Starting phenix.real_space_refine on Mon Jul 28 16:47:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcw_37112/07_2025/8kcw_37112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcw_37112/07_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_37112/07_2025/8kcw_37112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcw_37112/07_2025/8kcw_37112.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcw_37112/07_2025/8kcw_37112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcw_37112/07_2025/8kcw_37112.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.50, per 1000 atoms: 0.72 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: 3.09 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.24 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: 3.37 Time building geometry restraints manager: 3.64 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: 0.00 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.410 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP C 754 HIS 0.004 0.001 HIS A 594 PHE 0.013 0.001 PHE C 193 TYR 0.015 0.002 TYR A 481 ARG 0.002 0.000 ARG C 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00776 ( 8) link_NAG-ASN : angle 3.47649 ( 24) link_BETA1-4 : bond 0.00693 ( 12) link_BETA1-4 : angle 2.57678 ( 36) hydrogen bonds : bond 0.29380 ( 538) hydrogen bonds : angle 9.53662 ( 1536) metal coordination : bond 0.08799 ( 6) SS BOND : bond 0.00167 ( 8) SS BOND : angle 0.99524 ( 16) covalent geometry : bond 0.00468 (10770) covalent geometry : angle 0.81695 (14684) *********************** 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 : 1.183 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: 0.8626 time to fit residues: 282.0456 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 : 1.067 ------------------------------------------------------------------------------- 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 104 optimal weight: 6.9990 chunk 93 optimal weight: 0.3980 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 763 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.089941 restraints weight = 13080.613| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.62 r_work: 0.2826 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10804 Z= 0.182 Angle : 0.712 8.029 14760 Z= 0.349 Chirality : 0.048 0.285 1740 Planarity : 0.005 0.039 1772 Dihedral : 14.412 82.724 2032 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.97 % Allowed : 13.98 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.21), residues: 1232 helix: -1.59 (0.18), residues: 560 sheet: 1.09 (0.29), residues: 270 loop : -1.77 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 446 HIS 0.006 0.001 HIS C 594 PHE 0.016 0.002 PHE C 632 TYR 0.015 0.002 TYR C 81 ARG 0.002 0.001 ARG C 776 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 8) link_NAG-ASN : angle 2.28058 ( 24) link_BETA1-4 : bond 0.00471 ( 12) link_BETA1-4 : angle 2.43849 ( 36) hydrogen bonds : bond 0.05511 ( 538) hydrogen bonds : angle 4.45733 ( 1536) metal coordination : bond 0.00360 ( 6) SS BOND : bond 0.00153 ( 8) SS BOND : angle 0.98256 ( 16) covalent geometry : bond 0.00412 (10770) covalent geometry : angle 0.69628 (14684) *********************** 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 278 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9272 (mttt) cc_final: 0.9069 (mttm) REVERT: A 240 MET cc_start: 0.9478 (ttt) cc_final: 0.8890 (tmm) REVERT: A 320 PHE cc_start: 0.9177 (m-80) cc_final: 0.8881 (m-80) REVERT: A 517 ARG cc_start: 0.7964 (tmt170) cc_final: 0.7713 (ttp-170) REVERT: A 541 HIS cc_start: 0.8862 (m-70) cc_final: 0.8565 (m90) REVERT: A 713 MET cc_start: 0.9377 (mmt) cc_final: 0.8994 (mmm) REVERT: A 720 ASN cc_start: 0.9245 (m-40) cc_final: 0.8907 (m110) REVERT: A 781 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8714 (mm-30) REVERT: C 101 LYS cc_start: 0.9277 (mttt) cc_final: 0.9073 (mttm) REVERT: C 240 MET cc_start: 0.9476 (ttt) cc_final: 0.8889 (tmm) REVERT: C 320 PHE cc_start: 0.9154 (m-80) cc_final: 0.8863 (m-80) REVERT: C 517 ARG cc_start: 0.7952 (tmt170) cc_final: 