Starting phenix.real_space_refine on Sun Aug 4 12:55:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/08_2024/8kcw_37112.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/08_2024/8kcw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/08_2024/8kcw_37112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/08_2024/8kcw_37112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/08_2024/8kcw_37112.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/08_2024/8kcw_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 Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 820": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10484 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5051 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5051 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.06, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 4.42 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 791 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 795 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 791 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 563 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 795 " 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 48.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 302 through 316 removed outlier: 3.790A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.922A pdb=" N VAL A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 473 removed outlier: 3.649A pdb=" N PHE A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Proline residue: A 458 - end of helix removed outlier: 3.918A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 471 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 4.078A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.812A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 527 removed outlier: 3.951A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 563 removed outlier: 3.620A pdb=" N TYR A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 575 removed outlier: 3.703A pdb=" N ASP A 574 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 592 removed outlier: 4.132A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 620 removed outlier: 3.569A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 648 removed outlier: 3.538A pdb=" N TRP A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 631 " --> pdb=" O TRP A 627 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 640 " --> pdb=" O HIS A 636 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 705 removed outlier: 3.536A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 688 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 735 removed outlier: 3.520A pdb=" N LEU A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 763 removed outlier: 3.716A pdb=" N PHE A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 763 " --> pdb=" O TYR A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 789 through 812 removed outlier: 3.868A pdb=" N ALA A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 800 " --> pdb=" O PHE A 796 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 809 " --> pdb=" O SER A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.790A pdb=" N TYR C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 332 removed outlier: 3.922A pdb=" N VAL C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 473 removed outlier: 3.649A pdb=" N PHE C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) Proline residue: C 458 - end of helix removed outlier: 3.918A pdb=" N ILE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR C 465 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.078A pdb=" N ALA C 486 " --> pdb=" O PHE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 500 removed outlier: 3.812A pdb=" N ILE C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 527 removed outlier: 3.951A pdb=" N VAL C 505 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 509 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 522 " --> pdb=" O ARG C 518 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 563 removed outlier: 3.620A pdb=" N TYR C 546 " --> pdb=" O PHE C 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.703A pdb=" N ASP C 574 " --> pdb=" O PHE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 592 removed outlier: 4.132A pdb=" N MET C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 620 removed outlier: 3.569A pdb=" N TYR