS B 641 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 714 " - pdb=" SG CYS B 739 " distance=2.04 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 844 " distance=2.03 Simple disulfide: pdb=" SG CYS B 820 " - pdb=" SG CYS B 856 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 841 " distance=2.03 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 888 " distance=2.03 Simple disulfide: pdb=" SG CYS B 871 " - pdb=" SG CYS B 902 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1101 " - " ASN A 153 " " NAG A1102 " - " ASN A 576 " " NAG A1103 " - " ASN A 544 " " NAG B1101 " - " ASN B 153 " " NAG B1102 " - " ASN B 576 " " NAG B1103 " - " ASN B 544 " " NAG C 1 " - " ASN A 672 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN B 672 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 539.6 milliseconds Enol-peptide restraints added in 1.4 microseconds 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3018 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 46 sheets defined 3.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.885A pdb=" N ASP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.524A pdb=" N ALA A 677 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 709 Processing helix chain 'A' and resid 716 through 721 removed outlier: 4.520A pdb=" N ASP A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.542A pdb=" N MET A 749 " --> pdb=" O PRO A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.877A pdb=" N ASP B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.597A pdb=" N ALA B 677 " --> pdb=" O SER B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 745 through 750 removed outlier: 3.673A pdb=" N MET B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.997A pdb=" N ILE A 264 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 139 Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 167 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 339 removed outlier: 3.604A pdb=" N PHE A 336 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 386 through 387 removed outlier: 3.662A pdb=" N GLU A 395 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 401 through 402 Processing sheet with id=AB3, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AB4, first strand: chain 'A' and resid 433 through 438 removed outlier: 3.518A pdb=" N GLN A 554 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 510 " --> pdb=" O GLN A 554 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 526 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 515 " --> pdb=" O PRO A 524 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 495 through 497 removed outlier: 3.651A pdb=" N ALA A 495 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 501 through 502 removed outlier: 3.639A pdb=" N LYS A 571 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 609 through 611 Processing sheet with id=AB8, first strand: chain 'A' and resid 625 through 626 Processing sheet with id=AB9, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AC1, first strand: chain 'A' and resid 680 through 683 Processing sheet with id=AC2, first strand: chain 'A' and resid 680 through 683 removed outlier: 3.817A pdb=" N PHE A 696 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL A 738 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER A 761 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN A 740 " --> pdb=" O PRO A 759 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.622A pdb=" N ALA A 712 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 765 through 770 removed outlier: 5.658A pdb=" N LEU A 766 " --> pdb=" O ARG A 800 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG A 800 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR A 815 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TRP A 850 " --> pdb=" O THR A 815 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG A 817 " --> pdb=" O TRP A 850 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N SER A 852 " --> pdb=" O ARG A 817 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG A 819 " --> pdb=" O SER A 852 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 774 through 775 Processing sheet with id=AC6, first strand: chain 'A' and resid 864 through 865 removed outlier: 3.626A pdb=" N MET A 881 " --> pdb=" O HIS A 865 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 54 through 58 Processing sheet with id=AC8, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AC9, first strand: chain 'B' and resid 135 through 139 Processing sheet with id=AD1, first strand: chain 'B' and resid 229 through 234 Processing sheet with id=AD2, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AD3, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AD4, first strand: chain 'B' and resid 315 through 316 Processing sheet with id=AD5, first strand: chain 'B' and resid 335 through 339 removed outlier: 3.598A pdb=" N PHE B 336 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 353 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 386 through 387 removed outlier: 4.023A pdb=" N GLU B 395 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 401 through 403 Processing sheet with id=AD8, first strand: chain 'B' and resid 415 through 