0.7700 (ttp-170) REVERT: C 713 MET cc_start: 0.9381 (mmt) cc_final: 0.8996 (mmm) REVERT: C 720 ASN cc_start: 0.9239 (m-40) cc_final: 0.8898 (m110) REVERT: C 781 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8709 (mm-30) outliers start: 22 outliers final: 12 residues processed: 266 average time/residue: 1.2901 time to fit residues: 372.0553 Evaluate side-chains 232 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 748 VAL Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 807 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 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 48 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 22 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.131208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.088143 restraints weight = 13732.903| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.68 r_work: 0.2785 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10804 Z= 0.210 Angle : 0.665 8.424 14760 Z= 0.323 Chirality : 0.048 0.272 1740 Planarity : 0.004 0.039 1772 Dihedral : 10.643 62.061 2032 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.23 % Allowed : 16.31 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1232 helix: 0.08 (0.21), residues: 558 sheet: 1.30 (0.28), residues: 268 loop : -1.67 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.004 0.001 HIS C 594 PHE 0.020 0.002 PHE A 700 TYR 0.014 0.002 TYR C 188 ARG 0.004 0.001 ARG C 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 8) link_NAG-ASN : angle 2.08575 ( 24) link_BETA1-4 : bond 0.00710 ( 12) link_BETA1-4 : angle 2.26967 ( 36) hydrogen bonds : bond 0.05041 ( 538) hydrogen bonds : angle 4.11791 ( 1536) metal coordination : bond 0.00837 ( 6) SS BOND : bond 0.00159 ( 8) SS BOND : angle 0.92573 ( 16) covalent geometry : bond 0.00495 (10770) covalent geometry : angle 0.65084 (14684) *********************** 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 275 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 1.988 Fit side-chains REVERT: A 101 LYS cc_start: 0.9327 (mttt) cc_final: 0.9060 (mttm) REVERT: A 240 MET cc_start: 0.9570 (ttt) cc_final: 0.8886 (tmm) REVERT: A 524 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7406 (mtm-85) REVERT: A 548 MET cc_start: 0.8964 (mtm) cc_final: 0.8704 (mtp) REVERT: A 720 ASN cc_start: 0.9112 (m-40) cc_final: 0.8799 (m110) REVERT: A 769 GLU cc_start: 0.8469 (mp0) cc_final: 0.8088 (mp0) REVERT: A 781 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8576 (mm-30) REVERT: C 101 LYS cc_start: 0.9330 (mttt) cc_final: 0.9064 (mttm) REVERT: C 240 MET cc_start: 0.9565 (ttt) cc_final: 0.8877 (tmm) REVERT: C 524 ARG cc_start: 0.7604 (mtm-85) cc_final: 0.7398 (mtm-85) REVERT: C 548 MET cc_start: 0.8967 (mtm) cc_final: 0.8708 (mtp) REVERT: C 720 ASN cc_start: 0.9106 (m-40) cc_final: 0.8795 (m110) REVERT: C 769 GLU cc_start: 0.8467 (mp0) cc_final: 0.8087 (mp0) REVERT: C 781 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8558 (mm-30) outliers start: 36 outliers final: 18 residues processed: 257 average time/residue: 1.3451 time to fit residues: 376.1767 Evaluate side-chains 235 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 470 VAL Chi-restraints excluded: chain A residue 557 VAL 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 470 VAL Chi-restraints excluded: chain C residue 557 VAL 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 12 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.133485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.090575 restraints weight = 13445.259| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.67 r_work: 0.2839 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10804 Z= 0.117 Angle : 0.594 8.003 14760 Z= 0.285 Chirality : 0.044 0.275 1740 Planarity : 0.003 0.033 1772 Dihedral : 8.245 57.598 2032 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.05 % Allowed : 19.35 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1232 helix: 0.97 (0.22), residues: 558 sheet: 1.52 (0.28), residues: 270 loop : -1.57 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 