Starting phenix.real_space_refine on Tue May 13 12:17:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcw_37112/05_2025/8kcw_37112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcw_37112/05_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_37112/05_2025/8kcw_37112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcw_37112/05_2025/8kcw_37112.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcw_37112/05_2025/8kcw_37112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcw_37112/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.60, per 1000 atoms: 0.63 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 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: 0.99 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: 2.87 Time building geometry restraints manager: 3.04 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: 0.380 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.590 Find NCS groups from input model: 0.330 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.320 ------------------------------------------------------------------------------- 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 : 1.179 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: 0.8543 time to fit residues: 279.2959 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 : 1.182 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.089940 restraints weight = 13080.615| |-----------------------------------------------------------------------------| 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 : 1.169 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: 0.8889 (tmm) REVERT: A 320 PHE cc_start: 0.9176 (m-80) cc_final: 0.8882 (m-80) REVERT: A 517 ARG cc_start: 0.7966 (tmt170) cc_final: 0.7714 (ttp-170) REVERT: A 541 HIS cc_start: 0.8863 (m-70) cc_final: 0.8566 (m90) REVERT: A 713 MET cc_start: 0.9377 (mmt) cc_final: 0.8993 (mmm) REVERT: A 720 ASN cc_start: 0.9246 (m-40) cc_final: 0.8908 (m110) REVERT: A 781 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8714 (mm-30) REVERT: C 101 LYS cc_start: 0.9276 (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: 0.9155 (m-80) cc_final: 0.8864 (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: 0.9240 (m-40) cc_final: 0.8899 (m110) REVERT: C 781 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8708 (mm-30) outliers start: 22 outliers final: 12 residues processed: 266 average time/residue: 1.0221 time to fit residues: 295.8847 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 : 1.136 ------------------------------------------------------------------------------- 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: 2.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 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 = 0.3553 r_free = 0.3553 target = 0.131124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.087967 restraints weight = 13731.163| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.69 r_work: 0.2795 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10804 Z= 0.208 Angle : 0.670 8.655 14760 Z= 0.327 Chirality : 0.047 0.270 1740 Planarity : 0.004 0.039 1772 Dihedral : 10.080 58.025 2032 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.87 % Allowed : 16.85 % Favored : 80.29 % 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: -0.33 (0.23), residues: 1232 helix: 0.08 (0.21), residues: 558 sheet: 1.31 (0.28), residues: 268 loop : -1.64 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 106 HIS 0.004 0.001 HIS C 594 PHE 0.021 0.002 PHE A 700 TYR 0.015 0.002 TYR C 724 ARG 0.004 0.001 ARG C 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 8) link_NAG-ASN : angle 2.09079 ( 24) link_BETA1-4 : bond 0.00670 ( 12) link_BETA1-4 : angle 2.17927 ( 36) hydrogen bonds : bond 0.05018 ( 538) hydrogen bonds : angle 4.09775 ( 1536) metal coordination : bond 0.00805 ( 6) SS BOND : bond 0.00170 ( 8) SS BOND : angle 0.93061 ( 16) covalent geometry : bond 0.00491 (10770) covalent geometry : angle 0.65663 (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 270 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 1.207 Fit side-chains REVERT: A 101 LYS cc_start: 0.9332 (mttt) cc_final: 0.9064 (mttm) REVERT: A 240 MET cc_start: 0.9582 (ttt) cc_final: 0.8940 (tmm) REVERT: A 524 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7425 (mtm-85) REVERT: A 555 GLU cc_start: 0.9103 (tp30) cc_final: 0.8760 (tp30) REVERT: A 713 MET cc_start: 0.9339 (mmt) cc_final: 0.8969 (mmm) REVERT: A 720 ASN cc_start: 0.9106 (m-40) cc_final: 0.8793 (m110) REVERT: A 769 GLU cc_start: 0.8516 (mp0) cc_final: 0.8101 (mp0) REVERT: C 101 LYS cc_start: 0.9332 (mttt) cc_final: 0.9062 (mttm) REVERT: C 240 MET cc_start: 0.9575 (ttt) cc_final: 0.8931 (tmm) REVERT: C 524 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7416 (mtm-85) REVERT: C 555 GLU cc_start: 0.9102 (tp30) cc_final: 0.8756 (tp30) REVERT: C 713 MET cc_start: 0.9338 (mmt) cc_final: 0.8969 (mmm) REVERT: C 720 ASN cc_start: 0.9107 (m-40) cc_final: 0.8791 (m110) REVERT: C 769 GLU cc_start: 0.8521 (mp0) cc_final: 0.8105 (mp0) outliers start: 32 outliers final: 18 residues processed: 256 average time/residue: 0.9808 time to fit residues: 274.0950 Evaluate side-chains 232 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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: 3.9990 chunk 118 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 77 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.133157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.090033 restraints weight = 13442.821| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.69 r_work: 0.2822 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10804 Z= 0.121 Angle : 0.593 7.922 14760 Z= 0.285 Chirality : 0.044 0.273 1740 Planarity : 0.003 0.033 1772 Dihedral : 8.178 57.674 2032 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.24 % Allowed : 19.71 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.23), residues: 1232 helix: 1.02 (0.22), residues: 554 sheet: 1.55 (0.28), residues: 270 loop : -1.48 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 106 HIS 0.002 0.001 HIS A 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 0.00315 ( 8) link_NAG-ASN : angle 2.09236 ( 24) link_BETA1-4 : bond 0.00604 ( 12) link_BETA1-4 : angle 2.22689 ( 36) hydrogen bonds : bond 0.03993 ( 538) hydrogen bonds : angle 3.78930 ( 1536) metal coordination : bond 0.00358 ( 6) SS BOND : bond 0.00097 ( 8) SS BOND : angle 0.79276 ( 16) covalent geometry : bond 0.00266 (10770) covalent geometry : angle 0.57704 (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 269 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9339 (mttt) cc_final: 0.9068 (mttm) REVERT: A 123 GLN cc_start: 0.9041 (mt0) cc_final: 0.8747 (mm-40) REVERT: A 195 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8381 (mtpm) REVERT: A 240 MET cc_start: 0.9578 (ttt) cc_final: 0.8809 (tmm) REVERT: A 524 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.6921 (mmm-85) REVERT: A 555 GLU cc_start: 0.9060 (tp30) cc_final: 0.8608 (tp30) REVERT: A 713 MET cc_start: 0.9336 (mmt) cc_final: 0.9061 (mmm) REVERT: A 720 ASN cc_start: 0.8880 (m-40) cc_final: 0.8602 (m110) REVERT: C 101 LYS cc_start: 0.9340 (mttt) cc_final: 0.9056 (mttm) REVERT: C 123 GLN cc_start: 0.9040 (mt0) cc_final: 0.8741 (mm-40) REVERT: C 143 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: C 195 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8376 (mtpm) REVERT: C 240 MET cc_start: 0.9571 (ttt) cc_final: 0.8795 (tmm) REVERT: C 524 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.6909 (mmm-85) REVERT: C 555 GLU cc_start: 0.9059 (tp30) cc_final: 0.8607 (tp30) REVERT: C 713 MET cc_start: 0.9332 (mmt) cc_final: 0.9057 (mmm) REVERT: C 720 ASN cc_start: 0.8878 (m-40) cc_final: 0.8599 (m110) outliers start: 25 outliers final: 5 residues processed: 251 average time/residue: 0.9390 time to fit residues: 258.3086 Evaluate side-chains 234 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 684 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 143 GLN A 467 GLN A 541 HIS A 763 GLN C 121 ASN C 467 GLN C 541 HIS C 763 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.089107 restraints weight = 13562.079| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.66 r_work: 0.2796 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10804 Z= 0.154 Angle : 0.602 7.114 14760 Z= 0.292 Chirality : 0.045 0.275 1740 Planarity : 0.003 0.034 1772 Dihedral : 7.512 56.752 2032 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.32 % Allowed : 20.88 % Favored : 75.81 % 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: 0.88 (0.24), residues: 1232 helix: 1.49 (0.22), residues: 554 sheet: 1.60 (0.29), residues: 270 loop : -1.46 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.003 