Starting phenix.real_space_refine on Sat Aug 23 07:20:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcw_37112/08_2025/8kcw_37112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcw_37112/08_2025/8kcw_37112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kcw_37112/08_2025/8kcw_37112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcw_37112/08_2025/8kcw_37112.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcw_37112/08_2025/8kcw_37112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcw_37112/08_2025/8kcw_37112.cif" } resolution = 2.77 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 58 5.16 5 C 6934 2.51 5 N 1620 2.21 5 O 1870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 10484 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5051 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5051 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "I" 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: "J" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "O" 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: "P" 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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.19, per 1000 atoms: 0.21 Number of scatterers: 10484 At special positions: 0 Unit cell: (93.375, 85.905, 133.215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 58 16.00 O 1870 8.00 N 1620 7.00 C 6934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 479 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 782 " 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG G 1 " - " ASN A 83 " " NAG H 1 " - " ASN A 136 " " NAG I 1 " - " ASN A 67 " " NAG J 1 " - " ASN A 57 " " NAG M 1 " - " ASN C 83 " " NAG N 1 " - " ASN C 136 " " NAG O 1 " - " ASN C 67 " " NAG P 1 " - " ASN C 57 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 325.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 791 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 795 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 791 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 563 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 795 " 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 48.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 302 through 316 removed outlier: 3.790A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.922A pdb=" N VAL A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 473 removed outlier: 3.649A pdb=" N PHE A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Proline residue: A 458 - end of helix removed outlier: 3.918A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 471 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 4.078A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.812A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 527 removed outlier: 3.951A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 563 removed outlier: 3.620A pdb=" N TYR A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 575 removed outlier: 3.703A pdb=" N ASP A 574 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 592 removed outlier: 4.132A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 620 removed outlier: 3.569A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 648 removed outlier: 3.538A pdb=" N TRP A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 631 " --> pdb=" O TRP A 627 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 640 " --> pdb=" O HIS A 636 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 705 removed outlier: 3.536A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 688 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 735 removed outlier: 3.520A pdb=" N LEU A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 763 removed outlier: 3.716A pdb=" N PHE A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 763 " --> pdb=" O TYR A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 789 through 812 removed outlier: 3.868A pdb=" N ALA A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 800 " --> pdb=" O PHE A 796 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 809 " --> pdb=" O SER A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.790A pdb=" N TYR C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 332 removed outlier: 3.922A pdb=" N VAL C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 473 removed outlier: 3.649A pdb=" N PHE C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) Proline residue: C 458 - end of helix removed outlier: 3.918A pdb=" N ILE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR C 465 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.078A pdb=" N ALA C 486 " --> pdb=" O PHE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 500 removed outlier: 3.812A pdb=" N ILE C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 527 removed outlier: 3.951A pdb=" N VAL C 505 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 