416 Processing sheet with id=AD9, first strand: chain 'B' and resid 420 through 423 Processing sheet with id=AE1, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.515A pdb=" N GLY B 516 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 554 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 510 " --> pdb=" O GLN B 554 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 515 " --> pdb=" O PRO B 524 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 609 through 611 Processing sheet with id=AE3, first strand: chain 'B' and resid 625 through 626 Processing sheet with id=AE4, first strand: chain 'B' and resid 646 through 647 Processing sheet with id=AE5, first strand: chain 'B' and resid 680 through 683 Processing sheet with id=AE6, first strand: chain 'B' and resid 680 through 683 removed outlier: 3.634A pdb=" N PHE B 696 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL B 738 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER B 761 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLN B 740 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 712 through 714 removed outlier: 3.556A pdb=" N ALA B 712 " --> pdb=" O ALA B 736 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 765 through 770 removed outlier: 5.609A pdb=" N LEU B 766 " --> pdb=" O ARG B 800 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG B 800 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 770 " --> pdb=" O VAL B 796 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 815 " --> pdb=" O PHE B 848 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TRP B 850 " --> pdb=" O THR B 815 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG B 817 " --> pdb=" O TRP B 850 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER B 852 " --> pdb=" O ARG B 817 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 819 " --> pdb=" O SER B 852 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 774 through 775 Processing sheet with id=AF1, first strand: chain 'B' and resid 864 through 866 259 hydrogen bonds defined for protein. 606 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: 1.64 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2029 1.32 - 1.45: 3518 1.45 - 1.57: 6736 1.57 - 1.70: 0 1.70 - 1.82: 145 Bond restraints: 12428 Sorted by residual: bond pdb=" CA PHE B 501 " pdb=" C PHE B 501 " ideal model delta sigma weight residual 1.531 1.437 0.094 1.46e-02 4.69e+03 4.16e+01 bond pdb=" CA PHE A 501 " pdb=" C PHE A 501 " ideal model delta sigma weight residual 1.526 1.452 0.074 1.21e-02 6.83e+03 3.76e+01 bond pdb=" CA SER A 574 " pdb=" CB SER A 574 " ideal model delta sigma weight residual 1.530 1.433 0.097 1.69e-02 3.50e+03 3.31e+01 bond pdb=" CA SER A 536 " pdb=" CB SER A 536 " ideal model delta sigma weight residual 1.530 1.470 0.061 1.69e-02 3.50e+03 1.29e+01 bond pdb=" CA PHE B 499 " pdb=" C PHE B 499 " ideal model delta sigma weight residual 1.522 1.479 0.042 1.20e-02 6.94e+03 1.25e+01 ... (remaining 12423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 16940 5.40 - 10.80: 36 10.80 - 16.20: 5 16.20 - 21.60: 1 21.60 - 27.00: 2 Bond angle restraints: 16984 Sorted by residual: angle pdb=" C CYS B 739 " pdb=" CA CYS B 739 " pdb=" CB CYS B 739 " ideal model delta sigma weight residual 109.37 84.60 24.77 1.91e+00 2.74e-01 1.68e+02 angle pdb=" C CYS A 739 " pdb=" CA CYS A 739 " pdb=" CB CYS A 739 " ideal model delta sigma weight residual 109.38 82.38 27.00 2.09e+00 2.29e-01 1.67e+02 angle pdb=" CA PHE A 499 " pdb=" CB PHE A 499 " pdb=" CG PHE A 499 " ideal model delta sigma weight residual 113.80 125.64 -11.84 1.00e+00 1.00e+00 1.40e+02 angle pdb=" CA PHE B 499 " pdb=" CB PHE B 499 " pdb=" CG PHE B 499 " ideal model delta sigma weight residual 113.80 125.23 -11.43 1.00e+00 1.00e+00 1.31e+02 angle pdb=" N VAL B 500 " pdb=" CA VAL B 500 " pdb=" C VAL B 500 " ideal model delta sigma weight residual 108.17 94.09 14.08 1.40e+00 5.10e-01 1.01e+02 ... (remaining 16979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 6930 18.09 - 36.18: 479 36.18 - 54.28: 122 54.28 - 72.37: 45 72.37 - 90.46: 10 Dihedral angle restraints: 7586 sinusoidal: 2890 harmonic: 4696 Sorted by residual: dihedral pdb=" C CYS A 739 " pdb=" N CYS A 739 " pdb=" CA CYS A 739 " pdb=" CB CYS A 739 " ideal model delta harmonic sigma weight residual -122.60 -91.46 -31.14 0 2.50e+00 1.60e-01 1.55e+02 dihedral pdb=" C CYS B 739 " pdb=" N CYS B 739 " pdb=" CA CYS B 739 " pdb=" CB CYS B 739 " ideal model delta harmonic sigma weight residual -122.60 -94.29 -28.31 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" CB CYS B 411 " pdb=" SG CYS B 411 " pdb=" SG CYS B 588 " pdb=" CB CYS B 588 " ideal model delta sinusoidal sigma weight residual 93.00 -178.27 -88.73 1 1.00e+01 1.00e-02 9.39e+01 ... (remaining 7583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 1928 0.155 - 0.310: 30 0.310 - 0.465: 4 0.465 - 0.620: 2 0.620 - 0.775: 2 Chirality restraints: 1966 Sorted by residual: chirality pdb=" C1 NAG B1103 " pdb=" ND2 ASN B 544 " pdb=" C2 NAG B1103 " pdb=" O5 NAG B1103 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C1 NAG A1103 " pdb=" ND2 ASN A 544 " pdb=" C2 NAG A1103 " pdb=" O5 NAG A1103 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.91e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 