0.001 HIS C 487 PHE 0.020 0.001 PHE C 700 TYR 0.013 0.001 TYR C 188 ARG 0.002 0.000 ARG C 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 8) link_NAG-ASN : angle 2.06828 ( 24) link_BETA1-4 : bond 0.00584 ( 12) link_BETA1-4 : angle 2.33197 ( 36) hydrogen bonds : bond 0.04024 ( 538) hydrogen bonds : angle 3.79542 ( 1536) metal coordination : bond 0.00515 ( 6) SS BOND : bond 0.00110 ( 8) SS BOND : angle 0.76938 ( 16) covalent geometry : bond 0.00361 (10770) covalent geometry : angle 0.58614 (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: 37 poor density : 231 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8273 (p0) REVERT: A 101 LYS cc_start: 0.9324 (mttt) cc_final: 0.9040 (mttm) REVERT: A 123 GLN cc_start: 0.9061 (mt0) cc_final: 0.8715 (mm-40) REVERT: A 143 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: A 240 MET cc_start: 0.9550 (ttt) cc_final: 0.8892 (tmm) REVERT: A 524 ARG cc_start: 0.7665 (mtm-85) cc_final: 0.7415 (mmm-85) REVERT: A 555 GLU cc_start: 0.9107 (tp30) cc_final: 0.8650 (tp30) REVERT: A 577 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8731 (m-80) REVERT: A 588 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8537 (mmmt) REVERT: A 713 MET cc_start: 0.9354 (mmt) cc_final: 0.9059 (mmm) REVERT: A 769 GLU cc_start: 0.8566 (mp0) cc_final: 0.8114 (mp0) REVERT: A 781 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8490 (mm-30) REVERT: C 73 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8272 (p0) REVERT: C 101 LYS cc_start: 0.9327 (mttt) cc_final: 0.9044 (mttm) REVERT: C 123 GLN cc_start: 0.9061 (mt0) cc_final: 0.8711 (mm-40) REVERT: C 143 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: C 240 MET cc_start: 0.9539 (ttt) cc_final: 0.8885 (tmm) REVERT: C 524 ARG cc_start: 0.7661 (mtm-85) cc_final: 0.7414 (mmm-85) REVERT: C 555 GLU cc_start: 0.9100 (tp30) cc_final: 0.8635 (tp30) REVERT: C 577 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: C 588 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8535 (mmmt) REVERT: C 713 MET cc_start: 0.9357 (mmt) cc_final: 0.9062 (mmm) REVERT: C 769 GLU cc_start: 0.8564 (mp0) cc_final: 0.8115 (mp0) REVERT: C 781 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8463 (mm-30) outliers start: 37 outliers final: 11 residues processed: 246 average time/residue: 0.9998 time to fit residues: 268.6992 Evaluate side-chains 239 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 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 70 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 541 HIS A 636 HIS A 720 ASN A 763 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 HIS C 636 HIS C 720 ASN C 763 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.088270 restraints weight = 13608.019| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.66 r_work: 0.2780 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3816 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= 0.191 Angle : 0.612 7.217 14760 Z= 0.301 Chirality : 0.046 0.273 1740 Planarity : 0.003 0.035 1772 Dihedral : 7.291 56.487 2032 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.15 % Allowed : 22.40 % Favored : 75.45 % 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: 1.02 (0.24), residues: 1232 helix: 1.65 (0.22), residues: 554 sheet: 1.61 (0.29), residues: 270 loop : -1.41 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.003 0.001 HIS C 487 PHE 0.020 0.001 PHE C 632 TYR 0.013 0.001 TYR C 188 ARG 0.002 0.000 ARG C 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 8) link_NAG-ASN : angle 1.98996 ( 24) link_BETA1-4 : bond 0.00528 ( 12) link_BETA1-4 : angle 2.40726 ( 36) hydrogen bonds : bond 0.04133 ( 538) hydrogen bonds : angle 3.84201 ( 1536) metal coordination : bond 0.00622 ( 6) SS BOND : bond 0.00146 ( 8) SS BOND : angle 0.75551 ( 16) covalent geometry : bond 0.00457 (10770) covalent geometry : angle 0.59640 (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 253 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8311 (p0) REVERT: A 101 LYS cc_start: 0.9329 (mttt) cc_final: 0.9039 (mttm) REVERT: A 123 GLN cc_start: 0.9013 (mt0) cc_final: 0.8694 (mm-40) REVERT: A 240 MET cc_start: 0.9573 (ttt) cc_final: 0.8980 (tmm) REVERT: A 524 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7403 (mtm-85) REVERT: A 555 GLU cc_start: 0.9082 (tp30) cc_final: 0.8563 (tp30) REVERT: A 588 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8507 (mmmt) REVERT: A 781 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8492 (mm-30) REVERT: C 73 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8308 (p0) REVERT: C 101 LYS cc_start: 0.9321 (mttt) cc_final: 0.9030 (mttm) REVERT: C 123 GLN cc_start: 0.9007 (mt0) cc_final: 0.8684 (mm-40) REVERT: C 143 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: C 240 MET cc_start: 0.9560 (ttt) cc_final: 0.8962 (tmm) REVERT: C 524 ARG cc_start: 0.7650 (mtm-85) cc_final: 0.7394 (mtm-85) REVERT: C 555 GLU cc_start: 0.9078 (tp30) cc_final: 0.8558 (tp30) REVERT: C 588 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8492 (mmmt) REVERT: C 781 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8474 (mm-30) outliers start: 24 outliers final: 16 residues processed: 236 average time/residue: 1.0045 time to fit residues: 258.3660 Evaluate side-chains 248 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 332 TYR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 810 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 461 GLN A 541 HIS A 720 ASN A 763 GLN C 121 ASN C 461 GLN C 541 HIS C 720 ASN C 763 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.088319 restraints weight = 13651.007| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.67 r_work: 0.2799 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10804 Z= 0.187 Angle : 0.612 9.112 14760 Z= 0.299 Chirality : 0.045 0.269 1740 Planarity : 0.003 0.035 1772 Dihedral : 6.976 56.282 2032 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.24 % Allowed : 22.40 % Favored : 75.36 % 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: 1.12 (0.24), residues: 1232 helix: 1.77 (0.23), residues: 554 sheet: 1.63 (0.29), residues: 270 loop : -1.40 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 106 HIS 0.003 0.001 HIS C 487 PHE 0.023 0.001 PHE A 700 TYR 0.014 0.001 TYR C 81 ARG 0.002 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 8) link_NAG-ASN : angle 1.99542 ( 24) link_BETA1-4 : bond 0.00494 ( 12) link_BETA1-4 : angle 2.45285 ( 36) hydrogen bonds : bond 0.04116 ( 538) hydrogen bonds : angle 3.84232 ( 1536) metal coordination : bond 0.00608 ( 6) SS BOND : bond 0.00144 ( 8) SS BOND : angle 0.77961 ( 16) covalent geometry : bond 0.00445 (10770) covalent geometry : angle 0.59498 (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 253 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8051 (p0) REVERT: A 74 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7798 (mp-120) REVERT: A 101 LYS cc_start: 0.9322 (mttt) cc_final: 0.9049 (mttm) REVERT: A 219 ASN cc_start: 0.8741 (m-40) cc_final: 0.8348 (p0) REVERT: A 240 MET cc_start: 0.9570 (ttt) cc_final: 0.8987 (tmm) REVERT: A 524 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7441 (mtm-85) REVERT: A 555 GLU cc_start: 0.9084 (tp30) cc_final: 0.8565 (tp30) REVERT: A 588 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8581 (mmmt) REVERT: A 684 MET cc_start: 0.8005 (ptt) cc_final: 0.7726 (ptm) REVERT: A 781 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8486 (mm-30) REVERT: C 73 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8341 (p0) REVERT: C 101 LYS cc_start: 0.9320 (mttt) cc_final: 0.9036 (mttm) REVERT: C 143 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8137 (mt0) REVERT: C 240 MET cc_start: 0.9556 (ttt) cc_final: 0.8965 (tmm) REVERT: C 524 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7439 (mtm-85) REVERT: C 555 GLU cc_start: 0.9079 (tp30) cc_final: 0.8557 (tp30) REVERT: C 588 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8576 (mmmt) REVERT: C 684 MET cc_start: 0.7999 (ptt) cc_final: 0.7722 (ptm) REVERT: C 781 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8467 (mm-30) outliers start: 25 outliers final: 15 residues processed: 239 average time/residue: 1.0004 time to fit residues: 260.7673 Evaluate side-chains 235 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 332 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 810 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 120 optimal weight: 0.0010 chunk 122 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN C 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.093039 restraints weight = 13533.884| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.56 r_work: 0.2854 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10804 Z= 0.113 Angle : 0.582 