C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 615 " --> pdb=" O VAL C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 648 removed outlier: 3.538A pdb=" N TRP C 629 " --> pdb=" O ASP C 625 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE C 631 " --> pdb=" O TRP C 627 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 640 " --> pdb=" O HIS C 636 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR C 645 " --> pdb=" O LEU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 705 removed outlier: 3.536A pdb=" N LEU C 686 " --> pdb=" O ASP C 682 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 688 " --> pdb=" O MET C 684 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 735 removed outlier: 3.520A pdb=" N LEU C 714 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 726 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 729 " --> pdb=" O LEU C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 763 removed outlier: 3.716A pdb=" N PHE C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 763 " --> pdb=" O TYR C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 776 Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 789 through 812 removed outlier: 3.868A pdb=" N ALA C 799 " --> pdb=" O HIS C 795 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 800 " --> pdb=" O PHE C 796 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 809 " --> pdb=" O SER C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 815 No H-bonds generated for 'chain 'C' and resid 813 through 815' Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.656A pdb=" N ALA A 77 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.901A pdb=" N ARG A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.877A pdb=" N LYS A 192 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 56 removed outlier: 4.656A pdb=" N ALA C 77 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.901A pdb=" N ARG C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 170 through 171 removed outlier: 4.877A pdb=" N LYS C 192 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 177 through 181 538 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 4.63 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: 99.20 - 106.21: 262 106.21 - 113.21: 5882 113.21 - 120.22: 4148 120.22 - 127.23: 4288 127.23 - 134.24: 104 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: 1.120 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.710 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.730 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 1.172 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: 0.8489 time to fit residues: 276.8359 Evaluate side-chains 238 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 fitting. rotamer outliers: 24 poor density : 256 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9149 (mttt) cc_final: 0.8902 (mttm) REVERT: A 240 MET cc_start: 0.9611 (ttt) cc_final: 0.8985 (tmm) REVERT: A 320 PHE cc_start: 0.9101 (m-80) cc_final: 0.8866 (m-80) REVERT: A 517 ARG cc_start: 0.7777 (tmt170) cc_final: 0.7533 (ttp-170) REVERT: A 717 PHE cc_start: 0.9210 (m-80) cc_final: 0.8949 (m-80) REVERT: A 720 ASN cc_start: 0.9138 (m-40) cc_final: 0.8757 (m110) REVERT: A 781 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8632 (mm-30) REVERT: C 101 LYS cc_start: 0.9149 (mttt) cc_final: 0.8901 (mttm) REVERT: C 240 MET cc_start: 0.9611 (ttt) cc_final: 0.8986 (tmm) REVERT: C 320 PHE cc_start: 0.9101 (m-80) cc_final: 0.8866 (m-80) REVERT: C 517 ARG cc_start: 0.7776 (tmt170) cc_final: 0.7530 (ttp-170) REVERT: C 717 PHE cc_start: 0.9210 (m-80) cc_final: 0.8949 (m-80) REVERT: C 720 ASN cc_start: 0.9138 (m-40) cc_final: 0.8759 (m110) REVERT: C 781 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8633 (mm-30) outliers start: 24 outliers final: 10 residues processed: 268 average time/residue: 0.9839 time to fit residues: 287.3441 Evaluate side-chains 234 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.0570 chunk 112 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 HIS A 594 HIS C 447 ASN C 541 HIS C 594 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10770 Z= 0.177 Angle : 0.606 8.381 14684 Z= 0.295 Chirality : 0.046 0.264 1740 Planarity : 0.004 0.036 1772 Dihedral : 10.922 62.948 2032 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.15 % Allowed : 16.49 % Favored : 81.36 % 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: -0.34 (0.23), residues: 1232 helix: 0.04 (0.21), residues: 558 sheet: 1.34 (0.29), residues: 270 loop : -1.64 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.005 0.001 HIS A 594 PHE 0.017 0.001 PHE C 700 TYR 0.012 0.001 TYR C 481 ARG 0.003 0.000 ARG A 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 268 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 244 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9178 (mttt) cc_final: 0.8919 (mttm) REVERT: A 123 GLN cc_start: 0.8837 (mt0) cc_final: 0.8542 (mm-40) REVERT: A 240 MET cc_start: 0.9612 (ttt) cc_final: 0.9014 (tmm) REVERT: A 517 ARG cc_start: 0.7815 (tmt170) cc_final: 0.7598 (ttp-170) REVERT: A 524 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.6750 (mmm160) REVERT: A 548 MET cc_start: 0.8933 (mtm) cc_final: 0.8668 (mtp) REVERT: A 588 LYS cc_start: 0.8692 (tptp) cc_final: 0.8489 (tptp) REVERT: A 713 MET cc_start: 0.9329 (mmt) cc_final: 0.9043 (mmm) REVERT: A 717 PHE cc_start: 0.9228 (m-80) cc_final: 0.9020 (m-80) REVERT: A 720 ASN cc_start: 0.9024 (m-40) cc_final: 0.8668 (m110) REVERT: C 101 LYS cc_start: 0.9179 (mttt) cc_final: 0.8919 (mttm) REVERT: C 123 GLN cc_start: 0.8837 (mt0) cc_final: 0.8541 (mm-40) REVERT: C 240 MET cc_start: 0.9612 (ttt) cc_final: 0.9012 (tmm) REVERT: C 517 ARG cc_start: 0.7815 (tmt170) cc_final: 0.7598 (ttp-170) REVERT: C 524 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.6751 (mmm160) REVERT: C 548 MET cc_start: 0.8932 (mtm) cc_final: 0.8667 (mtp) REVERT: C 588 LYS cc_start: 0.8694 (tptp) cc_final: 0.8492 (tptp) REVERT: C 713 MET cc_start: 0.9325 (mmt) cc_final: 0.9039 (mmm) REVERT: C 717 PHE cc_start: 0.9227 (m-80) cc_final: 0.9019 (m-80) REVERT: C 720 ASN cc_start: 0.9022 (m-40) cc_final: 0.8668 (m110) outliers start: 24 outliers final: 14 residues processed: 256 average time/residue: 0.9873 time to fit residues: 276.0158 Evaluate side-chains 236 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 222 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 313 SER Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 74 GLN 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 748 VAL Chi-restraints excluded: chain C residue 766 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 541 HIS A 763 GLN C 447 ASN C 541 HIS C 763 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10770 Z= 0.252 Angle : 0.608 7.751 14684 Z= 0.300 Chirality : 0.045 0.278 1740 Planarity : 0.003 0.034 1772 Dihedral : 8.128 57.218 2032 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.30 % Allowed : 17.92 % Favored : 77.78 % 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: 0.53 (0.23), residues: 1232 helix: 1.07 (0.22), residues: 554 sheet: 1.53 (0.29), residues: 268 loop : -1.47 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 106 HIS 0.003 0.001 HIS A 487 PHE 0.018 0.001 PHE C 571 TYR 0.013 0.001 TYR A 188 ARG 0.003 0.000 ARG C 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 277 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 229 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9203 (mttt) cc_final: 0.8916 (mttm) REVERT: A 123 GLN cc_start: 0.8788 (mt0) cc_final: 0.8544 (mm-40) REVERT: A 143 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: A 152 MET cc_start: 0.9345 (ttm) cc_final: 0.9093 (mtt) REVERT: A 195 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8290 (mtpm) REVERT: A 208 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8478 (mtp) REVERT: A 240 MET cc_start: 0.9615 (ttt) cc_final: 0.9067 (tmm) REVERT: A 555 GLU cc_start: 0.8908 (tp30) cc_final: 0.8691 (tm-30) REVERT: A 713 MET cc_start: 0.9397 (mmt) cc_final: 0.9138 (mmm) REVERT: A 717 PHE cc_start: 0.9046 (m-80) cc_final: 0.8817 (m-80) REVERT: C 101 LYS cc_start: 0.9204 (mttt) cc_final: 0.8918 (mttm) REVERT: C 123 GLN cc_start: 0.8829 (mt0) cc_final: 0.8552 (mm-40) REVERT: C 143 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: C 152 MET cc_start: 0.9346 (ttm) cc_final: 0.9093 (mtt) REVERT: C 195 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8291 (mtpm) REVERT: C 208 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8455 (mtp) REVERT: C 240 MET cc_start: 0.9614 (ttt) cc_final: 0.9065 (tmm) REVERT: C 555 GLU cc_start: 0.8907 (tp30) cc_final: 0.8692 (tm-30) REVERT: C 713 MET cc_start: 0.9395 (mmt) cc_final: 0.9137 (mmm) REVERT: C 717 PHE cc_start: 0.9046 (m-80) cc_final: 0.8818 (m-80) outliers start: 48 outliers final: 24 residues processed: 247 average