509 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 522 " --> pdb=" O ARG C 518 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 563 removed outlier: 3.620A pdb=" N TYR C 546 " --> pdb=" O PHE C 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.703A pdb=" N ASP C 574 " --> pdb=" O PHE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 592 removed outlier: 4.132A pdb=" N MET C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 620 removed outlier: 3.569A pdb=" N TYR C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 615 " --> pdb=" O VAL C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 648 removed outlier: 3.538A pdb=" N TRP C 629 " --> pdb=" O ASP C 625 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE C 631 " --> pdb=" O TRP C 627 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 640 " --> pdb=" O HIS C 636 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR C 645 " --> pdb=" O LEU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 705 removed outlier: 3.536A pdb=" N LEU C 686 " --> pdb=" O ASP C 682 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 688 " --> pdb=" O MET C 684 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 735 removed outlier: 3.520A pdb=" N LEU C 714 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 726 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 729 " --> pdb=" O LEU C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 763 removed outlier: 3.716A pdb=" N PHE C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 763 " --> pdb=" O TYR C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 776 Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 789 through 812 removed outlier: 3.868A pdb=" N ALA C 799 " --> pdb=" O HIS C 795 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 800 " --> pdb=" O PHE C 796 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 809 " --> pdb=" O SER C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 815 No H-bonds generated for 'chain 'C' and resid 813 through 815' Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.656A pdb=" N ALA A 77 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.901A pdb=" N ARG A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.877A pdb=" N LYS A 192 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 56 removed outlier: 4.656A pdb=" N ALA C 77 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.901A pdb=" N ARG C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 170 through 171 removed outlier: 4.877A pdb=" N LYS C 192 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 177 through 181 538 hydrogen bonds defined for protein. 1536 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: 1.34 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3098 1.34 - 1.46: 2768 1.46 - 1.58: 4814 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 10770 Sorted by residual: bond pdb=" N ILE A 449 " pdb=" CA ILE A 449 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.21e+01 bond pdb=" N ILE C 449 " pdb=" CA ILE C 449 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.21e+01 bond pdb=" N ASP C 625 " pdb=" CA ASP C 625 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.18e-02 7.18e+03 9.62e+00 bond pdb=" N ASP A 625 " pdb=" CA ASP A 625 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.18e-02 7.18e+03 9.62e+00 bond pdb=" N ILE C 448 " pdb=" CA ILE C 448 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.33e-02 5.65e+03 8.11e+00 ... (remaining 10765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 14150 2.01 - 4.02: 458 4.02 - 6.03: 54 6.03 - 8.04: 18 8.04 - 10.05: 4 Bond angle restraints: 14684 Sorted by residual: angle pdb=" N GLN A 646 " pdb=" CA GLN A 646 " pdb=" C GLN A 646 " ideal model delta sigma weight residual 111.36 107.03 4.33 1.09e+00 8.42e-01 1.57e+01 angle pdb=" N GLN C 646 " pdb=" CA GLN C 646 " pdb=" C GLN C 646 " ideal model delta sigma weight residual 111.36 107.03 4.33 1.09e+00 8.42e-01 1.57e+01 angle pdb=" CB GLN A 646 " pdb=" CG GLN A 646 " pdb=" CD GLN A 646 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CB GLN C 646 " pdb=" CG GLN C 646 " pdb=" CD GLN C 646 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CA ASN C 624 " pdb=" C ASN C 624 " pdb=" O ASN C 624 " ideal model delta sigma weight residual 121.84 117.53 4.31 1.16e+00 7.43e-01 1.38e+01 ... (remaining 14679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 6222 21.92 - 43.84: 354 43.84 - 65.76: 56 65.76 - 87.67: 38 87.67 - 109.59: 50 Dihedral angle restraints: 6720 sinusoidal: 3004 harmonic: 3716 Sorted by residual: dihedral pdb=" CA ILE C 478 " pdb=" C ILE C 478 " pdb=" N CYS C 479 " pdb=" CA CYS C 479 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ILE A 478 " pdb=" C ILE A 478 " pdb=" N CYS A 479 " pdb=" CA CYS A 479 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS C 212 " pdb=" SG CYS C 212 " pdb=" SG