717 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.29e+00 ... (remaining 1963 not shown) Planarity restraints: 2179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1103 " -0.194 2.00e-02 2.50e+03 1.66e-01 3.45e+02 pdb=" C7 NAG A1103 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG A1103 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG A1103 " 0.277 2.00e-02 2.50e+03 pdb=" O7 NAG A1103 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 496 " -0.478 9.50e-02 1.11e+02 2.14e-01 2.81e+01 pdb=" NE ARG A 496 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 496 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 496 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 496 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 502 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C GLU A 502 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU A 502 " -0.027 2.00e-02 2.50e+03 pdb=" N THR A 503 " -0.026 2.00e-02 2.50e+03 ... (remaining 2176 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 293 2.67 - 3.23: 11801 3.23 - 3.79: 17870 3.79 - 4.34: 24102 4.34 - 4.90: 40102 Nonbonded interactions: 94168 Sorted by model distance: nonbonded pdb=" OH TYR B 195 " pdb=" O ILE B 200 " model vdw 2.115 3.040 nonbonded pdb=" O PHE A 124 " pdb=" NE1 TRP A 127 " model vdw 2.161 3.120 nonbonded pdb=" OH TYR A 195 " pdb=" O ILE A 200 " model vdw 2.200 3.040 nonbonded pdb=" O PRO A 622 " pdb=" OG1 THR A 625 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR A 664 " pdb=" O ARG A 667 " model vdw 2.210 3.040 ... (remaining 94163 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' and (resid 50 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 131 or (resid 132 and (name N or n \ ame CA or name C or name O or name CB )) or resid 133 through 140 or resid 153 t \ hrough 171 or (resid 172 and (name N or name CA or name C or name O or name CB ) \ ) or resid 173 through 318 or (resid 319 and (name N or name CA or name C or nam \ e O or name CB )) or resid 320 through 324 or (resid 325 and (name N or name CA \ or name C or name O or name CB )) or resid 326 through 329 or (resid 330 and (na \ me N or name CA or name C or name O or name CB )) or resid 331 or (resid 332 and \ (name N or name CA or name C or name O or name CB )) or resid 333 through 348 o \ r (resid 349 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 50 through 495 or (resid 496 and (name N or name CA or name C or name O or name \ CB )) or resid 497 through 516 or (resid 517 through 518 and (name N or name CA \ or name C or name O or name CB )) or resid 519 through 520 or (resid 521 and (na \ me N or name CA or name C or name O or name CB )) or resid 522 through 542 or (r \ esid 543 and (name N or name CA or name C or name O or name CB )) or resid 544 t \ hrough 558 or (resid 559 through 560 and (name N or name CA or name C or name O \ or name CB )) or resid 562 through 567 or (resid 568 and (name N or name CA or n \ ame C or name O or name CB )) or resid 569 through 612 or (resid 613 and (name N \ or name CA or name C or name O or name CB )) or resid 614 through 629 or (resid \ 630 and (name N or name CA or name C or name O or name CB )) or resid 631 throu \ gh 822 or (resid 823 through 826 and (name N or name CA or name C or name O or n \ ame CB )) or resid 827 through 883 or (resid 884 and (name N or name CA or name \ C or name O or name CB )) or resid 885 through 1103)) selection = (chain 'B' and (resid 50 through 62 or (resid 63 through 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 or (resid 66 and (name N or nam \ e CA or name C or name O or name CB )) or resid 67 through 86 or (resid 87 and ( \ name N or name CA or name C or name O or name CB )) or resid 88 through 89 or (r \ esid 90 and (name N or name CA or name C or name O or name CB )) or resid 91 thr \ ough 92 or (resid 93 and (name N or name CA or name C or name O or name CB )) or \ resid 94 through 100 or (resid 101 through 105 and (name N or name CA or name C \ or name O or name CB )) or resid 106 through 108 or (resid 109 and (name N or n \ ame CA or name C or name O or name CB )) or resid 110 through 127 or (resid 128 \ and (name N or name CA or name C or name O or name CB )) or resid 129 through 22 \ 6 or resid 228 through 236 or (resid 237 and (name N or name CA or name C or nam \ e O or name CB )) or resid 238 through 261 or (resid 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 273 or (resid 274 and (na \ me N or name CA or name C or name O or name CB )) or resid 275 through 285 or (r \ esid 286 and (name N or name CA or name C or name O or name CB )) or resid 287 t \ hrough 292 or (resid 293 and (name N or name CA or name C or name O or name CB ) \ ) or resid 294 through 311 or (resid 312 through 315 and (name N or name CA or n \ ame C or name O or name CB )) or resid 316 through 333 or (resid 334 and (name N \ or name CA or name C or name O or name CB )) or resid 335 through 355 or (resid \ 356 and (name N or name CA or name C or name O or name CB )) or resid 357 throu \ gh 358 or (resid 359 and (name N or name CA or name C or name O or name CB )) or \ resid 360 through 386 or (resid 387 through 