106 HIS 0.002 0.001 HIS C 487 PHE 0.017 0.001 PHE C 571 TYR 0.012 0.001 TYR C 481 ARG 0.003 0.000 ARG C 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 8) link_NAG-ASN : angle 2.12353 ( 24) link_BETA1-4 : bond 0.00668 ( 12) link_BETA1-4 : angle 2.18722 ( 36) hydrogen bonds : bond 0.03937 ( 538) hydrogen bonds : angle 3.76682 ( 1536) metal coordination : bond 0.00375 ( 6) SS BOND : bond 0.00105 ( 8) SS BOND : angle 0.80912 ( 16) covalent geometry : bond 0.00254 (10770) covalent geometry : angle 0.57883 (14684) *********************** 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 282 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9344 (mttt) cc_final: 0.9070 (mttm) REVERT: A 123 GLN cc_start: 0.9027 (mt0) cc_final: 0.8735 (mm-40) REVERT: A 143 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: A 195 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8407 (mtpm) REVERT: A 240 MET cc_start: 0.9562 (ttt) cc_final: 0.8917 (tmm) REVERT: A 524 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.6895 (mmm-85) REVERT: A 577 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8629 (m-80) REVERT: A 713 MET cc_start: 0.9331 (mmt) cc_final: 0.9074 (mmm) REVERT: A 720 ASN cc_start: 0.8959 (m-40) cc_final: 0.8675 (m110) REVERT: C 101 LYS cc_start: 0.9341 (mttt) cc_final: 0.9063 (mttm) REVERT: C 123 GLN cc_start: 0.9033 (mt0) cc_final: 0.8737 (mm-40) REVERT: C 143 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: C 195 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8395 (mtpm) REVERT: C 240 MET cc_start: 0.9555 (ttt) cc_final: 0.8909 (tmm) REVERT: C 524 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.6875 (mmm-85) REVERT: C 577 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: C 713 MET cc_start: 0.9336 (mmt) cc_final: 0.9079 (mmm) REVERT: C 720 ASN cc_start: 0.8962 (m-40) cc_final: 0.8677 (m110) outliers start: 34 outliers final: 10 residues processed: 256 average time/residue: 1.3319 time to fit residues: 374.1579 Evaluate side-chains 240 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 GLN 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 C residue 70 SER Chi-restraints excluded: chain C residue 74 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 541 HIS A 636 HIS A 763 GLN C 121 ASN C 541 HIS C 636 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 = 0.3544 r_free = 0.3544 target = 0.130395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.087417 restraints weight = 13611.392| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.66 r_work: 0.2769 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10804 Z= 0.220 Angle : 0.636 7.232 14760 Z= 0.313 Chirality : 0.046 0.278 1740 Planarity : 0.003 0.036 1772 Dihedral : 7.773 56.879 2032 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.76 % Allowed : 19.71 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1232 helix: 1.34 (0.22), residues: 558 sheet: 1.59 (0.28), residues: 268 loop : -1.52 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.004 0.001 HIS A 487 PHE 0.020 0.002 PHE C 700 TYR 0.015 0.001 TYR A 188 ARG 0.002 0.000 ARG C 776 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 8) link_NAG-ASN : angle 2.01387 ( 24) link_BETA1-4 : bond 0.00645 ( 12) link_BETA1-4 : angle 2.39804 ( 36) hydrogen bonds : bond 0.04359 ( 538) hydrogen bonds : angle 3.90241 ( 1536) metal coordination : bond 0.00732 ( 6) SS BOND : bond 0.00171 ( 8) SS BOND : angle 0.81726 ( 16) covalent geometry : bond 0.00527 (10770) covalent geometry : angle 0.62072 (14684) *********************** 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 268 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8275 (p0) REVERT: A 101 LYS cc_start: 0.9333 (mttt) cc_final: 0.9053 (mttm) REVERT: A 123 GLN cc_start: 0.9051 (mt0) cc_final: 0.8720 (mm-40) REVERT: A 143 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: A 240 MET cc_start: 0.9569 (ttt) cc_final: 0.9017 (tmm) REVERT: A 524 ARG cc_start: 0.7650 (mtm-85) cc_final: 0.7403 (mmm-85) REVERT: A 577 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8691 (m-80) REVERT: A 588 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8500 (mmmt) REVERT: C 73 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8273 (p0) REVERT: C 101 LYS cc_start: 0.9323 (mttt) cc_final: 0.9035 (mttm) REVERT: C 123 GLN cc_start: 0.9048 (mt0) cc_final: 0.8714 (mm-40) REVERT: C 143 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: C 240 MET cc_start: 0.9561 (ttt) cc_final: 0.9005 (tmm) REVERT: C 524 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7396 (mmm-85) REVERT: C 577 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8683 (m-80) REVERT: C 588 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8507 (mmmt) outliers start: 42 outliers final: 18 residues processed: 242 average time/residue: 1.2418 time to fit residues: 328.7532 Evaluate side-chains 246 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 557 VAL Chi-restraints excluded: chain A residue 577 PHE 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 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 557 VAL Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 684 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 20 optimal weight: 0.0770 chunk 31 optimal weight: 0.0370 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 541 HIS A 720 ASN C 447 ASN C 541 HIS C 720 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.091323 restraints weight = 13545.655| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.69 r_work: 0.2828 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10804 Z= 0.111 Angle : 0.579 7.495 14760 Z= 0.280 Chirality : 0.044 0.267 1740 Planarity : 0.003 0.033 1772 Dihedral : 7.044 56.782 2032 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.15 % Allowed : 22.22 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1232 helix: 1.78 (0.23), residues: 554 sheet: 1.62 (0.29), residues: 270 loop : -1.43 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 768 HIS 0.001 0.000 HIS A 636 PHE 0.015 0.001 PHE C 632 TYR 0.012 0.001 TYR C 481 ARG 0.003 0.000 ARG C 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 8) link_NAG-ASN : angle 2.11246 ( 24) link_BETA1-4 : bond 0.00554 ( 12) link_BETA1-4 : angle 2.33780 ( 36) hydrogen bonds : bond 0.03693 ( 538) hydrogen bonds : angle 3.73233 ( 1536) metal coordination : bond 0.00342 ( 6) SS BOND : bond 0.00094 ( 8) SS BOND : angle 0.76769 ( 16) covalent geometry : bond 0.00241 (10770) covalent geometry : angle 0.56157 (14684) *********************** 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 256 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9329 (mttt) cc_final: 0.9044 (mttm) REVERT: A 123 GLN cc_start: 0.9060 (mt0) cc_final: 0.8674 (mm-40) REVERT: A 219 ASN cc_start: 0.8689 (m-40) cc_final: 0.8327 (p0) REVERT: A 240 MET cc_start: 0.9558 (ttt) cc_final: 0.8735 (tmm) REVERT: A 524 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.7393 (mtm-85) REVERT: A 586 MET cc_start: 0.8541 (mmm) cc_final: 0.8170 (mpp) REVERT: A 588 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8564 (mmmt) REVERT: A 781 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8441 (mm-30) REVERT: C 101 LYS cc_start: 0.9325 (mttt) cc_final: 0.9032 (mttm) REVERT: C 123 GLN cc_start: 0.9058 (mt0) cc_final: 0.8671 (mm-40) REVERT: C 219 ASN cc_start: 0.8696 (m-40) cc_final: 0.8332 (p0) REVERT: C 240 MET cc_start: 0.9556 (ttt) cc_final: 0.8726 (tmm) REVERT: C 325 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7295 (mp) REVERT: C 524 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: C 586 MET cc_start: 0.8538 (mmm) cc_final: 0.8165 (mpp) REVERT: C 588 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8552 (mmmt) REVERT: C 781 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8429 (mm-30) outliers start: 24 outliers final: 6 residues processed: 238 average time/residue: 1.2495 time to fit residues: 325.1441 Evaluate side-chains 225 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 684 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.0970 chunk 92 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN A 447 ASN A 467 GLN