Starting phenix.real_space_refine on Fri Feb 14 18:49:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcw_37112/02_2025/8kcw_37112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcw_37112/02_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_37112/02_2025/8kcw_37112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcw_37112/02_2025/8kcw_37112.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcw_37112/02_2025/8kcw_37112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcw_37112/02_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-5592/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: 6.19, per 1000 atoms: 0.59 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: 2.70 Conformation dependent library (CDL) restraints added in 1.3 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: 0.90 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: 3.11 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: 0.630 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.140 Find NCS groups from input model: 0.350 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- 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 0.042 10770 Z= 0.296 Angle : 0.817 10.047 14684 Z= 0.452 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 *********************** 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 : 1.127 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: 0.9014 time to fit residues: 294.1054 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 : 1.084 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.9990 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 763 GLN C 229 HIS C 447 ASN C 763 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.088886 restraints weight = 13126.132| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.63 r_work: 0.2806 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10770 Z= 0.337 Angle : 0.729 7.970 14684 Z= 0.365 Chirality : 0.048 0.294 1740 Planarity : 0.005 0.041 1772 Dihedral : 14.516 84.255 2032 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.15 % Allowed : 13.80 % 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: -1.71 (0.21), residues: 1232 helix: -1.64 (0.18), residues: 560 sheet: 1.09 (0.29), residues: 270 loop : -1.74 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 446 HIS 0.006 0.001 HIS A 594 PHE 0.017 0.002 PHE C 632 TYR 0.015 0.002 TYR A 724 ARG 0.004 0.001 ARG A 524 *********************** 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 280 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9312 (mttt) cc_final: 0.9109 (mttm) REVERT: A 240 MET cc_start: 0.9551 (ttt) cc_final: 0.8898 (tmm) REVERT: A 320 PHE cc_start: 0.9202 (m-80) cc_final: 0.8946 (m-80) REVERT: A 517 ARG cc_start: 0.7972 (tmt170) cc_final: 0.7746 (ttp-170) REVERT: A 700 PHE cc_start: 0.7992 (t80) cc_final: 0.7791 (t80) REVERT: A 717 PHE cc_start: 0.9280 (m-80) cc_final: 0.9035 (m-80) REVERT: A 720 ASN cc_start: 0.9245 (m-40) cc_final: 0.8893 (m110) REVERT: A 781 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8663 (mm-30) REVERT: C 101 LYS cc_start: 0.9316 (mttt) cc_final: 0.9114 (mttm) REVERT: C 240 MET cc_start: 0.9551 (ttt) cc_final: 0.8892 (tmm) REVERT: C 320 PHE cc_start: 0.9185 (m-80) cc_final: 0.8929 (m-80) REVERT: C 517 ARG cc_start: 0.7974 (tmt170) cc_final: 0.7750 (ttp-170) REVERT: C 700 PHE cc_start: 0.7993 (t80) cc_final: 0.7790 (t80) REVERT: C 717 PHE cc_start: 0.9279 (m-80) cc_final: 0.9026 (m-80) REVERT: C 720 ASN cc_start: 0.9239 (m-40) cc_final: 0.8884 (m110) REVERT: C 781 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8666 (mm-30) outliers start: 24 outliers final: 10 residues processed: 268 average time/residue: 1.0426 time to fit residues: 304.4549 Evaluate side-chains 234 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 696 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 748 VAL 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: 4.