time/residue: 0.9984 time to fit residues: 269.4279 Evaluate side-chains 249 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 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 70 SER 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 208 MET Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0270 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 0.0000 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 447 ASN A 541 HIS A 720 ASN C 121 ASN C 447 ASN C 541 HIS C 636 HIS C 720 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10770 Z= 0.153 Angle : 0.557 7.609 14684 Z= 0.273 Chirality : 0.043 0.271 1740 Planarity : 0.003 0.033 1772 Dihedral : 7.346 56.705 2032 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.87 % Allowed : 20.43 % Favored : 76.70 % 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: 0.96 (0.24), residues: 1232 helix: 1.58 (0.23), residues: 554 sheet: 1.61 (0.28), residues: 270 loop : -1.43 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 106 HIS 0.002 0.000 HIS C 487 PHE 0.020 0.001 PHE A 700 TYR 0.014 0.001 TYR A 81 ARG 0.002 0.000 ARG A 518 *********************** 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 261 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 1.180 Fit side-chains REVERT: A 73 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7951 (p0) REVERT: A 101 LYS cc_start: 0.9206 (mttt) cc_final: 0.8919 (mttm) REVERT: A 123 GLN cc_start: 0.8849 (mt0) cc_final: 0.8555 (mm-40) REVERT: A 143 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: A 152 MET cc_start: 0.9303 (ttm) cc_final: 0.9047 (mtt) REVERT: A 195 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8324 (mtpm) REVERT: A 219 ASN cc_start: 0.8711 (m-40) cc_final: 0.8447 (p0) REVERT: A 240 MET cc_start: 0.9615 (ttt) cc_final: 0.8937 (tmm) REVERT: A 524 ARG cc_start: 0.7388 (mtm-85) cc_final: 0.6683 (mmm-85) REVERT: A 555 GLU cc_start: 0.8888 (tp30) cc_final: 0.8686 (tp30) REVERT: A 577 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: A 588 LYS cc_start: 0.8797 (tptp) cc_final: 0.8537 (mmmt) REVERT: A 713 MET cc_start: 0.9412 (mmt) cc_final: 0.9053 (mmm) REVERT: A 781 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8439 (mm-30) REVERT: C 73 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7951 (p0) REVERT: C 101 LYS cc_start: 0.9204 (mttt) cc_final: 0.8919 (mttm) REVERT: C 123 GLN cc_start: 0.8870 (mt0) cc_final: 0.8562 (mm-40) REVERT: C 143 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: C 152 MET cc_start: 0.9304 (ttm) cc_final: 0.9047 (mtt) REVERT: C 195 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8325 (mtpm) REVERT: C 219 ASN cc_start: 0.8713 (m-40) cc_final: 0.8446 (p0) REVERT: C 240 MET cc_start: 0.9614 (ttt) cc_final: 0.8936 (tmm) REVERT: C 524 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.6686 (mmm-85) REVERT: C 555 GLU cc_start: 0.8888 (tp30) cc_final: 0.8685 (tp30) REVERT: C 577 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: C 588 LYS cc_start: 0.8797 (tptp) cc_final: 0.8539 (mmmt) REVERT: C 713 MET cc_start: 0.9413 (mmt) cc_final: 0.9054 (mmm) REVERT: C 781 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8440 (mm-30) outliers start: 32 outliers final: 8 residues processed: 241 average time/residue: 0.9344 time to fit residues: 246.4506 Evaluate side-chains 230 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 216 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 447 ASN Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain 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 447 ASN Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 684 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 447 ASN A 467 GLN A 541 HIS A 720 ASN C 121 ASN C 447 ASN C 467 GLN C 541 HIS C 720 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10770 Z= 0.245 Angle : 0.585 7.799 14684 Z= 0.288 Chirality : 0.045 0.275 1740 Planarity : 0.003 0.033 1772 Dihedral : 7.178 56.429 2032 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.87 % Allowed : 20.97 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1232 helix: 1.76 (0.23), residues: 554 sheet: 1.66 (0.28), residues: 270 loop : -1.38 (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 0.019 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 249 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 217 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8010 (p0) REVERT: A 101 LYS cc_start: 0.9206 (mttt) cc_final: 0.8913 (mttm) REVERT: A 123 GLN cc_start: 0.8820 (mt0) cc_final: 0.8558 (mm-40) REVERT: A 143 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: A 152 MET cc_start: 0.9340 (ttm) cc_final: 0.9103 (mtt) REVERT: A 219 ASN cc_start: 0.8710 (m-40) cc_final: 0.8419 (p0) REVERT: A 240 MET cc_start: 0.9604 (ttt) cc_final: 0.9038 (tmm) REVERT: A 555 GLU cc_start: 0.8914 (tp30) cc_final: 0.8522 (tp30) REVERT: A 577 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8762 (m-80) REVERT: A 713 MET cc_start: 0.9372 (mmt) cc_final: 0.9129 (mmm) REVERT: C 73 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8012 (p0) REVERT: C 101 LYS cc_start: 0.9204 (mttt) cc_final: 0.8911 (mttm) REVERT: C 123 GLN cc_start: 0.8843 (mt0) cc_final: 0.8556 (mm-40) REVERT: C 143 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: C 152 MET cc_start: 0.9341 (ttm) cc_final: 0.9103 (mtt) REVERT: C 219 ASN cc_start: 0.8711 (m-40) cc_final: 0.8418 (p0) REVERT: C 240 MET cc_start: 0.9603 (ttt) cc_final: 0.9037 (tmm) REVERT: C 555 GLU cc_start: 0.8914 (tp30) cc_final: 0.8523 (tp30) REVERT: C 577 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8762 (m-80) REVERT: C 713 MET cc_start: 0.9372 (mmt) cc_final: 0.9129 (mmm) outliers start: 32 outliers final: 12 residues processed: 231 average time/residue: 0.9359 time to fit residues: 236.6491 Evaluate side-chains 234 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 216 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 447 ASN 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 748 VAL 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 447 ASN 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 748 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 HIS A 720 ASN C 541 HIS C 720 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10770 Z= 0.191 Angle : 0.577 9.240 14684 Z= 0.283 Chirality : 0.044 0.269 1740 Planarity : 0.003 0.033 1772 Dihedral : 6.966 56.249 2032 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.15 % Allowed : 22.94 % Favored : 74.91 % 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: 1.88 (0.23), residues: 554 sheet: 1.70 (0.29), residues: 270 loop : -1.35 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 768 HIS 0.002 0.001 HIS C 487 PHE 0.020 0.001 PHE C 632 TYR 0.017 0.001 TYR A 590 ARG 0.002 0.000 ARG A 518 *********************** 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 251 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 227 time to evaluate : 1.171 Fit side-chains REVERT: A 73 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7762 (p0) REVERT: A 74 GLN cc_start: 0.8323 (mp10) cc_final: 0.8092 (mp10) REVERT: A 101 LYS cc_start: 0.9192 (mttt) cc_final: 0.8895 (mttm) REVERT: A 123 GLN cc_start: 0.8835 (mt0) cc_final: 0.8535 (mm-40) REVERT: A 152 MET cc_start: 0.9315 (ttm) cc_final: 0.9080 (mtt) REVERT: A 219 ASN cc_start: 0.8687 (m-40) cc_final: 0.8423 (p0) REVERT: A 240 MET cc_start: 0.9597 (ttt) cc_final: 0.9020 (tmm) REVERT: A 517 ARG cc_start: 0.7805 (tmt170) cc_final: 0.7571 (ttp-170) REVERT: A 524 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.6674 (mmm-85) REVERT: A 555 GLU cc_start: 0.8917 (tp30) cc_final: 0.8502 (tp30) REVERT: A 781 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8462 (mm-30) REVERT: C 73 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7765 (p0) REVERT: C 74 GLN cc_start: 0.8323 (mp10) cc_final: 0.8093 (mp10) REVERT: C 101 LYS cc_start: 0.9190 (mttt) cc_final: 0.8894 (mttm) REVERT: C 123 GLN cc_start: 0.8838 (mt0) cc_final: 0.8537 (mm-40) REVERT: C 152 MET cc_start: 0.9315 (ttm) cc_final: 0.9081 (mtt) REVERT: C 219 ASN cc_start: 0.8689 (m-40) cc_final: 0.8424 (p0) REVERT: C 240 MET cc_start: 0.9596 (ttt) cc_final: 0.9019 (tmm) REVERT: C 517 ARG cc_start: 0.7806 (tmt170) cc_final: 0.7571 (ttp-170) REVERT: C 524 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.6677 (mmm-85) REVERT: C 555 GLU cc_start: 0.8916 (tp30) cc_final: 0.8501 (tp30) REVERT: C 781 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8461 (mm-30) outliers start: 24 outliers final: 8 residues processed: 235 average time/residue: 0.9779 time to fit residues: 250.7994 Evaluate side-chains 226 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 216 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 577 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 0.0020 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 447 ASN A 