388 and (name N or name CA or name \ C or name O or name CB )) or resid 391 through 392 or (resid 393 and (name N or \ name CA or name C or name O or name CB )) or resid 394 or (resid 395 and (name N \ or name CA or name C or name O or name CB )) or resid 396 through 398 or (resid \ 399 and (name N or name CA or name C or name O or name CB )) or resid 400 throu \ gh 409 or (resid 410 and (name N or name CA or name C or name O or name CB )) or \ resid 411 through 485 or (resid 486 through 488 and (name N or name CA or name \ C or name O or name CB )) or resid 489 or (resid 490 through 493 and (name N or \ name CA or name C or name O or name CB )) or resid 494 through 580 or (resid 581 \ and (name N or name CA or name C or name O or name CB )) or resid 582 through 5 \ 93 or (resid 594 and (name N or name CA or name C or name O or name CB )) or res \ id 602 through 717 or (resid 718 and (name N or name CA or name C or name O or n \ ame CB )) or resid 719 through 745 or (resid 746 through 749 and (name N or name \ CA or name C or name O or name CB )) or resid 750 or resid 755 through 1103)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.590 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3280 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 : 0.005 0.097 12488 Z= 0.284 Angle : 0.944 26.998 17118 Z= 0.551 Chirality : 0.059 0.775 1966 Planarity : 0.008 0.214 2169 Dihedral : 13.599 90.461 4430 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.16 % Favored : 93.78 % Rotamer: Outliers : 0.80 % Allowed : 0.48 % Favored : 98.73 % Cbeta Deviations : 0.53 % 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: -0.95 (0.21), residues: 1592 helix: -1.80 (1.10), residues: 24 sheet: -0.98 (0.24), residues: 503 loop : -0.35 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 555 TYR 0.034 0.002 TYR A 459 PHE 0.027 0.002 PHE B 501 TRP 0.022 0.001 TRP B 68 HIS 0.010 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00482 (12428) covalent geometry : angle 0.89640 (16984) SS BOND : bond 0.00360 ( 46) SS BOND : angle 1.68831 ( 92) hydrogen bonds : bond 0.25015 ( 251) hydrogen bonds : angle 9.72941 ( 606) link_BETA1-4 : bond 0.00462 ( 4) link_BETA1-4 : angle 3.82717 ( 12) link_NAG-ASN : bond 0.00936 ( 10) link_NAG-ASN : angle 6.23467 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 300 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.6673 (pttt) cc_final: 0.6395 (ptmm) REVERT: A 823 MET cc_start: 0.3544 (ptp) cc_final: 0.3192 (mmm) REVERT: A 835 MET cc_start: 0.4468 (ppp) cc_final: 0.3926 (pmm) REVERT: B 271 TYR cc_start: 0.5245 (m-10) cc_final: 0.4997 (m-10) REVERT: B 693 LEU cc_start: 0.6182 (tp) cc_final: 0.5965 (tp) REVERT: B 799 PHE cc_start: 0.5416 (m-10) cc_final: 0.4674 (m-10) REVERT: B 816 ILE cc_start: 0.5952 (mt) cc_final: 0.5557 (mt) outliers start: 10 outliers final: 6 residues processed: 308 average time/residue: 0.0860 time to fit residues: 38.6313 Evaluate side-chains 175 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain B residue 499 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 HIS ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS B 427 ASN B 522 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN B 697 HIS B 740 GLN ** B 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.179022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.151681 restraints weight = 18520.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.151418 restraints weight = 20046.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.153778 restraints weight = 17092.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.153922 restraints weight = 12206.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154449 restraints weight = 12444.873| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4463 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12488 Z= 0.215 Angle : 0.848 14.381 17118 Z= 0.437 Chirality : 0.051 0.490 1966 Planarity : 0.006 0.073 2169 Dihedral : 8.131 76.663 2029 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.79 % Allowed : 13.23 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.17 (0.21), residues: 1592 helix: -2.01 (1.01), residues: 24 sheet: -1.15 (0.23), residues: 500 loop : -0.49 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 613 TYR 0.023 0.002 TYR A 610 PHE 0.029 0.003 PHE B 867 TRP 0.024 0.002 TRP B 252 HIS 0.016 0.002 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00469 (12428) covalent geometry : angle 0.79750 (16984) SS BOND : bond 0.00572 ( 46) SS BOND : angle 1.96866 ( 92) hydrogen bonds : bond 0.04719 ( 251) hydrogen bonds : angle 7.27462 ( 606) link_BETA1-4 : bond 0.00646 ( 4) link_BETA1-4 : angle 3.02169 ( 12) link_NAG-ASN : bond 0.01060 ( 10) link_NAG-ASN : angle 5.86239 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 PHE cc_start: 0.4017 (m-80) cc_final: 0.3583 (m-80) REVERT: A 835 MET cc_start: 0.4737 (ppp) cc_final: 0.4139 (pmm) REVERT: B 235 LEU cc_start: 0.3946 (mt) cc_final: 0.3007 (mt) REVERT: B 795 ILE cc_start: 0.4217 (mt) cc_final: 0.3611 (mt) REVERT: B 881 MET cc_start: 0.5844 (mpp) cc_final: 0.4298 (mmm) outliers start: 35 outliers final: 23 residues processed: 245 average time/residue: 0.0732 time to fit residues: 27.4603 Evaluate side-chains 187 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 894 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 chunk 122 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A 786 HIS ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS B 609 HIS B 647 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.180801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.157301 restraints weight = 18935.