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 22 optimal weight: 0.0470 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.130255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.087042 restraints weight = 13771.370| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.68 r_work: 0.2783 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10770 Z= 0.365 Angle : 0.669 8.735 14684 Z= 0.331 Chirality : 0.048 0.263 1740 Planarity : 0.004 0.041 1772 Dihedral : 10.488 61.781 2032 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.51 % Allowed : 17.38 % Favored : 80.11 % 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: -0.27 (0.23), residues: 1232 helix: 0.11 (0.21), residues: 558 sheet: 1.35 (0.28), residues: 268 loop : -1.59 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 106 HIS 0.004 0.001 HIS C 487 PHE 0.015 0.002 PHE A 571 TYR 0.015 0.002 TYR A 81 ARG 0.003 0.001 ARG C 518 *********************** 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 258 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 1.154 Fit side-chains REVERT: A 101 LYS cc_start: 0.9331 (mttt) cc_final: 0.9067 (mttm) REVERT: A 152 MET cc_start: 0.9411 (ttm) cc_final: 0.9145 (mtt) REVERT: A 240 MET cc_start: 0.9581 (ttt) cc_final: 0.8995 (tmm) REVERT: A 517 ARG cc_start: 0.8010 (tmt170) cc_final: 0.7774 (ttp-170) REVERT: A 524 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.6757 (mmm160) REVERT: A 548 MET cc_start: 0.8996 (mtm) cc_final: 0.8761 (mtp) REVERT: A 555 GLU cc_start: 0.9122 (tp30) cc_final: 0.8757 (tp30) REVERT: A 588 LYS cc_start: 0.8747 (tptp) cc_final: 0.8542 (tptp) REVERT: A 704 TYR cc_start: 0.8021 (m-80) cc_final: 0.7816 (m-10) REVERT: A 717 PHE cc_start: 0.9228 (m-80) cc_final: 0.9002 (m-80) REVERT: A 720 ASN cc_start: 0.9110 (m-40) cc_final: 0.8775 (m110) REVERT: C 101 LYS cc_start: 0.9326 (mttt) cc_final: 0.9059 (mttm) REVERT: C 152 MET cc_start: 0.9406 (ttm) cc_final: 0.9140 (mtt) REVERT: C 240 MET cc_start: 0.9572 (ttt) cc_final: 0.8984 (tmm) REVERT: C 517 ARG cc_start: 0.8010 (tmt170) cc_final: 0.7778 (ttp-170) REVERT: C 524 ARG cc_start: 0.7644 (mtm-85) cc_final: 0.6741 (mmm160) REVERT: C 548 MET cc_start: 0.8999 (mtm) cc_final: 0.8762 (mtp) REVERT: C 555 GLU cc_start: 0.9122 (tp30) cc_final: 0.8756 (tp30) REVERT: C 588 LYS cc_start: 0.8762 (tptp) cc_final: 0.8553 (tptp) REVERT: C 704 TYR cc_start: 0.8012 (m-80) cc_final: 0.7809 (m-10) REVERT: C 717 PHE cc_start: 0.9223 (m-80) cc_final: 0.9000 (m-80) REVERT: C 720 ASN cc_start: 0.9101 (m-40) cc_final: 0.8764 (m110) outliers start: 28 outliers final: 16 residues processed: 248 average time/residue: 1.0238 time to fit residues: 276.9880 Evaluate side-chains 228 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 118 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.132473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.089865 restraints weight = 13476.311| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.67 r_work: 0.2804 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10770 Z= 0.173 Angle : 0.582 8.099 14684 Z= 0.285 Chirality : 0.044 0.273 1740 Planarity : 0.003 0.036 1772 Dihedral : 8.467 58.704 2032 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.33 % Allowed : 19.18 % Favored : 78.49 % 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: 0.49 (0.23), residues: 1232 helix: 0.98 (0.22), residues: 558 sheet: 1.54 (0.29), residues: 270 loop : -1.47 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS C 487 PHE 0.016 0.001 PHE A 632 TYR 0.012 0.001 TYR C 481 ARG 0.003 0.000 ARG A 705 *********************** 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 264 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9343 (mttt) cc_final: 0.9068 (mttm) REVERT: A 123 GLN cc_start: 0.9035 (mt0) cc_final: 0.8692 (mm-40) REVERT: A 143 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: A 152 MET cc_start: 0.9382 (ttm) cc_final: 0.9125 (mtt) REVERT: A 195 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8406 (mtpm) REVERT: A 240 MET cc_start: 0.9546 (ttt) cc_final: 0.8778 (tmm) REVERT: A 524 ARG cc_start: 0.7592 (mtm-85) cc_final: 0.6779 (mmm-85) REVERT: A 541 HIS cc_start: 0.8761 (m-70) cc_final: 0.8551 (m90) REVERT: A 720 ASN cc_start: 0.8998 (m-40) cc_final: 0.8709 (m110) REVERT: A 769 GLU cc_start: 0.8453 (mp0) cc_final: 0.7994 (mp0) REVERT: C 101 LYS cc_start: 0.9337 (mttt) cc_final: 0.9056 (mttm) REVERT: C 123 GLN cc_start: 0.9031 (mt0) cc_final: 0.8686 (mm-40) REVERT: C 143 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: C 152 MET cc_start: 0.9370 (ttm) cc_final: 0.9111 (mtt) REVERT: C 195 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8405 (mtpm) REVERT: C 240 MET cc_start: 0.9535 (ttt) cc_final: 0.8761 (tmm) REVERT: C 524 ARG cc_start: 0.7572 (mtm-85) cc_final: 0.6757 (mmm-85) REVERT: C 541 HIS cc_start: 0.8758 (m-70) cc_final: 0.8546 (m90) REVERT: C 720 ASN cc_start: 0.8997 (m-40) cc_final: 0.8703 (m110) REVERT: C 769 GLU cc_start: 0.8454 (mp0) cc_final: 0.7993 (mp0) outliers start: 26 outliers final: 8 residues processed: 248 average time/residue: 0.9863 time to fit residues: 268.6998 Evaluate side-chains 236 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 226 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 766 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 636 HIS A 763 GLN C 121 ASN C 763 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.085944 restraints weight = 13671.351| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.67 r_work: 0.2767 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 10770 Z= 0.442 Angle : 0.655 7.279 14684 Z= 0.328 Chirality : 0.048 0.280 1740 Planarity : 0.004 0.039 1772 Dihedral : 8.113 57.881 2032 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.23 % Allowed : 20.70 % Favored : 76.08 % 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: 0.67 (0.23), residues: 1232 helix: 1.24 (0.22), residues: 558 sheet: 1.51 (0.28), residues: 268 loop : -1.45 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 106 HIS 0.004 0.001 HIS C 487 PHE 0.022 0.002 PHE C 700 TYR 0.016 0.002 TYR C 188 ARG 0.002 0.000 ARG A 705 *********************** 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 256 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 1.158 Fit side-chains REVERT: A 73 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8284 (p0) REVERT: A 101 LYS cc_start: 0.9334 (mttt) cc_final: 0.9059 (mttm) REVERT: A 143 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: A 152 MET cc_start: 0.9437 (ttm) cc_final: 0.9203 (mtt) REVERT: A 240 MET cc_start: 0.9561 (ttt) cc_final: 0.9001 (tmm) REVERT: A 517 ARG cc_start: 0.8040 (tmt170) cc_final: 0.7839 (ttp-170) REVERT: A 524 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.7318 (mmm-85) REVERT: A 763 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8642 (mm110) REVERT: A 781 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8513 (mm-30) REVERT: C 73 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8295 (p0) REVERT: C 101 LYS cc_start: 0.9327 (mttt) cc_final: 0.9049 (mttm) REVERT: C 143 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8220 (mt0) REVERT: C 152 MET cc_start: 0.9439 (ttm) cc_final: 0.9207 (mtt) REVERT: C 240 MET cc_start: 0.9552 (ttt) cc_final: 0.8988 (tmm) REVERT: C 524 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7328 (mmm-85) REVERT: C 763 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8656 (mm110) REVERT: C 781 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8502 (mm-30) outliers start: 36 outliers final: 18 residues processed: 234 average time/residue: 1.0422 time to fit residues: 265.6906 Evaluate side-chains 236 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 763 GLN 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 75 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 763 GLN 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: 4.9990 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 20 optimal weight: 0.0870 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 541 HIS A 720 ASN C 461 GLN C 541 HIS C 720 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.089851 restraints weight = 13528.757| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.65 r_work: 0.2818 rms_B_bonded: 3.02 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: 0.8344 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10770 Z= 0.164 Angle : 0.574 7.272 14684 Z= 0.284 Chirality : 0.044 0.270 1740 Planarity : 0.003 0.034 1772 Dihedral : 7.479 58.275 2032 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.15 % Allowed : 22.04 % 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: 1.05 (0.24), residues: 1232 helix: 1.68 (0.23), residues: 554 sheet: 1.54 (0.29), residues: 270 loop : -1.33 (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 0.019 0.001 PHE C 632 TYR 0.013 0.001 TYR C 590 ARG 0.002 0.000 ARG A 518 *********************** 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 244 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8269 (p0) REVERT: A 101 LYS cc_start: 0.9342 (mttt) cc_final: 0.9063 (mttm) REVERT: A 123 GLN cc_start: 0.8985 (mt0) cc_final: 0.8687 (mm-40) REVERT: A 