Starting phenix.real_space_refine on Mon Jul 28 03:49:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y63_33632/07_2025/7y63_33632.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y63_33632/07_2025/7y63_33632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y63_33632/07_2025/7y63_33632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y63_33632/07_2025/7y63_33632.map" model { file = "/net/cci-nas-00/data/ceres_data/7y63_33632/07_2025/7y63_33632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y63_33632/07_2025/7y63_33632.cif" } resolution = 3.16 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= 0.001 sd= 0.061 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 66 5.16 5 C 6430 2.51 5 N 1604 2.21 5 O 1822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9924 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4863 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 598} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 4, 'ARG:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4863 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 598} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 4, 'ARG:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "C" 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: "D" 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: "E" 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: "F" 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.06, per 1000 atoms: 0.61 Number of scatterers: 9924 At special positions: 0 Unit cell: (108.692, 80.1467, 133.944, 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 66 16.00 O 1822 8.00 N 1604 7.00 C 6430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 570 " distance=2.04 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 570 " distance=2.04 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 787 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 902 " - " ASN A 27 " " NAG A 903 " - " ASN A 141 " " NAG A 904 " - " ASN A 123 " " NAG B 902 " - " ASN B 27 " " NAG B 903 " - " ASN B 141 " " NAG B 904 " - " ASN B 123 " " NAG C 1 " - " ASN A 54 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN B 54 " " NAG F 1 " - " ASN B 165 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 568 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 568 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 45.7% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.538A pdb=" N VAL A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP A 320 " --> pdb=" O CYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 479 removed outlier: 3.579A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Proline residue: A 463 - end of helix removed outlier: 3.916A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.617A pdb=" N LEU A 504 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 505' Processing helix chain 'A' and resid 506 through 533 removed outlier: 3.972A pdb=" N ILE A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 549 through 561 removed outlier: 3.538A pdb=" N MET A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 599 removed outlier: 4.578A pdb=" N THR A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 626 Processing helix chain 'A' and resid 630 through 652 removed outlier: 3.851A pdb=" N THR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.966A pdb=" N LEU A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 693 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.906A pdb=" N LEU A 728 " --> pdb=" O CYS A 724 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 736 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 769 removed outlier: 3.556A pdb=" N CYS A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 755 " --> pdb=" O CYS A 751 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 763 " --> pdb=" O TRP A 759 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 769 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 794 through 818 removed outlier: 3.918A pdb=" N SER A 804 " --> pdb=" O HIS A 800 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 813 " --> pdb=" O GLY A 809 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.538A pdb=" N VAL