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.156959 restraints weight = 22017.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.158967 restraints weight = 19393.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.158770 restraints weight = 13932.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159039 restraints weight = 14427.815| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4840 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12488 Z= 0.159 Angle : 0.773 13.851 17118 Z= 0.386 Chirality : 0.048 0.468 1966 Planarity : 0.005 0.062 2169 Dihedral : 8.264 75.079 2023 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.95 % Allowed : 17.93 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.07 % 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: -1.20 (0.21), residues: 1592 helix: -1.20 (1.03), residues: 29 sheet: -1.29 (0.23), residues: 511 loop : -0.45 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 115 TYR 0.023 0.001 TYR A 300 PHE 0.020 0.002 PHE B 276 TRP 0.030 0.002 TRP B 252 HIS 0.007 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00341 (12428) covalent geometry : angle 0.72189 (16984) SS BOND : bond 0.00364 ( 46) SS BOND : angle 1.75508 ( 92) hydrogen bonds : bond 0.04351 ( 251) hydrogen bonds : angle 6.76117 ( 606) link_BETA1-4 : bond 0.00715 ( 4) link_BETA1-4 : angle 2.69628 ( 12) link_NAG-ASN : bond 0.01193 ( 10) link_NAG-ASN : angle 5.81147 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.4922 (m-80) cc_final: 0.4669 (m-80) REVERT: A 221 MET cc_start: 0.3867 (tpt) cc_final: 0.3600 (tpt) REVERT: A 835 MET cc_start: 0.4842 (ppp) cc_final: 0.4173 (pmm) REVERT: B 179 TYR cc_start: 0.6642 (t80) cc_final: 0.6271 (t80) REVERT: B 529 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7178 (mttp) REVERT: B 881 MET cc_start: 0.6474 (mpp) cc_final: 0.5083 (mmm) outliers start: 37 outliers final: 20 residues processed: 224 average time/residue: 0.0732 time to fit residues: 25.4697 Evaluate side-chains 187 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 899 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 83 optimal weight: 0.0030 chunk 107 optimal weight: 9.9990 chunk 157 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 147 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.181008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.154374 restraints weight = 19077.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.153293 restraints weight = 22038.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.155539 restraints weight = 19215.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155828 restraints weight = 13552.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.156030 restraints weight = 14083.146| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.7472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 12488 Z= 0.246 Angle : 0.877 15.427 17118 Z= 0.455 Chirality : 0.051 0.464 1966 Planarity : 0.006 0.082 2169 Dihedral : 8.569 93.212 2021 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 5.10 % Allowed : 18.73 % Favored : 76.18 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -1.37 (0.20), residues: 1592 helix: -1.07 (1.01), residues: 29 sheet: -1.40 (0.24), residues: 460 loop : -0.65 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 67 TYR 0.027 0.002 TYR B 880 PHE 0.034 0.003 PHE B 191 TRP 0.020 0.002 TRP A 244 HIS 0.073 0.004 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00550 (12428) covalent geometry : angle 0.83877 (16984) SS BOND : bond 0.00733 ( 46) SS BOND : angle 1.85720 ( 92) hydrogen bonds : bond 0.04311 ( 251) hydrogen bonds : angle 7.12558 ( 606) link_BETA1-4 : bond 0.00192 ( 4) link_BETA1-4 : angle 2.72137 ( 12) link_NAG-ASN : bond 0.01013 ( 10) link_NAG-ASN : angle 5.24443 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.6806 (t) cc_final: 0.6392 (t) REVERT: A 433 MET cc_start: 0.3957 (tmm) cc_final: 0.3383 (mmt) REVERT: A 835 MET cc_start: 0.5363 (ppp) cc_final: 0.5005 (pmm) REVERT: A 840 THR cc_start: 0.4664 (OUTLIER) cc_final: 0.4266 (p) REVERT: B 184 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8132 (tppt) REVERT: B 433 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7422 (mmt) REVERT: B 534 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7737 (tttp) REVERT: B 671 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: B 749 MET cc_start: 0.6457 (tmm) cc_final: 0.6155 (tmm) REVERT: B 881 MET cc_start: 0.7115 (mpp) cc_final: 0.6660 (mmm) outliers start: 64 outliers final: 25 residues processed: 241 average time/residue: 0.0652 time to fit residues: 24.3163 Evaluate side-chains 182 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 671 TYR Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 64 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 122 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 114 optimal weight: 0.0010 chunk 147 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN A 865 HIS B 706 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.180830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.156498 restraints weight = 19079.