461 GLN A 467 GLN A 720 ASN C 143 GLN C 447 ASN C 461 GLN C 467 GLN C 720 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3989 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= 0.193 Angle : 0.573 10.493 14684 Z= 0.282 Chirality : 0.044 0.262 1740 Planarity : 0.003 0.032 1772 Dihedral : 6.599 55.701 2032 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.97 % Allowed : 23.39 % 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: 1.33 (0.24), residues: 1232 helix: 1.96 (0.23), residues: 554 sheet: 1.74 (0.29), residues: 270 loop : -1.32 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 768 HIS 0.003 0.001 HIS C 636 PHE 0.019 0.001 PHE A 632 TYR 0.014 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 256 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 234 time to evaluate : 1.241 Fit side-chains REVERT: A 73 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7556 (p0) REVERT: A 101 LYS cc_start: 0.9183 (mttt) cc_final: 0.8893 (mttm) REVERT: A 123 GLN cc_start: 0.8840 (mt0) cc_final: 0.8537 (mm-40) REVERT: A 143 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: A 152 MET cc_start: 0.9309 (ttm) cc_final: 0.9080 (mtt) REVERT: A 219 ASN cc_start: 0.8622 (m-40) cc_final: 0.8414 (p0) REVERT: A 240 MET cc_start: 0.9592 (ttt) cc_final: 0.9030 (tmm) REVERT: A 524 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.6572 (mmm-85) REVERT: A 555 GLU cc_start: 0.8888 (tp30) cc_final: 0.8646 (tp30) REVERT: A 684 MET cc_start: 0.7908 (ptt) cc_final: 0.7601 (ptm) REVERT: A 781 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8471 (mm-30) REVERT: C 73 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7559 (p0) REVERT: C 101 LYS cc_start: 0.9183 (mttt) cc_final: 0.8894 (mttm) REVERT: C 123 GLN cc_start: 0.8840 (mt0) cc_final: 0.8536 (mm-40) REVERT: C 143 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: C 152 MET cc_start: 0.9309 (ttm) cc_final: 0.9079 (mtt) REVERT: C 219 ASN cc_start: 0.8620 (m-40) cc_final: 0.8413 (p0) REVERT: C 240 MET cc_start: 0.9590 (ttt) cc_final: 0.9029 (tmm) REVERT: C 524 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.6575 (mmm-85) REVERT: C 555 GLU cc_start: 0.8888 (tp30) cc_final: 0.8645 (tp30) REVERT: C 684 MET cc_start: 0.7911 (ptt) cc_final: 0.7604 (ptm) REVERT: C 781 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8470 (mm-30) outliers start: 22 outliers final: 10 residues processed: 242 average time/residue: 1.0051 time to fit residues: 266.0708 Evaluate side-chains 223 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 447 ASN 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 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 447 ASN Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 577 PHE 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 114 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 0.0010 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 447 ASN A 461 GLN A 541 HIS A 763 GLN C 143 GLN C 447 ASN C 461 GLN C 541 HIS C 763 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 10770 Z= 0.437 Angle : 0.655 11.046 14684 Z= 0.328 Chirality : 0.048 0.271 1740 Planarity : 0.004 0.038 1772 Dihedral : 6.866 55.501 2032 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.69 % Allowed : 23.39 % 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: 1.16 (0.24), residues: 1232 helix: 1.80 (0.22), residues: 554 sheet: 1.64 (0.29), residues: 270 loop : -1.36 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 446 HIS 0.004 0.001 HIS A 487 PHE 0.025 0.002 PHE A 632 TYR 0.016 0.002 TYR A 602 ARG 0.003 0.000 ARG A 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 246 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9191 (mttt) cc_final: 0.8892 (mttm) REVERT: A 152 MET cc_start: 0.9349 (ttm) cc_final: 0.9117 (mtt) REVERT: A 219 ASN cc_start: 0.8694 (m-40) cc_final: 0.8371 (p0) REVERT: A 240 MET cc_start: 0.9610 (ttt) cc_final: 0.9098 (tmm) REVERT: A 517 ARG cc_start: 0.7836 (tmt170) cc_final: 0.7572 (ttp-170) REVERT: A 555 GLU cc_start: 0.8919 (tp30) cc_final: 0.8409 (tp30) REVERT: A 708 ASP cc_start: 0.8294 (t0) cc_final: 0.7900 (t0) REVERT: A 781 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8531 (mm-30) REVERT: C 101 LYS cc_start: 0.9192 (mttt) cc_final: 0.8894 (mttm) REVERT: C 152 MET cc_start: 0.9348 (ttm) cc_final: 0.9116 (mtt) REVERT: C 219 ASN cc_start: 0.8694 (m-40) cc_final: 0.8371 (p0) REVERT: C 240 MET cc_start: 0.9608 (ttt) cc_final: 