B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP B 320 " --> pdb=" O CYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 479 removed outlier: 3.580A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Proline residue: B 463 - end of helix removed outlier: 3.917A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 467 " --> pdb=" O PRO B 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 476 " --> pdb=" O GLN B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.617A pdb=" N LEU B 504 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 500 through 505' Processing helix chain 'B' and resid 506 through 533 removed outlier: 3.972A pdb=" N ILE B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B 514 " --> pdb=" O ILE B 510 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 529 " --> pdb=" O ILE B 525 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 531 " --> pdb=" O HIS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 549 through 561 removed outlier: 3.539A pdb=" N MET B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 599 removed outlier: 4.578A pdb=" N THR B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 626 Processing helix chain 'B' and resid 630 through 652 removed outlier: 3.850A pdb=" N THR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 710 removed outlier: 3.966A pdb=" N LEU B 692 " --> pdb=" O ARG B 688 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 693 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.907A pdb=" N LEU B 728 " --> pdb=" O CYS B 724 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 736 " --> pdb=" O PHE B 732 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 737 " --> pdb=" O TYR B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 769 removed outlier: 3.555A pdb=" N CYS B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 755 " --> pdb=" O CYS B 751 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 763 " --> pdb=" O TRP B 759 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 769 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 794 through 818 removed outlier: 3.918A pdb=" N SER B 804 " --> pdb=" O HIS B 800 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 813 " --> pdb=" O GLY B 809 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 814 " --> pdb=" O SER B 810 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.849A pdb=" N ASP A 41 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.910A pdb=" N LYS A 106 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.602A pdb=" N PHE A 164 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 285 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.473A pdb=" N CYS A 197 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 43 removed outlier: 3.849A pdb=" N ASP B 41 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 115 Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.910A pdb=" N LYS B 106 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.601A pdb=" N PHE B 164 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 285 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.472A pdb=" N CYS B 197 " --> pdb=" O LYS B 250 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1386 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: 2.88 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3094 1.34 - 1.46: 2472 1.46 - 1.58: 4476 1.58 - 1.70: 0 1.70 - 1.83: 98 Bond restraints: 10140 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CA ARG B 85 " pdb=" CB ARG B 85 " ideal model delta sigma weight residual 1.528 1.500 0.027 1.39e-02 5.18e+03 3.91e+00 bond pdb=" CA ARG A 85 " pdb=" CB ARG A 85 " ideal model delta sigma weight residual 1.528 1.500 0.027 1.39e-02 5.18e+03 3.91e+00 bond pdb=" CA ARG B 235 " pdb=" C ARG B 235 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.80e-02 3.09e+03 2.60e+00 ... (remaining 10135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 13203 1.53 - 3.06: 487 3.06 - 4.60: 77 4.60 - 6.13: 15 6.13 - 7.66: 6 Bond angle restraints: 13788 Sorted by residual: angle pdb=" C ALA A 715 " pdb=" CA ALA A 715 " pdb=" CB ALA A 715 " ideal model delta sigma weight residual 110.88 116.78 -5.90 1.57e+00 4.06e-01 1.41e+01 