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.156236 restraints weight = 24470.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.157867 restraints weight = 20161.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.157790 restraints weight = 15043.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.157987 restraints weight = 14837.595| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.8255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12488 Z= 0.151 Angle : 0.744 12.660 17118 Z= 0.373 Chirality : 0.047 0.456 1966 Planarity : 0.005 0.055 2169 Dihedral : 8.230 92.698 2021 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.59 % Allowed : 21.59 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -1.27 (0.21), residues: 1592 helix: -0.99 (1.00), residues: 29 sheet: -1.36 (0.23), residues: 485 loop : -0.53 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 819 TYR 0.021 0.001 TYR A 459 PHE 0.023 0.002 PHE B 785 TRP 0.031 0.002 TRP A 425 HIS 0.015 0.002 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00327 (12428) covalent geometry : angle 0.70274 (16984) SS BOND : bond 0.00341 ( 46) SS BOND : angle 1.62140 ( 92) hydrogen bonds : bond 0.03803 ( 251) hydrogen bonds : angle 6.62014 ( 606) link_BETA1-4 : bond 0.00954 ( 4) link_BETA1-4 : angle 2.64205 ( 12) link_NAG-ASN : bond 0.00858 ( 10) link_NAG-ASN : angle 5.07643 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 835 MET cc_start: 0.5378 (ppp) cc_final: 0.4910 (pmm) REVERT: A 840 THR cc_start: 0.5313 (OUTLIER) cc_final: 0.5015 (p) REVERT: B 184 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8276 (ttpt) REVERT: B 433 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7437 (mmt) REVERT: B 514 MET cc_start: 0.7318 (mtt) cc_final: 0.7102 (mtm) REVERT: B 671 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: B 779 VAL cc_start: 0.7328 (t) cc_final: 0.7091 (p) outliers start: 45 outliers final: 30 residues processed: 197 average time/residue: 0.0662 time to fit residues: 20.8794 Evaluate side-chains 180 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 671 TYR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 899 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 55 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 139 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 383 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.179979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.153927 restraints weight = 18740.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.155383 restraints weight = 22245.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.156455 restraints weight = 16174.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.155973 restraints weight = 12589.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.156130 restraints weight = 13586.846| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.9067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12488 Z= 0.142 Angle : 0.723 12.212 17118 Z= 0.361 Chirality : 0.046 0.450 1966 Planarity : 0.005 0.048 2169 Dihedral : 8.007 93.777 2021 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.90 % Allowed : 22.23 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -1.24 (0.21), residues: 1592 helix: -0.87 (1.00), residues: 29 sheet: -1.37 (0.23), residues: 487 loop : -0.49 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 245 TYR 0.029 0.002 TYR A 193 PHE 0.025 0.002 PHE A 202 TRP 0.042 0.002 TRP A 425 HIS 0.010 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00322 (12428) covalent geometry : angle 0.68329 (16984) SS BOND : bond 0.00366 ( 46) SS BOND : angle 1.56358 ( 92) hydrogen bonds : bond 0.03352 ( 251) hydrogen bonds : angle 6.22932 ( 606) link_BETA1-4 : bond 0.00404 ( 4) link_BETA1-4 : angle 2.57733 ( 12) link_NAG-ASN : bond 0.00859 ( 10) link_NAG-ASN : angle 4.91456 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 300 TYR cc_start: 0.6616 (m-10) cc_final: 0.6390 (m-10) REVERT: A 835 MET cc_start: 0.5463 (ppp) cc_final: 0.4952 (pmm) REVERT: B 671 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: B 749 MET cc_start: 0.6268 (tmm) cc_final: 0.5881 (tmm) outliers start: 49 outliers final: 30 residues processed: 184 average time/residue: 0.0687 time to fit residues: 20.6677 Evaluate side-chains 166 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 671 TYR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 899 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 22 optimal weight: 0.0670 chunk 99 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 619 HIS B 427 ASN B 758 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.179998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.153563 restraints weight = 18633.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.153638 restraints weight = 23533.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.155406 restraints weight = 19098.