0.9096 (tmm) REVERT: C 517 ARG cc_start: 0.7836 (tmt170) cc_final: 0.7572 (ttp-170) REVERT: C 555 GLU cc_start: 0.8921 (tp30) cc_final: 0.8409 (tp30) REVERT: C 708 ASP cc_start: 0.8298 (t0) cc_final: 0.7903 (t0) REVERT: C 781 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8530 (mm-30) outliers start: 30 outliers final: 10 residues processed: 228 average time/residue: 0.9440 time to fit residues: 235.3166 Evaluate side-chains 223 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET 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 C residue 221 MET 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 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 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 447 ASN A 461 GLN A 541 HIS C 143 GLN C 447 ASN C 461 GLN C 541 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4108 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= 0.185 Angle : 0.605 12.361 14684 Z= 0.295 Chirality : 0.044 0.254 1740 Planarity : 0.003 0.035 1772 Dihedral : 6.586 55.950 2032 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.43 % Allowed : 25.00 % 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: 1.37 (0.24), residues: 1232 helix: 1.98 (0.23), residues: 554 sheet: 1.70 (0.29), residues: 270 loop : -1.25 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 768 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 0.002 0.000 ARG C 705 ********************** 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 232 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 216 time to evaluate : 1.200 Fit side-chains REVERT: A 101 LYS cc_start: 0.9178 (mttt) cc_final: 0.8889 (mttm) REVERT: A 143 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: A 152 MET cc_start: 0.9314 (ttm) cc_final: 0.9095 (mtt) REVERT: A 219 ASN cc_start: 0.8618 (m-40) cc_final: 0.8388 (p0) REVERT: A 240 MET cc_start: 0.9593 (ttt) cc_final: 0.9017 (tmm) REVERT: A 332 TYR cc_start: 0.5570 (OUTLIER) cc_final: 0.5263 (t80) REVERT: A 517 ARG cc_start: 0.7802 (tmt170) cc_final: 0.7528 (ttp-170) REVERT: A 524 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.6585 (mmm-85) REVERT: A 555 GLU cc_start: 0.8925 (tp30) cc_final: 0.8451 (tp30) REVERT: A 708 ASP cc_start: 0.8280 (t0) cc_final: 0.7889 (t0) REVERT: A 781 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8447 (mm-30) REVERT: C 101 LYS cc_start: 0.9178 (mttt) cc_final: 0.8891 (mttm) REVERT: C 143 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8221 (mt0) REVERT: C 152 MET cc_start: 0.9312 (ttm) cc_final: 0.9092 (mtt) REVERT: C 219 ASN cc_start: 0.8618 (m-40) cc_final: 0.8388 (p0) REVERT: C 240 MET cc_start: 0.9592 (ttt) cc_final: 0.9018 (tmm) REVERT: C 332 TYR cc_start: 0.5569 (OUTLIER) cc_final: 0.5263 (t80) REVERT: C 517 ARG cc_start: 0.7803 (tmt170) cc_final: 0.7529 (ttp-170) REVERT: C 524 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.6590 (mmm-85) REVERT: C 555 GLU cc_start: 0.8924 (tp30) cc_final: 0.8450 (tp30) REVERT: C 708 ASP cc_start: 0.8283 (t0) cc_final: 0.7892 (t0) REVERT: C 781 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8446 (mm-30) outliers start: 16 outliers final: 8 residues processed: 224 average time/residue: 0.9597 time to fit residues: 235.2981 Evaluate side-chains 224 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 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 104 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.0270 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 461 GLN A 541 HIS C 143 GLN C 461 GLN C 541 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091733 restraints weight = 13485.465| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.50 r_work: 0.2852 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 10770 Z= 0.277 Angle : 1.433 59.200 14684 Z= 0.866 Chirality : 0.049 0.499 1740 Planarity : 0.003 0.034 1772 Dihedral : 6.635 55.976 2032 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.81 % Allowed : 25.36 % Favored : 73.84 % Cbeta Deviations : 0.17 % 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: 1.29 (0.24), residues: 1232 helix: 1.90 (0.23), residues: 554 sheet: 1.65 (0.29), residues: 270 loop : -1.24 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 446 HIS 0.002 0.001 HIS C 487 PHE 0.019 0.001 PHE A 632 TYR 0.012 0.001 TYR A 590 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: 4463.14 seconds wall clock time: 78 minutes 24.04 seconds (4704.04 seconds total)