angle pdb=" N PHE A 195 " pdb=" CA PHE A 195 " pdb=" C PHE A 195 " ideal model delta sigma weight residual 109.81 117.47 -7.66 2.21e+00 2.05e-01 1.20e+01 angle pdb=" N PHE B 195 " pdb=" CA PHE B 195 " pdb=" C PHE B 195 " ideal model delta sigma weight residual 109.81 117.46 -7.65 2.21e+00 2.05e-01 1.20e+01 angle pdb=" N SER A 716 " pdb=" CA SER A 716 " pdb=" C SER A 716 " ideal model delta sigma weight residual 111.75 115.84 -4.09 1.28e+00 6.10e-01 1.02e+01 angle pdb=" C ALA B 194 " pdb=" N PHE B 195 " pdb=" CA PHE B 195 " ideal model delta sigma weight residual 121.80 114.40 7.40 2.44e+00 1.68e-01 9.19e+00 ... (remaining 13783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.21: 5690 23.21 - 46.42: 346 46.42 - 69.63: 69 69.63 - 92.83: 25 92.83 - 116.04: 30 Dihedral angle restraints: 6160 sinusoidal: 2526 harmonic: 3634 Sorted by residual: dihedral pdb=" CA PHE A 195 " pdb=" C PHE A 195 " pdb=" N PRO A 196 " pdb=" CA PRO A 196 " ideal model delta harmonic sigma weight residual 180.00 127.86 52.14 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA PHE B 195 " pdb=" C PHE B 195 " pdb=" N PRO B 196 " pdb=" CA PRO B 196 " ideal model delta harmonic sigma weight residual 180.00 127.89 52.11 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CB CYS B 197 " pdb=" SG CYS B 197 " pdb=" SG CYS B 256 " pdb=" CB CYS B 256 " ideal model delta sinusoidal sigma weight residual 93.00 172.68 -79.68 1 1.00e+01 1.00e-02 7.88e+01 ... (remaining 6157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1574 0.104 - 0.207: 61 0.207 - 0.311: 5 0.311 - 0.415: 2 0.415 - 0.519: 2 Chirality restraints: 1644 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 54 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 54 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1641 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 195 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO A 196 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 195 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO B 196 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 78 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 79 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.036 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1457 2.75 - 3.29: 9676 3.29 - 3.83: 15673 3.83 - 4.36: 19202 4.36 - 4.90: 32813 Nonbonded interactions: 78821 Sorted by model distance: nonbonded pdb=" NH2 ARG A 59 " pdb=" O LYS A 122 " model vdw 2.214 3.120 nonbonded pdb=" NH2 ARG B 59 " pdb=" O LYS B 122 " model vdw 2.214 3.120 nonbonded pdb=" O THR A 224 " pdb=" NH1 ARG A 781 " model vdw 2.221 3.120 nonbonded pdb=" O THR B 224 " pdb=" NH1 ARG B 781 " model vdw 2.221 3.120 nonbonded pdb=" CD2 LEU A 81 " pdb=" CG2 VAL B 90 " model vdw 2.228 3.880 ... (remaining 78816 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.250 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: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.380 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.006 0.083 10168 Z= 0.249 Angle : 0.739 9.947 13846 Z= 0.391 Chirality : 0.053 0.519 1644 Planarity : 0.005 0.098 1718 Dihedral : 18.687 116.042 3784 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -2.24 (0.23), residues: 1218 helix: -1.22 (0.23), residues: 468 sheet: -1.13 (0.30), residues: 296 loop : -1.79 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 700 HIS 0.003 0.001 HIS A 492 PHE 0.016 0.002 PHE A 576 TYR 0.018 0.002 TYR A 173 ARG 0.003 0.000 ARG A 785 Details of bonding type rmsd link_NAG-ASN : bond 0.00798 ( 10) link_NAG-ASN : angle 4.72251 ( 30) link_BETA1-4 : bond 0.00878 ( 4) link_BETA1-4 : angle 2.29671 ( 12) hydrogen bonds : bond 0.26634 ( 478) hydrogen bonds : angle 9.30574 ( 1386) metal coordination : bond 0.00190 ( 6) SS BOND : bond 0.00295 ( 8) SS BOND : angle 1.50042 ( 16) covalent geometry : bond 0.00551 (10140) covalent geometry : angle 0.70238 (13788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.025 Fit side-chains REVERT: A 694 MET cc_start: 0.5732 (mpp) cc_final: 0.5361 (mpp) REVERT: A 728 LEU cc_start: 0.9087 (mt) cc_final: 0.8840 (mt) REVERT: A 749 LEU cc_start: 0.8529 (tp) cc_final: 0.8255 (pp) REVERT: B 694 MET