Starting phenix.real_space_refine on Sat Jan 20 16:15:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryz_24749/01_2024/7ryz_24749_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryz_24749/01_2024/7ryz_24749.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryz_24749/01_2024/7ryz_24749_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryz_24749/01_2024/7ryz_24749_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryz_24749/01_2024/7ryz_24749_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryz_24749/01_2024/7ryz_24749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryz_24749/01_2024/7ryz_24749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryz_24749/01_2024/7ryz_24749_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryz_24749/01_2024/7ryz_24749_updated.pdb" } resolution = 4.15 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= 0.001 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 10196 2.51 5 N 2556 2.21 5 O 2882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1089": "NH1" <-> "NH2" Residue "A ARG 1111": "NH1" <-> "NH2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 715": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 715": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1089": "NH1" <-> "NH2" Residue "C ARG 1111": "NH1" <-> "NH2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 715": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15742 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4652 Classifications: {'peptide': 597} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 578} Chain breaks: 3 Chain: "B" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3193 Classifications: {'peptide': 410} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 396} Chain breaks: 1 Chain: "C" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4652 Classifications: {'peptide': 597} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 578} Chain breaks: 3 Chain: "D" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3193 Classifications: {'peptide': 410} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 396} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.80, per 1000 atoms: 0.56 Number of scatterers: 15742 At special positions: 0 Unit cell: (108.73, 126.99, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2882 8.00 N 2556 7.00 C 10196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1099 " - pdb=" SG CYS A1110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1099 " - pdb=" SG CYS C1110 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " 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 Time building additional restraints: 5.47 Conformation dependent library (CDL) restraints added in 3.0 seconds 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3684 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 16 sheets defined 50.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.569A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 546 removed outlier: 3.687A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.528A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 626 removed outlier: 3.520A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.856A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.550A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 756 removed outlier: 3.939A pdb=" N THR A 744 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 745 - end of helix removed outlier: 3.693A pdb=" N LEU A 753 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 756 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.769A pdb=" N TYR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.897A pdb=" N LYS A 781 " --> pdb=" O ASP A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 821 removed outlier: 5.622A pdb=" N GLY A 794 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 800 " --> pdb=" O TYR A 797 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 801 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 805 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 807 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 811 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 813 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 814 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 818 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1028 Processing helix chain 'A' and resid 1119 through 1147 removed outlier: 3.816A pdb=" N GLY A1123 " --> pdb=" O ALA A1119 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL A1124 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1193 removed outlier: 3.858A pdb=" N LEU A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1232 removed outlier: 3.682A pdb=" N MET A1221 " --> pdb=" O PHE A1217 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR A1226 " --> pdb=" O ALA A1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 436 removed outlier: 3.821A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.608A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.548A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.758A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.680A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 625 removed outlier: 4.353A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.540A pdb=" N SER B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 636 through 640' Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 686 through 694 removed outlier: 3.655A pdb=" N ALA B 691 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.876A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 712 " --> pdb=" O MET B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 removed outlier: 4.073A pdb=" N THR B 744 " --> pdb=" O SER B 741 " (cutoff:3.500A) Proline residue: B 745 - end of helix removed outlier: 4.080A pdb=" N LEU B 753 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.858A pdb=" N LYS B 765 " --> pdb=" O LYS B 761 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 779 Processing helix chain 'B' and resid 793 through 819 removed outlier: 3.641A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.568A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 546 removed outlier: 3.687A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 545 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.528A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 626 removed outlier: 3.520A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 654 through 660 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.857A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.549A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 756 removed outlier: 3.939A pdb=" N THR C 744 " --> pdb=" O SER C 741 " (cutoff:3.500A) Proline residue: C 745 - end of helix removed outlier: 3.692A pdb=" N LEU C 753 " --> pdb=" O VAL C 750 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN C 756 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 769 removed outlier: 3.770A pdb=" N TYR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 781 removed outlier: 3.896A pdb=" N LYS C 781 " --> pdb=" O ASP C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 821 removed outlier: 5.621A pdb=" N GLY C 794 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 800 " --> pdb=" O TYR C 797 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 801 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 805 " --> pdb=" O GLY C 802 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET C 807 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 811 " --> pdb=" O LEU C 808 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 813 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 814 " --> pdb=" O LEU C 811 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 818 " --> pdb=" O CYS C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1028 Processing helix chain 'C' and resid 1119 through 1147 removed outlier: 3.816A pdb=" N GLY C1123 " --> pdb=" O ALA C1119 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL C1124 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1193 removed outlier: 3.858A pdb=" N LEU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1232 removed outlier: 3.682A pdb=" N MET C1221 " --> pdb=" O PHE C1217 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR C1226 " --> pdb=" O ALA C1222 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.821A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.609A pdb=" N GLU D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 519 removed outlier: 3.549A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 516 through 519' Processing helix chain 'D' and resid 523 through 546 removed outlier: 3.758A pdb=" N CYS D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.678A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 removed outlier: 4.353A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.539A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 636 through 640' Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 686 through 694 removed outlier: 3.654A pdb=" N ALA D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.876A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 712 " --> pdb=" O MET D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 755 removed outlier: 4.074A pdb=" N THR D 744 " --> pdb=" O SER D 741 " (cutoff:3.500A) Proline residue: D 745 - end of helix removed outlier: 4.079A pdb=" N LEU D 753 " --> pdb=" O VAL