A 541 HIS A 720 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 447 ASN C 467 GLN C 541 HIS C 720 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.089446 restraints weight = 13643.764| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.66 r_work: 0.2802 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10804 Z= 0.152 Angle : 0.597 8.419 14760 Z= 0.291 Chirality : 0.044 0.266 1740 Planarity : 0.003 0.032 1772 Dihedral : 6.831 55.909 2032 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.15 % Allowed : 23.48 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1232 helix: 1.85 (0.23), residues: 554 sheet: 1.66 (0.29), residues: 270 loop : -1.41 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 768 HIS 0.003 0.001 HIS C 487 PHE 0.021 0.001 PHE A 700 TYR 0.014 0.001 TYR A 590 ARG 0.002 0.000 ARG C 705 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 8) link_NAG-ASN : angle 1.97210 ( 24) link_BETA1-4 : bond 0.00505 ( 12) link_BETA1-4 : angle 2.43592 ( 36) hydrogen bonds : bond 0.03899 ( 538) hydrogen bonds : angle 3.76621 ( 1536) metal coordination : bond 0.00514 ( 6) SS BOND : bond 0.00106 ( 8) SS BOND : angle 0.73808 ( 16) covalent geometry : bond 0.00356 (10770) covalent geometry : angle 0.57999 (14684) *********************** 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 255 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 1.127 Fit side-chains REVERT: A 101 LYS cc_start: 0.9333 (mttt) cc_final: 0.9051 (mttm) REVERT: A 123 GLN cc_start: 0.9004 (mt0) cc_final: 0.8675 (mm-40) REVERT: A 143 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: A 219 ASN cc_start: 0.8702 (m-40) cc_final: 0.8329 (p0) REVERT: A 240 MET cc_start: 0.9549 (ttt) cc_final: 0.8920 (tmm) REVERT: A 524 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7376 (mtm-85) REVERT: A 588 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8575 (mmmt) REVERT: A 781 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8506 (mm-30) REVERT: C 101 LYS cc_start: 0.9330 (mttt) cc_final: 0.9045 (mttm) REVERT: C 123 GLN cc_start: 0.8997 (mt0) cc_final: 0.8665 (mm-40) REVERT: C 143 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: C 219 ASN cc_start: 0.8710 (m-40) cc_final: 0.8341 (p0) REVERT: C 240 MET cc_start: 0.9542 (ttt) cc_final: 0.8907 (tmm) REVERT: C 524 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7370 (mtm-85) REVERT: C 588 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8562 (mmmt) REVERT: C 781 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8474 (mm-30) outliers start: 24 outliers final: 10 residues processed: 239 average time/residue: 1.1477 time to fit residues: 299.0914 Evaluate side-chains 232 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 577 PHE 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 16 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN A 447 ASN A 461 GLN A 541 HIS A 763 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 447 ASN C 461 GLN C 541 HIS C 763 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.090970 restraints weight = 13648.072| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.56 r_work: 0.2818 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10804 Z= 0.199 Angle : 0.625 9.542 14760 Z= 0.308 Chirality : 0.046 0.267 1740 Planarity : 0.003 0.035 1772 Dihedral : 6.839 55.944 2032 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.51 % Allowed : 23.66 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1232 helix: 1.84 (0.23), residues: 556 sheet: 1.63 (0.29), residues: 270 loop : -1.43 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 768 HIS 0.003 0.001 HIS C 487 PHE 0.021 0.001 PHE C 632 TYR 0.017 0.001 TYR A 590 ARG 0.002 0.000 ARG C 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 8) link_NAG-ASN : angle 1.93281 ( 24) link_BETA1-4 : bond 0.00518 ( 12) link_BETA1-4 : angle 2.42104 ( 36) hydrogen bonds : bond 0.04051 ( 538) hydrogen bonds : angle 3.84209 ( 1536) metal coordination : bond 0.00645 ( 6) SS BOND : bond 0.00144 ( 8) SS BOND : angle 0.70643 ( 16) covalent geometry : bond 0.00477 (10770) covalent