cc_start: 0.5776 (mpp) cc_final: 0.5413 (mpp) REVERT: B 728 LEU cc_start: 0.9073 (mt) cc_final: 0.8828 (mt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2323 time to fit residues: 51.3067 Evaluate side-chains 132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.0060 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 699 ASN A 774 GLN B 110 GLN B 699 ASN B 774 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.161126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107126 restraints weight = 13679.081| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.79 r_work: 0.3348 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10168 Z= 0.173 Angle : 0.737 11.638 13846 Z= 0.360 Chirality : 0.049 0.295 1644 Planarity : 0.005 0.087 1718 Dihedral : 14.864 90.464 1620 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.95 % Allowed : 7.58 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.53 (0.24), residues: 1218 helix: -0.41 (0.22), residues: 508 sheet: -0.95 (0.30), residues: 296 loop : -1.60 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 PHE 0.014 0.002 PHE A 582 TYR 0.025 0.002 TYR B 584 ARG 0.005 0.000 ARG B 781 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 10) link_NAG-ASN : angle 4.63438 ( 30) link_BETA1-4 : bond 0.00550 ( 4) link_BETA1-4 : angle 2.31736 ( 12) hydrogen bonds : bond 0.06410 ( 478) hydrogen bonds : angle 5.99799 ( 1386) metal coordination : bond 0.00117 ( 6) SS BOND : bond 0.00289 ( 8) SS BOND : angle 1.11543 ( 16) covalent geometry : bond 0.00369 (10140) covalent geometry : angle 0.70227 (13788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.983 Fit side-chains REVERT: A 104 GLN cc_start: 0.8861 (pm20) cc_final: 0.8435 (pm20) REVERT: A 297 MET cc_start: 0.7496 (ptt) cc_final: 0.6764 (ptt) REVERT: A 694 MET cc_start: 0.5919 (mpp) cc_final: 0.5648 (mpp) REVERT: A 714 PHE cc_start: 0.8350 (t80) cc_final: 0.8142 (t80) REVERT: A 728 LEU cc_start: 0.9019 (mt) cc_final: 0.8792 (mt) REVERT: B 104 GLN cc_start: 0.8852 (pm20) cc_final: 0.8472 (pm20) REVERT: B 297 MET cc_start: 0.7492 (ptt) cc_final: 0.6780 (ptt) REVERT: B 694 MET cc_start: 0.5921 (mpp) cc_final: 0.5668 (mpp) REVERT: B 728 LEU cc_start: 0.9029 (mt) cc_final: 0.8812 (mt) outliers start: 10 outliers final: 5 residues processed: 147 average time/residue: 0.3607 time to fit residues: 80.0481 Evaluate side-chains 132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 0.0980 chunk 46 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.161061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109160 restraints weight = 13520.918| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.63 r_work: 0.3334 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10168 Z= 0.226 Angle : 0.721 11.292 13846 Z= 0.348 Chirality : 0.048 0.272 1644 Planarity : 0.005 0.088 1718 Dihedral : 10.885 67.148 1620 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.42 % Allowed : 12.03 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.18 (0.24), residues: 1218 helix: 0.02 (0.23), residues: 512 sheet: -0.80 (0.30), residues: 296 loop : -1.61 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 320 HIS 0.003 0.001 HIS A 527 PHE 0.018 0.002 PHE B 304 TYR 0.020 0.002 TYR A 485 ARG 0.003 0.000 ARG B 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 10) link_NAG-ASN : angle 4.34968 ( 30) link_BETA1-4 : bond 0.00373 ( 4) link_BETA1-4 : angle 2.70023 ( 12) hydrogen bonds : bond 0.05338 ( 478) hydrogen bonds : angle 5.48858 ( 1386) metal coordination : bond 0.00285 ( 6) SS BOND : bond 0.00149 ( 8) SS BOND : angle 1.28679 ( 16) covalent geometry : bond 0.00530 (10140) covalent geometry : angle 0.68772 (13788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.061 Fit side-chains REVERT: A 61 ARG cc_start: 0.6861 (mpt180) cc_final: 0.6513 (mtm-85) REVERT: A 94 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7771 (pp30) REVERT: A 297 MET cc_start: 0.7564 (ptt) cc_final: 0.6867 (ptt) REVERT: A 728 LEU cc_start: 0.9020 (mt) cc_final: 0.8800 (mt) REVERT: A 779 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8378 (mt-10) REVERT: B 61 ARG cc_start: 0.6877 (mpt180) cc_final: 0.6530 (mtm-85) REVERT: B 94 