D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 769 removed outlier: 3.858A pdb=" N LYS D 765 " --> pdb=" O LYS D 761 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 779 Processing helix chain 'D' and resid 793 through 819 removed outlier: 3.641A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.061A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.375A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1033 through 1039 Processing sheet with id= E, first strand: chain 'A' and resid 1097 through 1100 Processing sheet with id= F, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 499 removed outlier: 4.118A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU B 498 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.291A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= J, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.059A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.376A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 1033 through 1039 Processing sheet with id= M, first strand: chain 'C' and resid 1097 through 1100 Processing sheet with id= N, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= O, first strand: chain 'D' and resid 496 through 499 removed outlier: 4.119A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU D 498 " --> pdb=" O LYS D 730 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.290A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 1860 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: 4.50 Time building geometry restraints manager: 5.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4829 1.35 - 1.47: 4215 1.47 - 1.60: 6872 1.60 - 1.72: 4 1.72 - 1.85: 174 Bond restraints: 16094 Sorted by residual: bond pdb=" C05 QUS B1301 " pdb=" O19 QUS B1301 " ideal model delta sigma weight residual 1.185 1.451 -0.266 2.00e-02 2.50e+03 1.76e+02 bond pdb=" C05 QUS D1301 " pdb=" O19 QUS D1301 " ideal model delta sigma weight residual 1.185 1.450 -0.265 2.00e-02 2.50e+03 1.76e+02 bond pdb=" C05 QUS A1401 " pdb=" O19 QUS A1401 " ideal model delta sigma weight residual 1.185 1.448 -0.263 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C05 QUS C1401 " pdb=" O19 QUS C1401 " ideal model delta sigma weight residual 1.185 1.448 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C04 QUS D1301 " pdb=" O18 QUS D1301 " ideal model delta sigma weight residual 1.185 1.411 -0.226 2.00e-02 2.50e+03 1.28e+02 ... (remaining 16089 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.09: 314 106.09 - 113.31: 8806 113.31 - 120.54: 6603 120.54 - 127.76: 5883 127.76 - 134.99: 148 Bond angle restraints: 21754 Sorted by residual: angle pdb=" CA PRO D 679 " pdb=" C PRO D 679 " pdb=" O PRO D 679 " ideal model delta sigma weight residual 122.12 115.48 6.64 1.24e+00 6.50e-01 2.87e+01 angle pdb=" CA PRO B 679 " pdb=" C PRO B 679 " pdb=" O PRO B 679 " ideal model delta sigma weight residual 122.12 115.48 6.64 1.24e+00 6.50e-01 2.87e+01 angle pdb=" C SER A1153 " pdb=" N SER A1154 " pdb=" CA SER A1154 " ideal model delta sigma weight residual 121.19 129.34 -8.15 1.59e+00 3.96e-01 2.63e+01 angle pdb=" C SER C1153 " pdb=" N SER C1154 " pdb=" CA SER C1154 " ideal model delta sigma weight residual 121.19 129.34 -8.15 1.59e+00 3.96e-01 2.63e+01 angle pdb=" C GLU C1197 " pdb=" N ASP C1198 " pdb=" CA ASP C1198 " ideal model delta sigma weight residual 125.66 134.99 -9.33 1.85e+00 2.92e-01 2.54e+01 ... (remaining 21749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 8865 15.01 - 30.02: 418 30.02 - 45.02: 163 45.02 - 60.03: 28 60.03 - 75.04: 4 Dihedral angle restraints: 9478 sinusoidal: 3704 harmonic: 5774 Sorted by residual: dihedral pdb=" CA GLU B 678 " pdb=" C GLU B 678 " pdb=" N PRO B 679 " pdb=" CA PRO B 679 " ideal model delta harmonic sigma weight residual 180.00 130.01 49.99 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA GLU D 678 " pdb=" C GLU D 678 " pdb=" N PRO D 679 " pdb=" CA PRO D 679 " ideal model delta harmonic sigma weight residual 180.00 130.02 49.98 0 5.00e+00 4.00e-02 9.99e+01 dihedral pdb=" CA PRO A1118 " pdb=" C PRO A1118 " pdb=" N ALA A1119 " pdb=" CA ALA A1119 " ideal model delta harmonic sigma weight residual -180.00 -154.15 -25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 9475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1871 0.052 - 0.104: 471 0.104 - 0.156: 82 0.156 - 0.208: 16 0.208 - 0.260: 2 Chirality restraints: 2442 Sorted by residual: chirality pdb=" CG LEU A 498 " pdb=" CB LEU A 498 " pdb=" CD1 LEU A 498 " pdb=" CD2 LEU A 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CG LEU C 498 " pdb=" CB LEU C 498 " pdb=" CD1 LEU C 498 " pdb=" CD2 LEU C 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA CYS D 718 " pdb=" N CYS D 718 " pdb=" C CYS D 718 " pdb=" CB CYS D 718 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2439 not shown) Planarity restraints: 2678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 519 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO A 520 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 519 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO C 520 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 493 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO D 494 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 494 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 494 " 0.027 5.00e-02 4.00e+02 ... (remaining 2675 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2898 2.76 - 3.30: 14875 3.30 - 3.83: 25996 3.83 - 4.37: 30837 4.37 - 4.90: 51296 Nonbonded interactions: 125902 Sorted by model distance: nonbonded pdb=" OG SER A 729 " pdb=" OG SER D 729 " model vdw 2.225 2.440 nonbonded pdb=" OG1 THR C 655 " pdb=" O18 QUS C1401 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR A 655 " pdb=" O18 QUS A1401 " model vdw 2.278 2.440 nonbonded pdb=" OE1 GLN A1186 " pdb=" OH TYR B 797 " model vdw 2.286 2.440 nonbonded pdb=" O LEU A 639 " pdb=" OH TYR A 647 " model vdw 2.289 2.440 ... (remaining 125897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 11.910 Check model and map are aligned: 0.000 Set scattering table: 0.050 Process input model: 43.980 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.120 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.008 0.266 16094 Z= 0.512 Angle : 0.946 13.680 21754 Z= 0.538 Chirality : 0.048 0.260 2442 Planarity : 0.006 0.050 2678 Dihedral : 10.877 75.040 5776 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.24 % Allowed : 5.37 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -4.55 (0.13), residues: 1990 helix: -3.45 (0.09), residues: 1072 sheet: -1.98 (0.34), residues: 180 loop : -2.24 (0.18), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A1032 HIS 0.004 0.002 HIS C1092 PHE 0.021 0.002 PHE D 574 TYR 0.021 0.002 TYR C1135 ARG 0.010 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 653 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ILE cc_start: 0.8827 (tt) cc_final: 0.8603 (mt) REVERT: A 434 LYS cc_start: 0.8915 (tptt) cc_final: 0.8454 (tmmt) REVERT: A 435 HIS cc_start: 0.7819 (t-90) cc_final: 0.7581 (t-170) REVERT: A 482 THR cc_start: 0.8631 (m) cc_final: 0.8328 (p) REVERT: A 509 LYS cc_start: 0.7353 (pmtt) cc_final: 0.7098 (mmmt) REVERT: A 537 SER cc_start: 0.9256 (p) cc_final: 0.8485 (t) REVERT: A 585 MET cc_start: 0.8203 (mmt) cc_final: 0.7775 (mmt) REVERT: A 611 ILE cc_start: 0.9288 (mm) cc_final: 0.9068 (mm) REVERT: A 626 VAL cc_start: 0.9123 (t) cc_final: 0.8807 (p) REVERT: A 637 GLU cc_start: 0.8190 (tt0) cc_final: 0.7628 (tp30) REVERT: A 642 GLN cc_start: 0.7326 (tt0) cc_final: 0.7006 (pp30) REVERT: A 720 THR cc_start: 0.8012 (p) cc_final: 0.7087 (p) REVERT: A 1015 LEU cc_start: 0.8668 (mt) cc_final: 0.8458 (mt) REVERT: A 1016 ASN cc_start: 0.8338 (m-40) cc_final: 0.7754 (t0) REVERT: A 1022 PHE cc_start: 0.8235 (m-10) cc_final: 0.7150 (m-10) REVERT: A 1131 SER cc_start: 0.9290 (m) cc_final: 0.9085 (p) REVERT: A 1141 VAL cc_start: 0.8890 (t) cc_final: 0.8673 (t) REVERT: A 1175 LEU cc_start: 0.9458 (mt) cc_final: 0.9140 (tp) REVERT: A 1211 CYS cc_start: 0.8755 (m) cc_final: 0.8538 (p) REVERT: A 1219 CYS cc_start: 0.8768 (m) cc_final: 0.8286 (m) REVERT: B 407 MET cc_start: 0.8413 (mtp) cc_final: 0.8051 (mtp) REVERT: B 408 MET cc_start: 0.7183 (mmm) cc_final: 0.6940 (mmm) REVERT: B 445 VAL cc_start: 0.7895 (p) cc_final: 0.7640 (p) REVERT: B 498 LEU cc_start: 0.9019 (pt) cc_final: 0.8760 (pt) REVERT: B 504 ILE cc_start: 0.8946 (pt) cc_final: 0.8634 (pt) REVERT: B 505 LYS cc_start: 0.7833 (tmtm) cc_final: 0.7252 (tptp) REVERT: B 506 LYS cc_start: 0.7906 (ttmp) cc_final: 0.7573 (mtpt) REVERT: B 509 LYS cc_start: 0.7725 (pmtt) cc_final: 0.7174 (tppt) REVERT: B 637 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7854 (tm-30) REVERT: B 670 MET cc_start: 0.8816 (mtp) cc_final: 0.8317 (mtp) REVERT: B 761 LYS cc_start: 0.8375 (mtpp) cc_final: 0.7689 (pttt) REVERT: B 807 MET cc_start: 0.9199 (mmm) cc_final: 0.8657 (mmt) REVERT: C 399 THR cc_start: 0.8006 (t) cc_final: 0.7792 (t) REVERT: C 408 MET cc_start: 0.6750 (tpp) cc_final: 0.6242 (tpt) REVERT: C 434 LYS cc_start: 0.8999 (tptt) cc_final: 0.8478 (pttp) REVERT: C 435 HIS cc_start: 0.7534 (t-90) cc_final: 0.7308 (t-170) REVERT: C 537 SER cc_start: 0.9218 (p) cc_final: 0.8410 (t) REVERT: C 540 LEU cc_start: 0.9181 (tt) cc_final: 0.8969 (mm) REVERT: C 585 MET cc_start: 0.8451 (mmt) cc_final: 0.7885 (mmt) REVERT: C 591 ILE cc_start: 0.8350 (mp) cc_final: 0.7969 (mt) REVERT: C 626 VAL