CYS C 271 " pdb=" CB CYS C 271 " ideal model delta sinusoidal sigma weight residual 93.00 57.12 35.88 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 6717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1468 0.070 - 0.141: 238 0.141 - 0.211: 28 0.211 - 0.281: 2 0.281 - 0.352: 4 Chirality restraints: 1740 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 57 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 1737 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 460 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ILE C 460 " 0.054 2.00e-02 2.50e+03 pdb=" O ILE C 460 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN C 461 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 460 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ILE A 460 " -0.054 2.00e-02 2.50e+03 pdb=" O ILE A 460 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN A 461 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 457 " 0.045 5.00e-02 4.00e+02 6.69e-02 7.17e+00 pdb=" N PRO A 458 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.038 5.00e-02 4.00e+02 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 170 2.68 - 3.24: 9382 3.24 - 3.79: 15779 3.79 - 4.35: 22578 4.35 - 4.90: 36146 Nonbonded interactions: 84055 Sorted by model distance: nonbonded pdb=" OD1 ASP A 574 " pdb="ZN ZN A 901 " model vdw 2.126 2.230 nonbonded pdb=" OD1 ASP C 574 " pdb="ZN ZN C 901 " model vdw 2.126 2.230 nonbonded pdb=" O SER C 640 " pdb=" OG SER C 644 " model vdw 2.298 3.040 nonbonded pdb=" O SER A 640 " pdb=" OG SER A 644 " model vdw 2.298 3.040 nonbonded pdb=" OD1 ASN C 501 " pdb=" OG SER C 559 " model vdw 2.313 3.040 ... (remaining 84050 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.410 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 0.115 10804 Z= 0.266 Angle : 0.837 10.047 14760 Z= 0.456 Chirality : 0.055 0.352 1740 Planarity : 0.006 0.067 1772 Dihedral : 18.783 109.593 4296 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -4.23 (0.19), residues: 1232 helix: -4.34 (0.09), residues: 552 sheet: 0.45 (0.29), residues: 280 loop : -2.56 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 289 TYR 0.015 0.002 TYR A 481 PHE 0.013 0.001 PHE C 193 TRP 0.009 0.001 TRP C 754 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00468 (10770) covalent geometry : angle 0.81695 (14684) SS BOND : bond 0.00167 ( 8) SS BOND : angle 0.99524 ( 16) hydrogen bonds : bond 0.29380 ( 538) hydrogen bonds : angle 9.53662 ( 1536) metal coordination : bond 0.08799 ( 6) link_BETA1-4 : bond 0.00693 ( 12) link_BETA1-4 : angle 2.57678 ( 36) link_NAG-ASN : bond 0.00776 ( 8) link_NAG-ASN : angle 3.47649 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 0.291 Fit side-chains REVERT: A 517 ARG cc_start: 0.8020 (tmt170) cc_final: 0.7716 (ttp-170) REVERT: A 684 MET cc_start: 0.6582 (mmt) cc_final: 0.5214 (ttt) REVERT: A 695 TRP cc_start: 0.8404 (m-10) cc_final: 0.8056 (m-10) REVERT: A 708 ASP cc_start: 0.8277 (t0) cc_final: 0.7877 (t0) REVERT: C 101 LYS cc_start: 0.8960 (mttt) cc_final: 0.8686 (mmtt) REVERT: C 517 ARG cc_start: 0.8020 (tmt170) cc_final: 0.7716 (ttp-170) REVERT: C 684 MET cc_start: 0.6584 (mmt) cc_final: 0.5219 (ttt) REVERT: C 695 TRP cc_start: 0.8404 (m-10) cc_final: 0.8055 (m-10) REVERT: C 708 ASP cc_start: 0.8274 (t0) cc_final: 0.7877 (t0) outliers start: 2 outliers final: 2 residues processed: 296 average time/residue: 0.3746 time to fit residues: 121.9496 Evaluate side-chains 238 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain C residue 332 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 447 ASN A 541 HIS A 763 GLN C 229 HIS C 447 ASN C 541 HIS C 763 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.091417 restraints weight = 13134.591| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.64 r_work: 0.2851 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10804 Z= 0.149 Angle : 0.698 7.623 14760 Z= 0.341 Chirality : 0.047 0.302 1740 Planarity : 0.005 0.040 1772 Dihedral : 14.338 82.048 2032 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.51 % Allowed : 13.26 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.79 (0.21), residues: 1232 helix: -1.70 (0.18), residues: 560 sheet: 1.07 (0.29), residues: 270 loop : -1.81 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 524 TYR 0.015 0.002 TYR A 81 PHE 0.016 0.001 PHE C 632 TRP 0.012 0.001 TRP A 446 HIS 0.006 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00317 (10770) covalent geometry : angle 0.68279 (14684) SS BOND : bond 0.00124 ( 8) SS BOND : angle 0.93232 ( 16) hydrogen bonds : bond 0.05521 ( 538) hydrogen bonds : angle 4.45776 ( 1536) metal coordination : bond 0.00722 ( 6) link_BETA1-4 : bond 0.00403 ( 12) link_BETA1-4 : angle 2.33709 ( 36) link_NAG-ASN : bond 0.00419 ( 8) link_NAG-ASN : angle 2.36159 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.9379 (ttt) cc_final: 0.8826 (tmm) REVERT: A 320 PHE cc_start: 0.9143 (m-80) cc_final: 0.8895 (m-80) REVERT: A 475 ASN cc_start: 0.9491 (t0) cc_final: 0.9174 (t160) REVERT: A 541 HIS cc_start: 0.8851 (m-70) cc_final: 0.8559 (m90) REVERT: A 713 MET cc_start: 0.9359 (mmt) cc_final: 0.9147 (mmm) REVERT: A 781 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8654 (mm-30) REVERT: C 240 MET cc_start: 0.9375 (ttt) cc_final: 0.8821 (tmm) REVERT: C 320 PHE cc_start: 0.9126 (m-80) cc_final: 0.8878 (m-80) REVERT: C 475 ASN cc_start: 0.9491 (t0) cc_final: 0.9166 (t160) REVERT: C 541 HIS cc_start: 0.8852 (m-70) cc_final: 0.8561 (m90) REVERT: C 713 MET cc_start: 0.9359 (mmt) cc_final: 0.9145 (mmm) REVERT: C 781 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8656 (mm-30) outliers start: 28 outliers final: 18 residues processed: 276 average time/residue: 0.4143 time to fit residues: 124.2706 Evaluate side-chains 242 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 750 THR Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 594 HIS A 763 GLN C 447 ASN C 594 HIS C 763 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.087075 restraints weight = 13456.590| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.70 r_work: 0.2751 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 10804 Z= 0.282 Angle : 0.719 8.681 14760 Z= 0.353 Chirality : 0.049 0.271 1740 Planarity : 0.004 0.041 1772 Dihedral : 10.790 62.573 2032 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.87 % Allowed : 17.20 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.42 (0.23), residues: 1232 helix: -0.00 (0.21), residues: 558 sheet: 1.24 (0.28), residues: 268 loop : -1.64 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 518 TYR 0.019 0.002 TYR C 724 PHE 0.021 0.002 PHE C 700 TRP 0.011 0.001 TRP C 106 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00679 (10770) covalent geometry : angle 0.70566 (14684) SS BOND : bond 0.00218 ( 8) SS BOND : angle 1.05206 ( 16) hydrogen bonds : bond 0.05346 ( 538) hydrogen bonds : angle 4.21695 ( 1536) metal coordination : bond 0.00821 ( 6) link_BETA1-4 : bond 0.00614 ( 12) link_BETA1-4 : angle 2.37421 ( 36) link_NAG-ASN : bond 0.00164 ( 8) link_NAG-ASN : angle 2.02323 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.372 Fit side-chains REVERT: A 240 MET cc_start: 0.9551 (ttt) cc_final: 0.9002 (tmm) REVERT: A 524 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.6620 (mmm160) REVERT: A 555 GLU cc_start: 0.9090 (tp30) cc_final: 0.8754 (tp30) REVERT: A 681 MET cc_start: 0.6450 (tmm) cc_final: 0.6246 (tmm) REVERT: A 720 ASN cc_start: 0.8880 (m-40) cc_final: 0.8614 (m110) REVERT: A 769 GLU cc_start: 0.8400 (mp0) cc_final: 0.8017 (mp0) REVERT: A 781 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8624 (mm-30) REVERT: C 240 MET cc_start: 0.9542 (ttt) cc_final: 0.8992 (tmm) REVERT: C 524 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.6604 (mmm160) REVERT: C 555 GLU cc_start: 0.9093 (tp30) cc_final: 0.8755 (tp30) REVERT: C 681 MET cc_start: 0.6447 (tmm) cc_final: 0.6244 (tmm) REVERT: C 720 ASN cc_start: 0.8875 (m-40) cc_final: 0.8611 (m110) REVERT: C 769 GLU cc_start: 0.8397 (mp0) cc_final: 0.8014 (mp0) REVERT: C 781 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8613 (mm-30) outliers start: 32 outliers final: 14 residues processed: 246 average time/residue: 0.4075 time to fit residues: 109.7303 Evaluate side-chains 226 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 810 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 HIS C 541 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.089706 restraints weight = 13402.960| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.69 r_work: 0.2790 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10804 Z= 0.147 Angle : 0.601 7.971 14760 Z= 0.291 Chirality : 0.045 0.273 1740 Planarity : 0.003 0.036 1772 Dihedral : 8.292 58.504 2032 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.87 % Allowed : 19.09 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.39 (0.23), residues: 1232 helix: 0.92 (0.22), residues: 558 sheet: 1.48 (0.28), residues: 270 loop : -1.54 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.017 0.001 TYR A 81 PHE 0.016 0.001 PHE C 571 TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00335 (10770) covalent geometry : angle 0.58619 (14684) SS BOND : bond 0.00104 ( 8) SS BOND : angle 0.85223 ( 16) hydrogen bonds : bond 0.04157 ( 538) hydrogen bonds : angle 3.86126 ( 1536) metal coordination : bond 0.00483 ( 6) link_BETA1-4 : bond 0.00624 ( 12) link_BETA1-4 : angle 2.23173 ( 36) link_NAG-ASN : bond 0.00308 ( 8) link_NAG-ASN : angle 2.07489 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.9060 (mt0) cc_final: 0.8700 (mm-40) REVERT: A 143 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: A 195 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8440 (mtpm) REVERT: A 240 MET cc_start: 0.9546 (ttt) cc_final: 0.8768 (tmm) REVERT: A 555 GLU cc_start: 0.9041 (tp30) cc_final: 0.8589 (tp30) REVERT: A 577 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: C 123 GLN cc_start: 0.9051 (mt0) cc_final: 0.8685 (mm-40) REVERT: C 143 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: C 195 LYS cc_start: 0.8784 (mtpp) cc_final: 0.8432 (mtpm) REVERT: C 240 MET cc_start: 0.9548 (ttt) cc_final: 0.8771 (tmm) REVERT: C 555 GLU cc_start: 0.9046 (tp30) cc_final: 0.8589 (tp30) REVERT: C 577 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8484 (m-80) outliers start: 32 outliers final: 12 residues processed: 244 average time/residue: 0.4206 time to fit residues: 111.9861 Evaluate side-chains 238 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 810 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 30 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 HIS A 720 ASN C 541 HIS C 720 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.090120 restraints weight = 13142.995| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.68 r_work: 0.2809 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10804 Z= 0.133 Angle : 0.584 7.149 14760 Z= 0.283 Chirality : 0.044 0.276 1740 Planarity : 0.003 0.034 1772 Dihedral : 7.410 57.008 2032 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.87 % Allowed : 21.86 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.85 (0.24), residues: 1232 helix: 1.46 (0.22), residues: 554 sheet: 1.57 (0.28), residues: 270 loop : -1.44 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 518 TYR 0.012 0.001 TYR C 188 PHE 0.019 0.001 PHE C 700 TRP 0.008 0.001 TRP C 106 HIS 0.002 0.001 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00303 (10770) covalent geometry : angle 0.56658 (14684) SS BOND : bond 0.00106 ( 8) SS BOND : angle 0.81842 ( 16) hydrogen bonds : bond 0.03947 ( 538) hydrogen bonds : angle 3.76156 ( 1536) metal coordination : bond 0.00474 ( 6) link_BETA1-4 : bond 0.00558 ( 12) link_BETA1-4 : angle 2.37783 ( 36) link_NAG-ASN : bond 0.00301 ( 8) link_NAG-ASN : angle 2.10319 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.400 Fit side-chains REVERT: A 73 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8019 (p0) REVERT: A 74 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7734 (mp-120) REVERT: A 123 GLN cc_start: 0.9006 (mt0) cc_final: 0.8618 (mm-40) REVERT: A 143 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: A 240 MET cc_start: 0.9533 (ttt) cc_final: 0.8813 (tmm) REVERT: A 524 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.6595 (mmm-85) REVERT: A 555 GLU cc_start: 0.9026 (tp30) cc_final: 0.8551 (tp30) REVERT: A 586 MET cc_start: 0.8427 (mmm) cc_final: 0.8078 (mpp) REVERT: A 588 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8432 (mmmt) REVERT: A 709 PHE cc_start: 0.8633 (t80) cc_final: 0.8317 (t80) REVERT: C 73 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8019 (p0) REVERT: C 74 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7744 (mp-120) REVERT: C 123 GLN cc_start: 0.9004 (mt0) cc_final: 0.8615 (mm-40) REVERT: C 143 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: C 240 MET cc_start: 0.9534 (ttt) cc_final: 0.8815 (tmm) REVERT: C 524 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.6584 (mmm-85) REVERT: C 555 GLU cc_start: 0.9036 (tp30) cc_final: 0.8561 (tp30) REVERT: C 586 MET cc_start: 0.8431 (mmm) cc_final: 0.8080 (mpp) REVERT: C 588 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8431 (mmmt) REVERT: C 709 PHE cc_start: 0.8644 (t80) cc_final: 0.8328 (t80) outliers start: 32 outliers final: 10 residues processed: 240 average time/residue: 0.3917 time to fit residues: 102.8454 Evaluate side-chains 244 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 467 GLN A 541 HIS A 636 HIS C 121 ASN C 467 GLN C 541 HIS C 636 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.090532 restraints weight = 13314.694| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.72 r_work: 0.2835 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10804 Z= 0.127 Angle : 0.573 7.393 14760 Z= 0.278 Chirality : 0.044 0.267 1740 Planarity : 0.003 0.033 1772 Dihedral : 6.974 56.745 2032 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.51 % Allowed : 22.40 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.08 (0.24), residues: 1232 helix: 1.73 (0.23), residues: 554 sheet: 1.61 (0.29), residues: 270 loop : -1.41 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.014 0.001 TYR C 81 PHE 0.016 0.001 PHE C 632 TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00289 (10770) covalent geometry : angle 0.55564 (14684) SS BOND : bond 0.00106 ( 8) SS BOND : angle 0.73030 ( 16) hydrogen bonds : bond 0.03765 ( 538) hydrogen bonds : angle 3.70300 ( 1536) metal coordination : bond 0.00428 ( 6) link_BETA1-4 : bond 0.00544 ( 12) link_BETA1-4 : angle 2.39512 ( 36) link_NAG-ASN : bond 0.00303 ( 