geometry : angle 0.61001 (14684) *********************** 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 250 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 1.460 Fit side-chains REVERT: A 73 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8007 (p0) REVERT: A 101 LYS cc_start: 0.9321 (mttt) cc_final: 0.9057 (mttm) REVERT: A 123 GLN cc_start: 0.9033 (mt0) cc_final: 0.8715 (mm-40) REVERT: A 219 ASN cc_start: 0.8712 (m-40) cc_final: 0.8373 (p0) REVERT: A 240 MET cc_start: 0.9607 (ttt) cc_final: 0.9049 (tmm) REVERT: A 524 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7416 (mtm-85) REVERT: A 781 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8505 (mm-30) REVERT: C 73 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7995 (p0) REVERT: C 101 LYS cc_start: 0.9318 (mttt) cc_final: 0.9050 (mttm) REVERT: C 219 ASN cc_start: 0.8721 (m-40) cc_final: 0.8390 (p0) REVERT: C 240 MET cc_start: 0.9605 (ttt) cc_final: 0.9041 (tmm) REVERT: C 524 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7416 (mtm-85) REVERT: C 781 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8496 (mm-30) outliers start: 28 outliers final: 15 residues processed: 235 average time/residue: 1.5117 time to fit residues: 387.3154 Evaluate side-chains 235 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 332 TYR 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 332 TYR Chi-restraints excluded: chain C residue 459 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 461 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 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 = 0.3570 r_free = 0.3570 target = 0.131931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.090560 restraints weight = 13828.473| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.52 r_work: 0.2823 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10804 Z= 0.178 Angle : 0.629 10.850 14760 Z= 0.309 Chirality : 0.046 0.262 1740 Planarity : 0.003 0.035 1772 Dihedral : 6.810 56.040 2032 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.06 % Allowed : 24.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1232 helix: 1.88 (0.23), residues: 556 sheet: 1.63 (0.29), residues: 270 loop : -1.43 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 768 HIS 0.003 0.001 HIS A 487 PHE 0.023 0.001 PHE A 632 TYR 0.015 0.001 TYR C 590 ARG 0.002 0.000 ARG C 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 8) link_NAG-ASN : angle 1.95541 ( 24) link_BETA1-4 : bond 0.00488 ( 12) link_BETA1-4 : angle 2.41833 ( 36) hydrogen bonds : bond 0.04038 ( 538) hydrogen bonds : angle 3.83588 ( 1536) metal coordination : bond 0.00590 ( 6) SS BOND : bond 0.00133 ( 8) SS BOND : angle 0.74572 ( 16) covalent geometry : bond 0.00426 (10770) covalent geometry : angle 0.61364 (14684) *********************** 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 238 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 1.117 Fit side-chains REVERT: A 73 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7999 (p0) REVERT: A 101 LYS cc_start: 0.9327 (mttt) cc_final: 0.9070 (mttm) REVERT: A 219 ASN cc_start: 0.8703 (m-40) cc_final: 0.8365 (p0) REVERT: A 240 MET cc_start: 0.9605 (ttt) cc_final: 0.9020 (tmm) REVERT: A 524 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7392 (mtm-85) REVERT: A 588 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8600 (mmmt) REVERT: A 781 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8491 (mm-30) REVERT: C 73 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8004 (p0) REVERT: C 101 LYS cc_start: 0.9322 (mttt) cc_final: 0.9062 (mttm) REVERT: C 219 ASN cc_start: 0.8717 (m-40) cc_final: 0.8380 (p0) REVERT: C 240 MET cc_start: 0.9600 (ttt) cc_final: 0.9006 (tmm) REVERT: C 524 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: C 588 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8599 (mmmt) REVERT: C 781 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8494 (mm-30) outliers start: 23 outliers final: 15 residues processed: 226 average time/residue: 1.1997 time to fit residues: 298.4282 Evaluate