10.269 14760 Z= 0.281 Chirality : 0.044 0.260 1740 Planarity : 0.003 0.033 1772 Dihedral : 6.612 55.873 2032 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.34 % Allowed : 24.19 % Favored : 74.46 % 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: 1.28 (0.24), residues: 1232 helix: 1.93 (0.23), residues: 554 sheet: 1.66 (0.29), residues: 270 loop : -1.32 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 106 HIS 0.002 0.000 HIS A 795 PHE 0.020 0.001 PHE A 632 TYR 0.014 0.001 TYR C 590 ARG 0.003 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 8) link_NAG-ASN : angle 2.02470 ( 24) link_BETA1-4 : bond 0.00493 ( 12) link_BETA1-4 : angle 2.41488 ( 36) hydrogen bonds : bond 0.03680 ( 538) hydrogen bonds : angle 3.69131 ( 1536) metal coordination : bond 0.00370 ( 6) SS BOND : bond 0.00100 ( 8) SS BOND : angle 0.78376 ( 16) covalent geometry : bond 0.00251 (10770) covalent geometry : angle 0.56464 (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 248 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9313 (mttt) cc_final: 0.9055 (mttm) REVERT: A 219 ASN cc_start: 0.8639 (m-40) cc_final: 0.8407 (p0) REVERT: A 240 MET cc_start: 0.9565 (ttt) cc_final: 0.8829 (tmm) REVERT: A 524 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7372 (mtm-85) REVERT: A 555 GLU cc_start: 0.9074 (tp30) cc_final: 0.8592 (tp30) REVERT: A 586 MET cc_start: 0.8456 (mmm) cc_final: 0.8253 (mpp) REVERT: A 684 MET cc_start: 0.7999 (ptt) cc_final: 0.7684 (ptm) REVERT: A 781 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8497 (mm-30) REVERT: C 101 LYS cc_start: 0.9315 (mttt) cc_final: 0.9056 (mttm) REVERT: C 219 ASN cc_start: 0.8652 (m-40) cc_final: 0.8408 (p0) REVERT: C 240 MET cc_start: 0.9558 (ttt) cc_final: 0.8810 (tmm) REVERT: C 524 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.7355 (mtm-85) REVERT: C 555 GLU cc_start: 0.9079 (tp30) cc_final: 0.8601 (tp30) REVERT: C 586 MET cc_start: 0.8457 (mmm) cc_final: 0.8245 (mpp) REVERT: C 684 MET cc_start: 0.7994 (ptt) cc_final: 0.7685 (ptm) REVERT: C 781 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8493 (mm-30) outliers start: 15 outliers final: 6 residues processed: 240 average time/residue: 0.9248 time to fit residues: 243.8501 Evaluate side-chains 223 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 217 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 577 PHE Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 577 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 763 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 GLN C 763 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.089271 restraints weight = 13763.286| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.50 r_work: 0.2806 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10804 Z= 0.243 Angle : 0.646 11.625 14760 Z= 0.317 Chirality : 0.046 0.267 1740 Planarity : 0.003 0.035 1772 Dihedral : 6.831 55.742 2032 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.34 % Allowed : 25.09 % Favored : 73.57 % 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 (0.22), residues: 554 sheet: 1.58 (0.29), residues: 270 loop : -1.33 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 629 HIS 0.004 0.001 HIS C 487 PHE 0.024 0.002 PHE C 632 TYR 0.015 0.002 TYR A 188 ARG 0.003 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 8) link_NAG-ASN : angle 1.92101 ( 24) link_BETA1-4 : bond 0.00489 ( 12) link_BETA1-4 : angle 2.43417 ( 36) hydrogen bonds : bond 0.04290 ( 538) hydrogen bonds : angle 3.87940 ( 1536) metal coordination : bond 0.00800 ( 6) SS BOND : bond 0.00169 ( 8) SS BOND : angle 0.80214 ( 16) covalent geometry : bond 0.00581 (10770) covalent geometry : angle 0.63101 (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 230 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8494 (p0) cc_final: 0.7798 (p0) REVERT: A 101 LYS cc_start: 0.9319 (mttt) cc_final: 0.9066 (mttm) REVERT: A 219 ASN cc_start: 0.8698 (m-40) cc_final: 0.8360 (p0) REVERT: A 240 MET cc_start: 0.9589 (ttt) cc_final: 0.9011 (tmm) REVERT: A 781 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8519 (mm-30) REVERT: C 101 LYS cc_start: 0.9314 (mttt) cc_final: 0.9052 (mttm) REVERT: C 219 ASN cc_start: 0.8723 (m-40) cc_final: 0.8374 (p0) REVERT: C 240 MET cc_start: 0.9588 (ttt) cc_final: 0.9013 (tmm) REVERT: C 781 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8514 (mm-30) outliers start: 