143 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: A 152 MET cc_start: 0.9386 (ttm) cc_final: 0.9158 (mtt) REVERT: A 240 MET cc_start: 0.9557 (ttt) cc_final: 0.8822 (tmm) REVERT: A 524 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7426 (mtm-85) REVERT: A 555 GLU cc_start: 0.9075 (tp30) cc_final: 0.8546 (tp30) REVERT: A 588 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8611 (mmmt) REVERT: A 781 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8475 (mm-30) REVERT: C 73 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8283 (p0) REVERT: C 101 LYS cc_start: 0.9340 (mttt) cc_final: 0.9058 (mttm) REVERT: C 123 GLN cc_start: 0.8975 (mt0) cc_final: 0.8674 (mm-40) REVERT: C 143 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: C 152 MET cc_start: 0.9385 (ttm) cc_final: 0.9158 (mtt) REVERT: C 240 MET cc_start: 0.9546 (ttt) cc_final: 0.8805 (tmm) REVERT: C 524 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7425 (mtm-85) REVERT: C 555 GLU cc_start: 0.9066 (tp30) cc_final: 0.8534 (tp30) REVERT: C 588 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8605 (mmmt) REVERT: C 781 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8451 (mm-30) outliers start: 24 outliers final: 4 residues processed: 228 average time/residue: 1.0636 time to fit residues: 263.7343 Evaluate side-chains 216 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 577 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.0980 chunk 92 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 720 ASN C 461 GLN C 720 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.089566 restraints weight = 13668.778| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.66 r_work: 0.2815 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10770 Z= 0.206 Angle : 0.578 8.598 14684 Z= 0.286 Chirality : 0.044 0.270 1740 Planarity : 0.003 0.034 1772 Dihedral : 7.037 57.419 2032 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.79 % Allowed : 23.12 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.24), residues: 1232 helix: 1.87 (0.23), residues: 554 sheet: 1.64 (0.29), residues: 270 loop : -1.30 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 106 HIS 0.002 0.001 HIS C 487 PHE 0.021 0.001 PHE C 700 TYR 0.016 0.001 TYR A 590 ARG 0.002 0.000 ARG C 705 *********************** 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 254 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 1.236 Fit side-chains REVERT: A 73 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8085 (p0) REVERT: A 74 GLN cc_start: 0.8163 (mp10) cc_final: 0.7776 (mp-120) REVERT: A 101 LYS cc_start: 0.9336 (mttt) cc_final: 0.9050 (mttm) REVERT: A 143 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: A 152 MET cc_start: 0.9401 (ttm) cc_final: 0.9182 (mtt) REVERT: A 219 ASN cc_start: 0.8704 (m-40) cc_final: 0.8340 (p0) REVERT: A 240 MET cc_start: 0.9561 (ttt) cc_final: 0.8879 (tmm) REVERT: A 524 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7459 (mtm-85) REVERT: A 555 GLU cc_start: 0.9088 (tp30) cc_final: 0.8588 (tp30) REVERT: A 588 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8513 (mmmt) REVERT: A 589 LEU cc_start: 0.9145 (tp) cc_final: 0.8940 (tp) REVERT: A 781 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8475 (mm-30) REVERT: C 73 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8084 (p0) REVERT: C 74 GLN cc_start: 0.8175 (mp10) cc_final: 0.7787 (mp-120) REVERT: C 101 LYS cc_start: 0.9333 (mttt) cc_final: 0.9042 (mttm) REVERT: C 143 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: C 152 MET cc_start: 0.9403 (ttm) cc_final: 0.9187 (mtt) REVERT: C 240 MET cc_start: 0.9548 (ttt) cc_final: 0.8863 (tmm) REVERT: C 524 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7448 (mtm-85) REVERT: C 555 GLU cc_start: 0.9087 (tp30) cc_final: 0.8584 (tp30) REVERT: C 588 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8501 (mmmt) REVERT: C 589 LEU cc_start: 0.9136 (tp) cc_final: 0.8932 (tp) REVERT: C 781 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8465 (mm-30) outliers start: 20 outliers final: 8 residues processed: 244 average time/residue: 1.0336 time to fit residues: 275.4466 Evaluate side-chains 237 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 225 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 108 VAL 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 721 