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7755 (pp30) REVERT: B 104 GLN cc_start: 0.8856 (pm20) cc_final: 0.8482 (pm20) REVERT: B 297 MET cc_start: 0.7578 (ptt) cc_final: 0.6865 (ptt) REVERT: B 728 LEU cc_start: 0.9021 (mt) cc_final: 0.8797 (mt) REVERT: B 779 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8402 (mt-10) outliers start: 15 outliers final: 8 residues processed: 146 average time/residue: 0.2056 time to fit residues: 43.2101 Evaluate side-chains 131 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 8 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.166107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112535 restraints weight = 13528.621| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.76 r_work: 0.3380 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10168 Z= 0.123 Angle : 0.627 9.954 13846 Z= 0.303 Chirality : 0.045 0.262 1644 Planarity : 0.004 0.076 1718 Dihedral : 7.671 51.052 1620 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.14 % Allowed : 13.83 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.94 (0.24), residues: 1218 helix: 0.41 (0.23), residues: 510 sheet: -0.74 (0.29), residues: 296 loop : -1.72 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 320 HIS 0.002 0.000 HIS B 492 PHE 0.014 0.001 PHE A 130 TYR 0.030 0.001 TYR A 584 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00810 ( 10) link_NAG-ASN : angle 4.07711 ( 30) link_BETA1-4 : bond 0.00232 ( 4) link_BETA1-4 : angle 2.75661 ( 12) hydrogen bonds : bond 0.04276 ( 478) hydrogen bonds : angle 5.05842 ( 1386) metal coordination : bond 0.00073 ( 6) SS BOND : bond 0.00101 ( 8) SS BOND : angle 0.81283 ( 16) covalent geometry : bond 0.00260 (10140) covalent geometry : angle 0.59311 (13788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.161 Fit side-chains REVERT: A 61 ARG cc_start: 0.6850 (mpt180) cc_final: 0.6563 (mtm-85) REVERT: A 297 MET cc_start: 0.7311 (ptt) cc_final: 0.6681 (ptt) REVERT: B 61 ARG cc_start: 0.6845 (mpt180) cc_final: 0.6543 (mtm-85) REVERT: B 104 GLN cc_start: 0.8804 (pm20) cc_final: 0.8455 (pm20) REVERT: B 297 MET cc_start: 0.7285 (ptt) cc_final: 0.6626 (ptt) outliers start: 12 outliers final: 4 residues processed: 142 average time/residue: 0.1845 time to fit residues: 39.0702 Evaluate side-chains 119 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 583 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.161701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107777 restraints weight = 13582.074| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.75 r_work: 0.3310 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10168 Z= 0.251 Angle : 0.668 9.256 13846 Z= 0.332 Chirality : 0.047 0.248 1644 Planarity : 0.005 0.088 1718 Dihedral : 7.529 56.264 1620 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.80 % Allowed : 16.00 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.83 (0.24), residues: 1218 helix: 0.47 (0.23), residues: 506 sheet: -0.69 (0.30), residues: 296 loop : -1.58 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 320 HIS 0.006 0.001 HIS A 527 PHE 0.014 0.002 PHE B 304 TYR 0.017 0.002 TYR B 173 ARG 0.003 0.000 ARG B 276 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 10) link_NAG-ASN : angle 3.90438 ( 30) link_BETA1-4 : bond 0.00117 ( 4) link_BETA1-4 : angle 2.47352 ( 12) hydrogen bonds : bond 0.04551 ( 478) hydrogen bonds : angle 5.15422 ( 1386) metal coordination : bond 0.00298 ( 6) SS BOND : bond 0.00183 ( 8) SS BOND : angle 1.20919 ( 16) covalent geometry : bond 0.00594 (10140) covalent geometry : angle 0.63879 (13788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.159 Fit side-chains REVERT: A 61 ARG cc_start: 0.6943 (mpt180) cc_final: 0.6683 (mtm-85) REVERT: A 94 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7759 (pp30) REVERT: A 297 MET cc_start: 0.7477 (ptt) cc_final: 0.6872 (ptt) REVERT: A 728 LEU cc_start: 0.9157 (mt) cc_final: 0.8784 (pp) REVERT: B 61 ARG cc_start: 0.6950 (mpt180) cc_final: 0.6686 (mtm-85) REVERT: B 94 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7747 (pp30) REVERT: B 104 GLN cc_start: 0.8844 (pm20) cc_final: 0.8494 (pm20) REVERT: B 297 MET cc_start: 0.7469 (ptt) cc_final: 