8) link_NAG-ASN : angle 2.03448 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.314 Fit side-chains REVERT: A 73 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8089 (p0) REVERT: A 74 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7781 (mp-120) REVERT: A 123 GLN cc_start: 0.9035 (mt0) cc_final: 0.8606 (mm-40) REVERT: A 143 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7932 (mt0) REVERT: A 145 ILE cc_start: 0.9408 (mt) cc_final: 0.9186 (mm) REVERT: A 219 ASN cc_start: 0.8690 (m-40) cc_final: 0.8248 (p0) REVERT: A 240 MET cc_start: 0.9527 (ttt) cc_final: 0.8774 (tmm) REVERT: A 555 GLU cc_start: 0.9033 (tp30) cc_final: 0.8790 (tp30) REVERT: A 588 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8462 (mmmt) REVERT: A 709 PHE cc_start: 0.8636 (t80) cc_final: 0.8388 (t80) REVERT: A 781 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8448 (mm-30) REVERT: C 73 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8096 (p0) REVERT: C 74 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7779 (mp-120) REVERT: C 123 GLN cc_start: 0.9019 (mt0) cc_final: 0.8605 (mm-40) REVERT: C 143 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: C 145 ILE cc_start: 0.9406 (mt) cc_final: 0.9181 (mm) REVERT: C 219 ASN cc_start: 0.8699 (m-40) cc_final: 0.8248 (p0) REVERT: C 240 MET cc_start: 0.9525 (ttt) cc_final: 0.8771 (tmm) REVERT: C 555 GLU cc_start: 0.9043 (tp30) cc_final: 0.8800 (tp30) REVERT: C 588 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8460 (mmmt) REVERT: C 709 PHE cc_start: 0.8636 (t80) cc_final: 0.8390 (t80) REVERT: C 781 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8439 (mm-30) outliers start: 28 outliers final: 10 residues processed: 240 average time/residue: 0.4066 time to fit residues: 106.7679 Evaluate side-chains 239 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 23 optimal weight: 0.0370 chunk 46 optimal weight: 6.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 541 HIS A 763 GLN C 461 GLN C 541 HIS C 763 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.089702 restraints weight = 13234.925| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.68 r_work: 0.2826 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10804 Z= 0.166 Angle : 0.598 8.210 14760 Z= 0.291 Chirality : 0.045 0.267 1740 Planarity : 0.003 0.034 1772 Dihedral : 6.815 56.116 2032 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.23 % Allowed : 22.76 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.17 (0.24), residues: 1232 helix: 1.82 (0.23), residues: 554 sheet: 1.63 (0.28), residues: 270 loop : -1.37 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 518 TYR 0.013 0.001 TYR C 188 PHE 0.020 0.001 PHE C 700 TRP 0.009 0.001 TRP C 106 HIS 0.003 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00393 (10770) covalent geometry : angle 0.58134 (14684) SS BOND : bond 0.00130 ( 8) SS BOND : angle 0.75961 ( 16) hydrogen bonds : bond 0.03984 ( 538) hydrogen bonds : angle 3.77153 ( 1536) metal coordination : bond 0.00558 ( 6) link_BETA1-4 : bond 0.00496 ( 12) link_BETA1-4 : angle 2.43249 ( 36) link_NAG-ASN : bond 0.00274 ( 8) link_NAG-ASN : angle 1.98455 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.373 Fit side-chains REVERT: A 73 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8055 (p0) REVERT: A 74 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7768 (mp-120) REVERT: A 123 GLN cc_start: 0.8945 (mt0) cc_final: 0.8607 (mm-40) REVERT: A 143 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: A 145 ILE cc_start: 0.9420 (mt) cc_final: 0.9203 (mm) REVERT: A 219 ASN cc_start: 0.8687 (m-40) cc_final: 0.8255 (p0) REVERT: A 240 MET cc_start: 0.9543 (ttt) cc_final: 0.8910 (tmm) REVERT: A 524 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.6602 (mmm-85) REVERT: A 555 GLU cc_start: 0.9037 (tp30) cc_final: 0.8540 (tp30) REVERT: A 708 ASP cc_start: 0.8309 (t0) cc_final: 0.7859 (t0) REVERT: A 781 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8469 (mm-30) REVERT: C 73 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8071 (p0) REVERT: C 74 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7761 (mp-120) REVERT: C 123 GLN cc_start: 0.8946 (mt0) cc_final: 0.8605 (mm-40) REVERT: C 143 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: C 145 ILE cc_start: 0.9422 (mt) cc_final: 0.9206 (mm) REVERT: C 219 ASN cc_start: 0.8711 (m-40) cc_final: 0.8242 (p0) REVERT: C 240 MET cc_start: 0.9539 (ttt) cc_final: 0.8907 (tmm) REVERT: C 524 ARG cc_start: 0.7372 (mtm-85) cc_final: 0.6590 (mmm-85) REVERT: C 555 GLU cc_start: 0.9046 (tp30) cc_final: 0.8547 (tp30) REVERT: C 708 ASP cc_start: 0.8313 (t0) cc_final: 0.7865 (t0) REVERT: C 781 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8452 (mm-30) outliers start: 36 outliers final: 18 residues processed: 244 average time/residue: 0.4268 time to fit residues: 113.5437 Evaluate side-chains 