side-chains 228 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 459 VAL 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 C residue 73 ASP Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 447 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 110 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 720 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 GLN C 720 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.090570 restraints weight = 13693.550| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.52 r_work: 0.2823 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10804 Z= 0.198 Angle : 1.070 59.197 14760 Z= 0.628 Chirality : 0.046 0.262 1740 Planarity : 0.003 0.034 1772 Dihedral : 6.840 56.042 2032 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.52 % Allowed : 25.00 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1232 helix: 1.80 (0.23), residues: 556 sheet: 1.62 (0.29), residues: 270 loop : -1.42 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 768 HIS 0.003 0.001 HIS C 487 PHE 0.021 0.001 PHE A 632 TYR 0.013 0.001 TYR C 590 ARG 0.002 0.000 ARG C 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 8) link_NAG-ASN : angle 1.95449 ( 24) link_BETA1-4 : bond 0.00526 ( 12) link_BETA1-4 : angle 2.43562 ( 36) hydrogen bonds : bond 0.04102 ( 538) hydrogen bonds : angle 3.84039 ( 1536) metal coordination : bond 0.00559 ( 6) SS BOND : bond 0.00123 ( 8) SS BOND : angle 0.73256 ( 16) covalent geometry : bond 0.00437 (10770) covalent geometry : angle 1.06230 (14684) ********************** 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 230 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 1.212 Fit side-chains REVERT: A 101 LYS cc_start: 0.9325 (mttt) cc_final: 0.9066 (mttm) REVERT: A 219 ASN cc_start: 0.8699 (m-40) cc_final: 0.8365 (p0) REVERT: A 240 MET cc_start: 0.9604 (ttt) cc_final: 0.9020 (tmm) REVERT: A 588 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8570 (mmmt) REVERT: A 781 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8481 (mm-30) REVERT: C 101 LYS cc_start: 0.9317 (mttt) cc_final: 0.9054 (mttm) REVERT: C 219 ASN cc_start: 0.8718 (m-40) cc_final: 0.8382 (p0) REVERT: C 240 MET cc_start: 0.9598 (ttt) cc_final: 0.9007 (tmm) REVERT: C 588 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8575 (mmmt) REVERT: C 781 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8492 (mm-30) outliers start: 17 outliers final: 13 residues processed: 218 average time/residue: 1.0880 time to fit residues: 259.5220 Evaluate side-chains 223 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 459 VAL 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 C residue 332 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 461 GLN A 720 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN C 461 GLN C 720 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.091225 restraints weight = 13674.676| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.56 r_work: 0.2819 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 10804 Z= 0.214 Angle : 1.065 58.314 14760 Z= 0.607 Chirality : 0.046 0.262 1740 Planarity : 0.003 0.035 1772 Dihedral : 6.824 56.051 2032 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.52 % Allowed : 25.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1232 helix: 1.79 (0.23), residues: 556 sheet: 1.62 (0.29), residues: 270 loop : -1.42 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 768 HIS 0.003 0.001 HIS A 487 PHE 0.021 0.001 PHE C 632 TYR 0.013 0.001 TYR A 188 ARG 0.002 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 8) link_NAG-ASN : angle 1.95308 ( 24) link_BETA1-4 : bond 0.00519 ( 12) link_BETA1-4 : angle 2.41122 ( 36) hydrogen bonds : bond 0.04036 ( 538) hydrogen bonds : angle 3.86045 ( 1536) metal coordination : bond 0.00615 ( 6) SS BOND : bond 0.00135 ( 8) SS BOND : angle 0.75493 ( 16) covalent geometry : bond 0.00503 (10770) covalent geometry : angle 1.05733 (14684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9789.22 seconds wall clock time: 179 minutes 35.69 seconds (10775.69 seconds total)