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 108 VAL 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 721 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 1.9990 chunk 115 optimal weight: 0.0470 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 461 GLN C 121 ASN C 461 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.090204 restraints weight = 13301.217| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.66 r_work: 0.2798 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10770 Z= 0.184 Angle : 0.571 10.269 14684 Z= 0.280 Chirality : 0.044 0.262 1740 Planarity : 0.003 0.032 1772 Dihedral : 6.716 56.591 2032 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.61 % Allowed : 23.75 % Favored : 74.64 % 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: 2.01 (0.23), residues: 554 sheet: 1.60 (0.29), residues: 270 loop : -1.25 (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 0.020 0.001 PHE C 632 TYR 0.018 0.001 TYR A 590 ARG 0.002 0.000 ARG C 705 *********************** 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 246 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 1.144 Fit side-chains REVERT: A 73 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.7858 (p0) REVERT: A 101 LYS cc_start: 0.9299 (mttt) cc_final: 0.9004 (mttm) REVERT: A 145 ILE cc_start: 0.9390 (mt) cc_final: 0.9164 (mm) REVERT: A 152 MET cc_start: 0.9340 (ttm) cc_final: 0.9096 (mtt) REVERT: A 219 ASN cc_start: 0.8650 (m-40) cc_final: 0.8222 (p0) REVERT: A 240 MET cc_start: 0.9510 (ttt) cc_final: 0.8644 (tmm) REVERT: A 524 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7333 (mtm-85) REVERT: A 555 GLU cc_start: 0.8985 (tp30) cc_final: 0.8719 (tp30) REVERT: A 684 MET cc_start: 0.7904 (ptt) cc_final: 0.7614 (ptm) REVERT: A 781 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8472 (mm-30) REVERT: C 73 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.7847 (p0) REVERT: C 101 LYS cc_start: 0.9285 (mttt) cc_final: 0.8985 (mttm) REVERT: C 152 MET cc_start: 0.9343 (ttm) cc_final: 0.9100 (mtt) REVERT: C 219 ASN cc_start: 0.8660 (m-40) cc_final: 0.8233 (p0) REVERT: C 240 MET cc_start: 0.9515 (ttt) cc_final: 0.8675 (tmm) REVERT: C 524 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7322 (mtm-85) REVERT: C 555 GLU cc_start: 0.8998 (tp30) cc_final: 0.8736 (tp30) REVERT: C 684 MET cc_start: 0.7904 (ptt) cc_final: 0.7616 (ptm) REVERT: C 781 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8444 (mm-30) outliers start: 18 outliers final: 10 residues processed: 238 average time/residue: 1.0150 time to fit residues: 264.6078 Evaluate side-chains 234 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 222 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 748 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 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: 2.9990 chunk 101 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 763 GLN 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 = 0.3547 r_free = 0.3547 target = 0.131161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.087363 restraints weight = 13656.798| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.69 r_work: 0.2794 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10770 Z= 0.345 Angle : 0.625 10.853 14684 Z= 0.312 Chirality : 0.046 0.267 1740 Planarity : 0.003 0.035 1772 Dihedral : 6.908 56.762 2032 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.33 % Allowed : 23.39 % Favored : 74.28 % 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: 1.23 (0.24), residues: 1232 helix: 1.88 (0.22), residues: 554 sheet: 1.57 (0.29), residues: 268 loop : -1.27 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 106 HIS 0.005 0.001 HIS A 487 PHE 0.023 0.002 PHE C 632 TYR 0.020 0.002 TYR C 590 ARG 0.002 0.000 ARG C 79 *********************** 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 252 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7990 (p0) REVERT: A 101 LYS cc_start: 0.9303 (mttt) cc_final: 0.9016 (mttm) REVERT: A 152 MET cc_start: 0.9375 (ttm) cc_final: 0.9137 (mtt) REVERT: A 240 MET cc_start: 0.9551 (ttt) cc_final: 0.9004 (tmm) REVERT: A 781 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8520 (mm-30) REVERT: C 73 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7980 (p0) REVERT: C 101 LYS cc_start: 0.9286 (mttt) cc_final: 0.8993 (mttm) REVERT: C 152 MET