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.155197 restraints weight = 14176.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155367 restraints weight = 13188.343| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 1.0306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12488 Z= 0.182 Angle : 0.770 12.155 17118 Z= 0.392 Chirality : 0.047 0.432 1966 Planarity : 0.005 0.067 2169 Dihedral : 8.187 96.815 2021 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.82 % Allowed : 22.23 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -1.39 (0.21), residues: 1592 helix: -0.50 (1.07), residues: 29 sheet: -1.42 (0.23), residues: 499 loop : -0.63 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 662 TYR 0.027 0.002 TYR A 459 PHE 0.025 0.003 PHE A 202 TRP 0.047 0.002 TRP A 127 HIS 0.007 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00410 (12428) covalent geometry : angle 0.73065 (16984) SS BOND : bond 0.00399 ( 46) SS BOND : angle 1.82938 ( 92) hydrogen bonds : bond 0.03681 ( 251) hydrogen bonds : angle 6.33129 ( 606) link_BETA1-4 : bond 0.00443 ( 4) link_BETA1-4 : angle 2.44032 ( 12) link_NAG-ASN : bond 0.00787 ( 10) link_NAG-ASN : angle 4.87974 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TRP cc_start: 0.7219 (m-10) cc_final: 0.6906 (m-10) REVERT: A 264 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8192 (mm) REVERT: A 835 MET cc_start: 0.5809 (ppp) cc_final: 0.5003 (pmm) REVERT: A 858 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6191 (mp) REVERT: B 497 ILE cc_start: 0.8969 (mp) cc_final: 0.8721 (mp) REVERT: B 671 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.7763 (m-80) outliers start: 48 outliers final: 30 residues processed: 192 average time/residue: 0.0669 time to fit residues: 20.9712 Evaluate side-chains 167 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 671 TYR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 899 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 19 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 239 ASN A 383 ASN A 706 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.177534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.152325 restraints weight = 18649.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.150366 restraints weight = 23446.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.152073 restraints weight = 22749.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.152261 restraints weight = 16840.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.152553 restraints weight = 17076.777| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 1.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12488 Z= 0.176 Angle : 0.765 11.650 17118 Z= 0.381 Chirality : 0.047 0.432 1966 Planarity : 0.005 0.043 2169 Dihedral : 8.218 97.210 2021 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.03 % Allowed : 23.98 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -1.47 (0.21), residues: 1592 helix: -0.99 (1.16), residues: 24 sheet: -1.56 (0.23), residues: 497 loop : -0.63 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 662 TYR 0.033 0.002 TYR A 300 PHE 0.028 0.003 PHE B 421 TRP 0.040 0.002 TRP A 127 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00415 (12428) covalent geometry : angle 0.72466 (16984) SS BOND : bond 0.00522 ( 46) SS BOND : angle 1.97011 ( 92) hydrogen bonds : bond 0.03388 ( 251) hydrogen bonds : angle 6.25846 ( 606) link_BETA1-4 : bond 0.00608 ( 4) link_BETA1-4 : angle 2.42144 ( 12) link_NAG-ASN : bond 0.00839 ( 10) link_NAG-ASN : angle 4.69000 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.453 Fit side-chains REVERT: A 127 TRP cc_start: 0.7467 (m-10) cc_final: 0.7217 (m-10) REVERT: A 264 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8276 (mm) REVERT: A 835 MET cc_start: 0.6016 (ppp) cc_final: 0.5178 (pmm) REVERT: A 881 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6827 (mtm) outliers start: 38 outliers final: 27 residues processed: 168 average time/residue: 0.0809 time to fit residues: 21.4934 Evaluate side-chains 150 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 899 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 0.0770 chunk 87 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.178372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.154786 restraints weight = 18622.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.153311 restraints weight = 22562.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.155021 restraints weight = 22701.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.155185 restraints weight = 16059.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.155504 restraints weight = 15045.053| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 1.