0.6860 (ptt) REVERT: B 728 LEU cc_start: 0.9157 (mt) cc_final: 0.8781 (pp) outliers start: 19 outliers final: 14 residues processed: 150 average time/residue: 0.1809 time to fit residues: 41.0271 Evaluate side-chains 139 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 761 PHE Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 52 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.163933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109905 restraints weight = 13683.694| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.77 r_work: 0.3341 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.004 0.036 10168 Z= 0.164 Angle : 0.602 8.704 13846 Z= 0.300 Chirality : 0.045 0.237 1644 Planarity : 0.004 0.077 1718 Dihedral : 6.960 53.342 1620 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.61 % Allowed : 17.90 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.75 (0.24), residues: 1218 helix: 0.63 (0.23), residues: 500 sheet: -0.69 (0.29), residues: 296 loop : -1.61 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 320 HIS 0.002 0.001 HIS A 492 PHE 0.020 0.001 PHE A 714 TYR 0.014 0.001 TYR A 173 ARG 0.002 0.000 ARG B 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 10) link_NAG-ASN : angle 3.61395 ( 30) link_BETA1-4 : bond 0.00200 ( 4) link_BETA1-4 : angle 2.22637 ( 12) hydrogen bonds : bond 0.04148 ( 478) hydrogen bonds : angle 5.00651 ( 1386) metal coordination : bond 0.00160 ( 6) SS BOND : bond 0.00110 ( 8) SS BOND : angle 0.92546 ( 16) covalent geometry : bond 0.00374 (10140) covalent geometry : angle 0.57445 (13788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6996 (mpt180) cc_final: 0.6699 (mtm-85) REVERT: A 94 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7711 (pp30) REVERT: A 104 GLN cc_start: 0.8821 (pm20) cc_final: 0.8474 (pm20) REVERT: A 297 MET cc_start: 0.7400 (ptt) cc_final: 0.6821 (ptt) REVERT: B 61 ARG cc_start: 0.7002 (mpt180) cc_final: 0.6702 (mtm-85) REVERT: B 94 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7701 (pp30) REVERT: B 104 GLN cc_start: 0.8827 (pm20) cc_final: 0.8496 (pm20) REVERT: B 297 MET cc_start: 0.7409 (ptt) cc_final: 0.6810 (ptt) REVERT: B 812 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8205 (mp) outliers start: 17 outliers final: 9 residues processed: 140 average time/residue: 0.1772 time to fit residues: 37.4165 Evaluate side-chains 133 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 30.0000 chunk 111 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.164334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110256 restraints weight = 13756.044| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.78 r_work: 0.3347 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10168 Z= 0.153 Angle : 0.592 8.161 13846 Z= 0.295 Chirality : 0.044 0.229 1644 Planarity : 0.004 0.083 1718 Dihedral : 6.592 53.794 1620 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.75 % Allowed : 17.23 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.59 (0.24), residues: 1218 helix: 0.81 (0.23), residues: 508 sheet: -0.60 (0.29), residues: 296 loop : -1.65 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 PHE 0.017 0.001 PHE A 714 TYR 0.014 0.001 TYR A 173 ARG 0.002 0.000 ARG B 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 10) link_NAG-ASN : angle 3.45292 ( 30) link_BETA1-4 : bond 0.00206 ( 4) link_BETA1-4 : angle 2.02326 ( 12) hydrogen bonds : bond 0.04003 ( 478) hydrogen bonds : angle 4.91146 ( 1386) metal coordination : bond 0.00152 ( 6) SS BOND : bond 0.00124 ( 8) SS BOND : angle 0.91999 ( 16) covalent geometry : bond 0.00350 (10140) covalent geometry : angle 0.56686 (13788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7040 (mpt180) cc_final: 0.6702 (mtm-85) REVERT: A 94 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7698 (pp30) REVERT: A 313 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7783 (tp) REVERT: A 812 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8221 (mp) REVERT: B 61 ARG cc_start: 0.7040 (mpt180) cc_final: 0.6698 (mtm-85) REVERT: B 94 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7685 (pp30) REVERT: B 313 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7776 (tp) outliers start: 29 outliers final: 14 residues processed: 152 average time/residue: 0.1800 time to fit residues: 41.1427 Evaluate side-chains 142 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 761 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.164030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109863 restraints weight = 13652.332| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.76 r_work: 0.3349 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10168 Z= 0.175 Angle : 0.606 7.728 13846 Z= 0.304 Chirality : 0.045 0.226 1644 Planarity : 0.004 0.077 1718 Dihedral : 6.498 54.453 1620 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.18 % Allowed : 18.28 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.48 (0.24), residues: 1218 helix: 0.93 (0.23), residues: 508 sheet: -0.56 (0.29), residues: 296 loop : -1.63 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 PHE 0.022 0.001 PHE A 304 TYR 0.015 0.001 TYR B 173 ARG 0.002 0.000 ARG B 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 10) link_NAG-ASN : angle 3.32392 ( 30) link_BETA1-4 : bond 0.00221 ( 4) link_BETA1-4 : angle 1.85761 ( 12) hydrogen bonds : bond 0.04024 ( 478) hydrogen bonds : angle 4.89607 ( 1386) metal coordination : bond 0.00141 ( 6) SS BOND : bond 0.00133 ( 8) SS BOND : angle 0.94979 ( 16) covalent geometry : bond 0.00407 (10140) covalent geometry : angle 0.58323 (13788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7057 (mpt180) cc_final: 0.6706 (mtm-85) REVERT: A 94 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7734 (pp30) REVERT: A 313 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7803 (tp) REVERT: A 521 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7847 (tp) REVERT: A 812 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8243 (mp) REVERT: B 61 ARG cc_start: 0.7057 (mpt180) cc_final: 0.6700 (mtm-85) REVERT: B 94 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7731 (pp30) REVERT: B 313 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7773 (tp) REVERT: B 521 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7840 (tp) REVERT: B 714 PHE cc_start: 0.8374 (t80) cc_final: 0.8166 (t80) REVERT: B 728 LEU cc_start: 0.9153 (mt) cc_final: 0.8849 (pp) REVERT: B 812 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8203 (mp) outliers start: 23 outliers final: 12 residues processed: 134 average time/residue: 0.1773 time to fit residues: 36.0257 Evaluate side-chains 138 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 0.0370 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.166027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112069 restraints weight = 13644.123| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.77 r_work: 0.3381 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10168 Z= 0.124 Angle : 0.577 7.496 13846 Z= 0.289 Chirality : 0.043 0.234 1644 Planarity : 0.004 0.081 1718 Dihedral : 6.082 52.002 1620 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.70 % Allowed : 18.94 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 (0.24), residues: 1218 helix: 1.18 (0.23), residues: 504 sheet: -0.54 (0.29), residues: 296 loop : -1.53 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 320 HIS 0.004 0.001 HIS A 527 PHE 0.022 0.001 PHE A 714 TYR 0.013 0.001 TYR A 173 ARG 0.002 0.000 ARG A 781 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 10) link_NAG-ASN : angle 3.19794 ( 30) link_BETA1-4 : bond 0.00275 ( 4) link_BETA1-4 : angle 1.73340 ( 12) hydrogen bonds : bond 0.03775 ( 478) hydrogen bonds : angle 4.82176 ( 1386) metal coordination : bond 0.00095 ( 6) SS BOND : bond 0.00109 ( 8) SS BOND : angle 0.75644 ( 16) covalent geometry : bond 0.00275 (10140) covalent geometry : angle 0.55582 (13788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7074 (mpt180) cc_final: 0.6703 (mtm-85) REVERT: A 94 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7704 (pp30) REVERT: A 313 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7834 (tp) REVERT: A 585 MET cc_start: 0.8027 (tpp) cc_final: 0.7785 (tpt) REVERT: A 812 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8202 (mp) REVERT: B 61 ARG cc_start: 0.7043 (mpt180) cc_final: 0.6668 (mtm-85) REVERT: B 94 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7695 (pp30) REVERT: B 313 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7836 (tp) REVERT: B 714 PHE cc_start: 0.8401 (t80) cc_final: 0.8162 (t80) REVERT: B 812 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8174 (mp) outliers start: 18 outliers final: 9 residues processed: 141 average time/residue: 0.1956 time to fit residues: 40.7328 Evaluate side-chains 135 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 115 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.165941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112249 restraints weight = 13589.844| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.74 r_work: 0.3378 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10168 Z= 0.129 Angle : 0.575 7.181 13846 Z= 0.289 Chirality : 0.043 0.231 1644 Planarity : 0.004 0.076 1718 Dihedral : 5.964 53.308 1620 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.18 % Allowed : 18.84 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.13 (0.24), residues: 1218 helix: 1.29 (0.23), residues: 504 sheet: -0.42 (0.29), residues: 296 loop : -1.49 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 320 HIS 0.004 0.001 HIS A 527 PHE 0.021 0.001 PHE A 304 TYR 0.013 0.001 TYR A 173 ARG 0.002 0.000 ARG A 598 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 10) link_NAG-ASN : angle 3.10152 ( 30) link_BETA1-4 : bond 0.00189 ( 4) link_BETA1-4 : angle 1.61087 ( 12) hydrogen bonds : bond 0.03703 ( 478) hydrogen bonds : angle 4.75986 ( 1386) metal coordination : bond 0.00070 ( 6) SS BOND : bond 0.00122 ( 8) SS BOND : angle 0.79014 ( 16) covalent geometry : bond 0.00291 (10140) covalent geometry : angle 0.55543 (13788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7038 (mpt180) cc_final: 0.6677 (mtm-85) REVERT: A 94 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7681 (pp30) REVERT: A 313 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7855 (tp) REVERT: A 521 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7731 (tp) REVERT: A 559 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8279 (mmm) REVERT: A 585 MET cc_start: 0.7938 (tpp) cc_final: 0.7672 (tpt) REVERT: A 812 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8213 (mp) REVERT: B 61 ARG cc_start: 0.7028 (mpt180) cc_final: 0.6665 (mtm-85) REVERT: B 94 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: B 313 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7832 (tp) REVERT: B 521 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7775 (tp) REVERT: B 714 PHE cc_start: 0.8362 (t80) cc_final: 0.8107 (t80) REVERT: B 812 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8219 (mp) outliers start: 23 outliers final: 11 residues processed: 140 average time/residue: 0.1723 time to fit residues: 36.6080 Evaluate side-chains 136 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.165342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111405 restraints weight = 13587.602| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.76 r_work: 0.3366 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10168 Z= 0.150 Angle : 0.595 12.604 13846 Z= 0.296 Chirality : 0.044 0.222 1644 Planarity : 0.004 0.080 1718 Dihedral : 5.983 54.234 1620 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.89 % Allowed : 19.60 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.11 (0.24), residues: 1218 helix: 1.29 (0.23), residues: 504 sheet: -0.41 (0.29), residues: 296 loop : -1.45 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 PHE 0.026 0.001 PHE A 714 TYR 0.013 0.001 TYR B 173 ARG 0.005 0.000 ARG A 529 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 10) link_NAG-ASN : angle 3.03469 ( 30) link_BETA1-4 : bond 0.00209 ( 4) link_BETA1-4 : angle 1.56213 ( 12) hydrogen bonds : bond 0.03776 ( 478) hydrogen bonds : angle 4.79075 ( 1386) metal coordination : bond 0.00127 ( 6) SS BOND : bond 0.00133 ( 8) SS BOND : angle 0.87562 ( 16) covalent geometry : bond 0.00347 (10140) covalent geometry : angle 0.57635 (13788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5016.89 seconds wall clock time: 89 minutes 56.86 seconds (5396.86 seconds total)