cc_start: 0.9388 (ttm) cc_final: 0.9152 (mtt) REVERT: C 240 MET cc_start: 0.9544 (ttt) cc_final: 0.8865 (tmm) REVERT: C 781 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8506 (mm-30) outliers start: 26 outliers final: 14 residues processed: 242 average time/residue: 1.0040 time to fit residues: 265.4260 Evaluate side-chains 230 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 108 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 721 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 108 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 Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.133707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.090364 restraints weight = 13397.343| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.68 r_work: 0.2822 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10770 Z= 0.187 Angle : 0.604 12.392 14684 Z= 0.294 Chirality : 0.044 0.255 1740 Planarity : 0.003 0.033 1772 Dihedral : 6.576 56.687 2032 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.43 % Allowed : 24.64 % Favored : 73.92 % 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: 1.41 (0.24), residues: 1232 helix: 2.05 (0.23), residues: 554 sheet: 1.63 (0.29), residues: 270 loop : -1.19 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 106 HIS 0.002 0.001 HIS C 795 PHE 0.023 0.001 PHE A 632 TYR 0.014 0.001 TYR A 590 ARG 0.001 0.000 ARG A 79 ********************** 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 238 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 1.099 Fit side-chains REVERT: A 73 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7883 (p0) REVERT: A 101 LYS cc_start: 0.9309 (mttt) cc_final: 0.9023 (mttm) REVERT: A 145 ILE cc_start: 0.9405 (mt) cc_final: 0.9193 (mm) REVERT: A 152 MET cc_start: 0.9330 (ttm) cc_final: 0.9099 (mtt) REVERT: A 219 ASN cc_start: 0.8624 (m-40) cc_final: 0.8238 (p0) REVERT: A 221 MET cc_start: 0.9117 (mtp) cc_final: 0.8603 (ttp) REVERT: A 240 MET cc_start: 0.9530 (ttt) cc_final: 0.8694 (tmm) REVERT: A 332 TYR cc_start: 0.5391 (OUTLIER) cc_final: 0.4980 (t80) REVERT: A 466 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7563 (m-10) REVERT: A 555 GLU cc_start: 0.9011 (tp30) cc_final: 0.8512 (tp30) REVERT: A 781 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8498 (mm-30) REVERT: C 73 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7885 (p0) REVERT: C 101 LYS cc_start: 0.9296 (mttt) cc_final: 0.9006 (mttm) REVERT: C 145 ILE cc_start: 0.9401 (mt) cc_final: 0.9188 (mm) REVERT: C 152 MET cc_start: 0.9336 (ttm) cc_final: 0.9103 (mtt) REVERT: C 219 ASN cc_start: 0.8636 (m-40) cc_final: 0.8262 (p0) REVERT: C 221 MET cc_start: 0.9142 (mtp) cc_final: 0.8627 (ttp) REVERT: C 240 MET cc_start: 0.9531 (ttt) cc_final: 0.8709 (tmm) REVERT: C 332 TYR cc_start: 0.5386 (OUTLIER) cc_final: 0.4974 (t80) REVERT: C 466 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7569 (m-10) REVERT: C 555 GLU cc_start: 0.9025 (tp30) cc_final: 0.8531 (tp30) REVERT: C 781 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8479 (mm-30) outliers start: 16 outliers final: 8 residues processed: 228 average time/residue: 0.9791 time to fit residues: 244.2353 Evaluate side-chains 226 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 466 TYR Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 748 VAL 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: 0.8980 chunk 108 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 461 GLN C 121 ASN C 461 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.090158 restraints weight = 13297.873| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.69 r_work: 0.2839 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10770 Z= 0.195 Angle : 0.585 10.469 14684 Z= 0.288 Chirality : 0.044 0.253 1740 Planarity : 0.003 0.033 1772 Dihedral : 6.449 56.291 2032 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.43 % Allowed : 24.64 % Favored : 73.92 % 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: 1.45 (0.24), residues: 1232 helix: 2.07 (0.22), residues: 554 sheet: 1.65 (0.29), residues: 270 loop : -1.17 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS C 487 PHE 0.014 0.001 PHE C 571 TYR 0.012 0.001 TYR A 188 ARG 0.001 0.000 ARG C 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7886.11 seconds wall clock time: 139 minutes 51.71 seconds (8391.71 seconds total)