242 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 810 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 461 GLN A 541 HIS A 720 ASN C 121 ASN C 461 GLN C 541 HIS C 720 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.091143 restraints weight = 13411.789| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.53 r_work: 0.2831 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10804 Z= 0.144 Angle : 0.589 9.570 14760 Z= 0.287 Chirality : 0.044 0.259 1740 Planarity : 0.003 0.034 1772 Dihedral : 6.661 56.036 2032 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.33 % Allowed : 24.01 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.26 (0.24), residues: 1232 helix: 1.90 (0.23), residues: 554 sheet: 1.64 (0.28), residues: 270 loop : -1.30 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 518 TYR 0.015 0.001 TYR A 81 PHE 0.021 0.001 PHE C 632 TRP 0.007 0.001 TRP C 106 HIS 0.003 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00337 (10770) covalent geometry : angle 0.57238 (14684) SS BOND : bond 0.00101 ( 8) SS BOND : angle 0.72520 ( 16) hydrogen bonds : bond 0.03850 ( 538) hydrogen bonds : angle 3.74863 ( 1536) metal coordination : bond 0.00514 ( 6) link_BETA1-4 : bond 0.00506 ( 12) link_BETA1-4 : angle 2.42325 ( 36) link_NAG-ASN : bond 0.00302 ( 8) link_NAG-ASN : angle 1.97105 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.396 Fit side-chains REVERT: A 73 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8293 (p0) REVERT: A 123 GLN cc_start: 0.9008 (mt0) cc_final: 0.8693 (mm-40) REVERT: A 143 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: A 219 ASN cc_start: 0.8657 (m-40) cc_final: 0.8365 (p0) REVERT: A 240 MET cc_start: 0.9599 (ttt) cc_final: 0.8996 (tmm) REVERT: A 524 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.6635 (mmm-85) REVERT: A 555 GLU cc_start: 0.9082 (tp30) cc_final: 0.8587 (tp30) REVERT: A 586 MET cc_start: 0.8707 (mmm) cc_final: 0.8219 (mpp) REVERT: A 708 ASP cc_start: 0.8443 (t0) cc_final: 0.7948 (t0) REVERT: A 781 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8467 (mm-30) REVERT: C 73 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8291 (p0) REVERT: C 123 GLN cc_start: 0.9015 (mt0) cc_final: 0.8700 (mm-40) REVERT: C 143 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: C 219 ASN cc_start: 0.8677 (m-40) cc_final: 0.8371 (p0) REVERT: C 240 MET cc_start: 0.9594 (ttt) cc_final: 0.8985 (tmm) REVERT: C 524 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.6630 (mmm-85) REVERT: C 555 GLU cc_start: 0.9088 (tp30) cc_final: 0.8592 (tp30) REVERT: C 586 MET cc_start: 0.8705 (mmm) cc_final: 0.8218 (mpp) REVERT: C 708 ASP cc_start: 0.8442 (t0) cc_final: 0.7946 (t0) REVERT: C 781 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8476 (mm-30) outliers start: 26 outliers final: 14 residues processed: 237 average time/residue: 0.4257 time to fit residues: 110.3995 Evaluate side-chains 228 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 461 GLN A 691 ASN C 74 GLN C 461 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.092442 restraints weight = 13418.701| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.55 r_work: 0.2851 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10804 Z= 0.117 Angle : 0.581 10.582 14760 Z= 0.281 Chirality : 0.044 0.254 1740 Planarity : 0.003 0.033 1772 Dihedral : 6.490 55.653 2032 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.97 % Allowed : 24.64 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.37 (0.24), residues: 1232 helix: 1.99 (0.23), residues: 554 sheet: 1.72 (0.29), residues: 270 loop : -1.27 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.015 0.001 TYR A 590 PHE 0.020 0.001 PHE A 632 TRP 0.007 0.001 TRP A 106 HIS 0.002 0.001 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00264 (10770) covalent geometry : angle 0.56378 (14684) SS BOND : bond 0.00088 ( 8) SS BOND : angle 0.73358 ( 16) hydrogen bonds : bond 0.03686 ( 538) hydrogen bonds : angle 3.67560 ( 1536) metal coordination : bond 0.00389 ( 6) link_BETA1-4 : bond 0.00472 ( 12) link_BETA1-4 : angle 2.40298 ( 36) link_NAG-ASN : bond 0.00307 ( 8) link_NAG-ASN : angle 1.96685 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8264 (p0) REVERT: A 123 GLN cc_start: 0.9013 (mt0) cc_final: 0.8707 (mm-40) REVERT: A 219 ASN cc_start: 0.8626 (m-40) cc_final: 0.8379 (p0) REVERT: A 240 MET cc_start: 0.9561 (ttt) cc_final: 0.8878 (tmm) REVERT: A 524 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.6580 (mmm-85) REVERT: A 555 GLU cc_start: 0.9015 (tp30) cc_final: 0.8520 (tp30) REVERT: A 586 MET cc_start: 0.8721 (mmm) cc_final: 0.8310 (mpp) REVERT: A 708 ASP cc_start: 0.8455 (t0) cc_final: 0.7928 (t0) REVERT: A 781 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8454 (mm-30) REVERT: C 73 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8263 (p0) REVERT: C 123 GLN cc_start: 0.9014 (mt0) cc_final: 0.8707 (mm-40) REVERT: C 219 ASN cc_start: 0.8645 (m-40) cc_final: 0.8382 (p0) REVERT: C 240 MET cc_start: 0.9554 (ttt) cc_final: 0.8865 (tmm) REVERT: C 524 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.6577 (mmm-85) REVERT: C 555 GLU cc_start: 0.9022 (tp30) cc_final: 0.8529 (tp30) REVERT: C 586 MET cc_start: 0.8725 (mmm) cc_final: 0.8313 (mpp) REVERT: C 708 ASP cc_start: 0.8446 (t0) cc_final: 0.7920 (t0) REVERT: C 781 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8470 (mm-30) outliers start: 22 outliers final: 12 residues processed: 235 average time/residue: 0.4122 time to fit residues: 105.9405 Evaluate side-chains 228 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 0.0370 chunk 62 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 143 GLN A 461 GLN C 121 ASN C 143 GLN C 461 GLN C 541 HIS C 691 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093014 restraints weight = 13259.550| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.52 r_work: 0.2864 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10804 Z= 0.113 Angle : 0.581 11.867 14760 Z= 0.280 Chirality : 0.043 0.250 1740 Planarity : 0.003 0.032 1772 Dihedral : 6.393 55.385 2032 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.25 % Allowed : 25.45 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.39 (0.24), residues: 1232 helix: 2.01 (0.22), residues: 554 sheet: 1.74 (0.29), residues: 270 loop : -1.28 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 518 TYR 0.013 0.001 TYR A 81 PHE 0.023 0.001 PHE A 632 TRP 0.007 0.001 TRP C 629 HIS 0.002 0.001 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00251 (10770) covalent geometry : angle 0.56432 (14684) SS BOND : bond 0.00066 ( 8) SS BOND : angle 0.69867 ( 16) hydrogen bonds : bond 0.03627 ( 538) hydrogen bonds : angle 3.65043 ( 1536) metal coordination : bond 0.00405 ( 6) link_BETA1-4 : bond 0.00474 ( 12) link_BETA1-4 : angle 2.38104 ( 36) link_NAG-ASN : bond 0.00304 ( 8) link_NAG-ASN : angle 1.92843 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 0.285 Fit side-chains REVERT: A 123 GLN cc_start: 0.9005 (mt0) cc_final: 0.8698 (mm-40) REVERT: A 143 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: A 219 ASN cc_start: 0.8575 (m-40) cc_final: 0.8353 (p0) REVERT: A 240 MET cc_start: 0.9559 (ttt) cc_final: 0.8857 (tmm) REVERT: A 524 ARG cc_start: 0.7393 (mtm-85) cc_final: 0.6535 (mmm-85) REVERT: A 555 GLU cc_start: 0.8994 (tp30) cc_final: 0.8499 (tp30) REVERT: A 586 MET cc_start: 0.8699 (mmm) cc_final: 0.8343 (mpp) REVERT: A 708 ASP cc_start: 0.8439 (t0) cc_final: 0.7917 (t0) REVERT: A 781 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8483 (mm-30) REVERT: C 123 GLN cc_start: 0.9010 (mt0) cc_final: 0.8704 (mm-40) REVERT: C 143 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: C 219 ASN cc_start: 0.8590 (m-40) cc_final: 0.8361 (p0) REVERT: C 240 MET cc_start: 0.9551 (ttt) cc_final: 0.8842 (tmm) REVERT: C 524 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.6535 (mmm-85) REVERT: C 555 GLU cc_start: 0.9004 (tp30) cc_final: 0.8514 (tp30) REVERT: C 586 MET cc_start: 0.8702 (mmm) cc_final: 0.8344 (mpp) REVERT: C 708 ASP cc_start: 0.8434 (t0) cc_final: 0.7914 (t0) REVERT: C 781 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8482 (mm-30) outliers start: 14 outliers final: 6 residues processed: 220 average time/residue: 0.4254 time to fit residues: 102.3025 Evaluate side-chains 216 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 461 GLN C 121 ASN C 461 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092828 restraints weight = 13429.921| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.54 r_work: 0.2861 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.348 10804 Z= 0.348 Angle : 1.039 65.900 14760 Z= 0.619 Chirality : 0.044 0.329 1740 Planarity : 0.008 0.266 1772 Dihedral : 6.164 50.981 2028 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.99 % Allowed : 25.99 % Favored : 73.03 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 12.50 % 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: 1.38 (0.24), residues: 1232 helix: 2.01 (0.22), residues: 554 sheet: 1.73 (0.29), residues: 270 loop : -1.28 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 79 TYR 0.013 0.001 TYR A 81 PHE 0.017 0.001 PHE A 632 TRP 0.007 0.001 TRP C 106 HIS 0.002 0.001 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00772 (10770) covalent geometry : angle 1.03195 (14684) SS BOND : bond 0.00092 ( 8) SS BOND : angle 0.69747 ( 16) hydrogen bonds : bond 0.03703 ( 538) hydrogen bonds : angle 3.67085 ( 1536) metal coordination : bond 0.00442 ( 6) link_BETA1-4 : bond 0.00653 ( 12) link_BETA1-4 : angle 2.40495 ( 36) link_NAG-ASN : bond 0.00309 ( 8) link_NAG-ASN : angle 1.92889 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.31 seconds wall clock time: 62 minutes 6.18 seconds (3726.18 seconds total)