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12488 Z= 0.136 Angle : 0.732 11.356 17118 Z= 0.359 Chirality : 0.046 0.418 1966 Planarity : 0.005 0.042 2169 Dihedral : 8.093 98.089 2021 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.71 % Allowed : 25.02 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -1.37 (0.21), residues: 1592 helix: -0.99 (1.16), residues: 24 sheet: -1.41 (0.23), residues: 473 loop : -0.63 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 662 TYR 0.026 0.001 TYR A 459 PHE 0.029 0.002 PHE A 291 TRP 0.028 0.002 TRP A 551 HIS 0.004 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00310 (12428) covalent geometry : angle 0.69749 (16984) SS BOND : bond 0.00309 ( 46) SS BOND : angle 1.42378 ( 92) hydrogen bonds : bond 0.03312 ( 251) hydrogen bonds : angle 6.06247 ( 606) link_BETA1-4 : bond 0.00672 ( 4) link_BETA1-4 : angle 2.63339 ( 12) link_NAG-ASN : bond 0.00946 ( 10) link_NAG-ASN : angle 4.62080 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.438 Fit side-chains REVERT: A 178 MET cc_start: 0.7853 (mtt) cc_final: 0.7527 (mtm) REVERT: A 835 MET cc_start: 0.6010 (ppp) cc_final: 0.5619 (pmm) REVERT: A 881 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6731 (mtm) outliers start: 34 outliers final: 26 residues processed: 160 average time/residue: 0.0691 time to fit residues: 18.0721 Evaluate side-chains 149 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 899 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 107 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 137 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS B 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.178280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.151949 restraints weight = 18601.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.150804 restraints weight = 25038.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.152677 restraints weight = 22175.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.152819 restraints weight = 17127.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.153049 restraints weight = 15412.970| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 1.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12488 Z= 0.133 Angle : 0.729 11.212 17118 Z= 0.358 Chirality : 0.046 0.418 1966 Planarity : 0.005 0.044 2169 Dihedral : 8.012 97.136 2021 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.47 % Allowed : 25.02 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -1.31 (0.21), residues: 1592 helix: -0.93 (1.16), residues: 24 sheet: -1.24 (0.24), residues: 460 loop : -0.68 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 115 TYR 0.031 0.001 TYR A 300 PHE 0.029 0.002 PHE A 291 TRP 0.039 0.002 TRP A 127 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00309 (12428) covalent geometry : angle 0.69525 (16984) SS BOND : bond 0.00326 ( 46) SS BOND : angle 1.43085 ( 92) hydrogen bonds : bond 0.03157 ( 251) hydrogen bonds : angle 6.10517 ( 606) link_BETA1-4 : bond 0.00411 ( 4) link_BETA1-4 : angle 2.60241 ( 12) link_NAG-ASN : bond 0.00810 ( 10) link_NAG-ASN : angle 4.54404 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.459 Fit side-chains REVERT: A 178 MET cc_start: 0.7805 (mtt) cc_final: 0.7562 (mtm) REVERT: A 348 THR cc_start: 0.5804 (t) cc_final: 0.5354 (p) REVERT: A 397 CYS cc_start: 0.2058 (OUTLIER) cc_final: 0.1721 (p) REVERT: A 438 LEU cc_start: 0.7366 (tp) cc_final: 0.7035 (tt) REVERT: A 881 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7136 (mtm) REVERT: B 221 MET cc_start: 0.5648 (mmm) cc_final: 0.5232 (mmm) outliers start: 31 outliers final: 27 residues processed: 154 average time/residue: 0.0703 time to fit residues: 17.9541 Evaluate side-chains 151 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 899 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 35 optimal weight: 0.0770 chunk 154 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 156 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 0.0040 chunk 69 optimal weight: 0.1980 chunk 151 optimal weight: 0.2980 overall best weight: 0.1550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.181892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.153205 restraints weight = 18590.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153047 restraints weight = 19867.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.154707 restraints weight = 17989.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155143 restraints weight = 14237.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.155178 restraints weight = 13385.295| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 1.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12488 Z= 0.110 Angle : 0.699 10.926 17118 Z= 0.340 Chirality : 0.045 0.411 1966 Planarity : 0.005 0.042 2169 Dihedral : 7.724 96.315 2021 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.99 % Allowed : 25.82 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -1.15 (0.21), residues: 1592 helix: -0.86 (1.16), residues: 24 sheet: -1.09 (0.23), residues: 472 loop : -0.57 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 162 TYR 0.019 0.001 TYR A 243 PHE 0.034 0.002 PHE A 291 TRP 0.025 0.002 TRP A 551 HIS 0.003 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00247 (12428) covalent geometry : angle 0.66757 (16984) SS BOND : bond 0.00277 ( 46) SS BOND : angle 1.18919 ( 92) hydrogen bonds : bond 0.03073 ( 251) hydrogen bonds : angle 5.93909 ( 606) link_BETA1-4 : bond 0.00524 ( 4) link_BETA1-4 : angle 2.66399 ( 12) link_NAG-ASN : bond 0.00816 ( 10) link_NAG-ASN : angle 4.38594 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.45 seconds wall clock time: 31 minutes 13.19 seconds (1873.19 seconds total)