15 outliers final: 8 residues processed: 221 average time/residue: 0.9384 time to fit residues: 226.8498 Evaluate side-chains 218 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 210 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 577 PHE Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 577 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.091704 restraints weight = 13533.571| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.49 r_work: 0.2845 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10804 Z= 0.131 Angle : 0.614 12.214 14760 Z= 0.299 Chirality : 0.044 0.256 1740 Planarity : 0.003 0.033 1772 Dihedral : 6.669 55.888 2032 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.08 % Allowed : 25.99 % Favored : 72.94 % 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: 1.35 (0.24), residues: 1232 helix: 1.99 (0.23), residues: 554 sheet: 1.65 (0.29), residues: 270 loop : -1.26 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 629 HIS 0.003 0.001 HIS C 487 PHE 0.023 0.001 PHE C 632 TYR 0.014 0.001 TYR A 590 ARG 0.002 0.000 ARG A 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 8) link_NAG-ASN : angle 1.97879 ( 24) link_BETA1-4 : bond 0.00493 ( 12) link_BETA1-4 : angle 2.37472 ( 36) hydrogen bonds : bond 0.03899 ( 538) hydrogen bonds : angle 3.76150 ( 1536) metal coordination : bond 0.00405 ( 6) SS BOND : bond 0.00092 ( 8) SS BOND : angle 0.74824 ( 16) covalent geometry : bond 0.00298 (10770) covalent geometry : angle 0.59803 (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: 12 poor density : 218 time to evaluate : 1.088 Fit side-chains REVERT: A 101 LYS cc_start: 0.9313 (mttt) cc_final: 0.9060 (mttm) REVERT: A 219 ASN cc_start: 0.8638 (m-40) cc_final: 0.8370 (p0) REVERT: A 240 MET cc_start: 0.9575 (ttt) cc_final: 0.8941 (tmm) REVERT: A 332 TYR cc_start: 0.5426 (OUTLIER) cc_final: 0.4977 (t80) REVERT: A 466 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: A 555 GLU cc_start: 0.9096 (tp30) cc_final: 0.8588 (tp30) REVERT: A 684 MET cc_start: 0.8042 (ptt) cc_final: 0.7717 (ptm) REVERT: A 781 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8516 (mm-30) REVERT: C 73 ASP cc_start: 0.8485 (p0) cc_final: 0.7789 (p0) REVERT: C 101 LYS cc_start: 0.9309 (mttt) cc_final: 0.9046 (mttm) REVERT: C 219 ASN cc_start: 0.8664 (m-40) cc_final: 0.8378 (p0) REVERT: C 240 MET cc_start: 0.9568 (ttt) cc_final: 0.8928 (tmm) REVERT: C 332 TYR cc_start: 0.5422 (OUTLIER) cc_final: 0.4975 (t80) REVERT: C 466 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: C 555 GLU cc_start: 0.9102 (tp30) cc_final: 0.8598 (tp30) REVERT: C 684 MET cc_start: 0.8039 (ptt) cc_final: 0.7720 (ptm) REVERT: C 781 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8502 (mm-30) outliers start: 12 outliers final: 4 residues processed: 225 average time/residue: 0.9361 time to fit residues: 232.7460 Evaluate side-chains 221 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 466 TYR Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 466 TYR Chi-restraints excluded: chain C residue 577 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091555 restraints weight = 13421.874| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.48 r_work: 0.2835 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4212 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= 0.165 Angle : 0.634 11.617 14760 Z= 0.309 Chirality : 0.045 0.256 1740 Planarity : 0.003 0.034 1772 Dihedral : 6.674 55.847 2032 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.34 % Allowed : 25.36 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.35 (0.24), residues: 1232 helix: 1.98 (0.22), residues: 554 sheet: 1.63 (0.28), residues: 270 loop : -1.23 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.003 0.001 HIS C 487 PHE 0.024 0.001 PHE C 632 TYR 0.013 0.001 TYR C 188 ARG 0.002 0.000 ARG C 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 8) link_NAG-ASN : angle 1.90954 ( 24) link_BETA1-4 : bond 0.00478 ( 12) link_BETA1-4 : angle 2.36818 ( 36) hydrogen bonds : bond 0.03994 ( 538) hydrogen bonds : angle 3.77721 ( 1536) metal coordination : bond 0.00552 ( 6) SS BOND : bond 0.00123 ( 8) SS BOND : angle 0.77865 ( 16) covalent geometry : bond 0.00389 (10770) covalent geometry : angle 0.61966 (14684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8487.75 seconds wall clock time: 146 minutes 40.59 seconds (8800.59 seconds total)