cc_start: 0.9100 (t) cc_final: 0.8779 (p) REVERT: C 637 GLU cc_start: 0.8316 (tt0) cc_final: 0.7421 (mp0) REVERT: C 709 ASN cc_start: 0.8712 (t0) cc_final: 0.8139 (t0) REVERT: C 710 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8540 (mt-10) REVERT: C 714 GLN cc_start: 0.7352 (mt0) cc_final: 0.6352 (tp40) REVERT: C 720 THR cc_start: 0.8071 (p) cc_final: 0.7010 (p) REVERT: C 728 ASP cc_start: 0.7544 (t70) cc_final: 0.6763 (t70) REVERT: C 1016 ASN cc_start: 0.8676 (m-40) cc_final: 0.8331 (t0) REVERT: C 1022 PHE cc_start: 0.8333 (m-10) cc_final: 0.7397 (m-10) REVERT: C 1175 LEU cc_start: 0.9327 (mt) cc_final: 0.9043 (mt) REVERT: C 1219 CYS cc_start: 0.8562 (m) cc_final: 0.7983 (m) REVERT: D 408 MET cc_start: 0.7245 (mmm) cc_final: 0.6945 (mmm) REVERT: D 418 ASN cc_start: 0.6580 (m-40) cc_final: 0.4628 (p0) REVERT: D 497 SER cc_start: 0.8654 (m) cc_final: 0.8317 (t) REVERT: D 504 ILE cc_start: 0.8978 (pt) cc_final: 0.8662 (mt) REVERT: D 509 LYS cc_start: 0.7906 (pmtt) cc_final: 0.7510 (tppt) REVERT: D 569 ASN cc_start: 0.5652 (m-40) cc_final: 0.5202 (m-40) REVERT: D 590 ASP cc_start: 0.7646 (p0) cc_final: 0.7371 (m-30) REVERT: D 591 ILE cc_start: 0.8505 (pt) cc_final: 0.8279 (pt) REVERT: D 710 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8115 (mt-10) REVERT: D 747 ASN cc_start: 0.8795 (t0) cc_final: 0.8573 (t0) REVERT: D 807 MET cc_start: 0.8962 (mmm) cc_final: 0.8693 (mmt) outliers start: 4 outliers final: 2 residues processed: 655 average time/residue: 0.2823 time to fit residues: 265.9294 Evaluate side-chains 372 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 370 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 181 optimal weight: 0.1980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN A 575 ASN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 GLN B 586 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN C 508 GLN C 587 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1186 GLN D 586 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16094 Z= 0.210 Angle : 0.570 7.108 21754 Z= 0.307 Chirality : 0.041 0.151 2442 Planarity : 0.005 0.042 2678 Dihedral : 5.904 58.362 2178 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.12 % Allowed : 4.25 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.93 (0.16), residues: 1990 helix: -0.79 (0.14), residues: 1054 sheet: -1.65 (0.38), residues: 154 loop : -1.72 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 766 HIS 0.005 0.001 HIS A1181 PHE 0.013 0.002 PHE C1188 TYR 0.023 0.002 TYR A 732 ARG 0.004 0.001 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 470 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8890 (tptt) cc_final: 0.8541 (tmmt) REVERT: A 537 SER cc_start: 0.9048 (p) cc_final: 0.8765 (t) REVERT: A 585 MET cc_start: 0.8433 (mmt) cc_final: 0.7824 (mmt) REVERT: A 589 CYS cc_start: 0.7184 (t) cc_final: 0.6673 (t) REVERT: A 591 ILE cc_start: 0.8237 (mp) cc_final: 0.7911 (pt) REVERT: A 619 ASN cc_start: 0.8693 (t0) cc_final: 0.8380 (t0) REVERT: A 637 GLU cc_start: 0.8096 (tt0) cc_final: 0.7530 (mp0) REVERT: A 708 MET cc_start: 0.8248 (mpp) cc_final: 0.6844 (mpp) REVERT: A 1022 PHE cc_start: 0.8530 (m-10) cc_final: 0.8313 (m-10) REVERT: A 1169 PHE cc_start: 0.8192 (m-80) cc_final: 0.7871 (m-80) REVERT: A 1175 LEU cc_start: 0.9370 (mt) cc_final: 0.8860 (tp) REVERT: A 1219 CYS cc_start: 0.8880 (m) cc_final: 0.8666 (m) REVERT: B 407 MET cc_start: 0.8201 (mtp) cc_final: 0.7963 (mtp) REVERT: B 503 MET cc_start: 0.8954 (tmm) cc_final: 0.8605 (tmm) REVERT: B 509 LYS cc_start: 0.7771 (pttm) cc_final: 0.7562 (tppt) REVERT: B 542 LEU cc_start: 0.8616 (mt) cc_final: 0.8369 (mt) REVERT: B 546 PHE cc_start: 0.6717 (m-10) cc_final: 0.6460 (m-80) REVERT: B 637 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7764 (tm-30) REVERT: B 638 ASP cc_start: 0.7434 (m-30) cc_final: 0.7228 (m-30) REVERT: B 761 LYS cc_start: 0.8607 (mtpp) cc_final: 0.7720 (mtmm) REVERT: B 807 MET cc_start: 0.8920 (mmm) cc_final: 0.8401 (mmt) REVERT: C 434 LYS cc_start: 0.8974 (tptt) cc_final: 0.8610 (tmmt) REVERT: C 476 ILE cc_start: 0.8973 (mp) cc_final: 0.8702 (mp) REVERT: C 585 MET cc_start: 0.8564 (mmt) cc_final: 0.7869 (mmt) REVERT: C 591 ILE cc_start: 0.8198 (mp) cc_final: 0.7850 (pt) REVERT: C 637 GLU cc_start: 0.8081 (tt0) cc_final: 0.7446 (mp0) REVERT: C 720 THR cc_start: 0.8449 (p) cc_final: 0.6928 (p) REVERT: C 734 ILE cc_start: 0.9068 (mt) cc_final: 0.8738 (mt) REVERT: C 1022 PHE cc_start: 0.8602 (m-10) cc_final: 0.8319 (m-10) REVERT: C 1219 CYS cc_start: 0.8720 (m) cc_final: 0.8207 (m) REVERT: D 408 MET cc_start: 0.7174 (mmm) cc_final: 0.6903 (mmm) REVERT: D 411 ASN cc_start: 0.7191 (t0) cc_final: 0.6976 (t0) REVERT: D 418 ASN cc_start: 0.6577 (m-40) cc_final: 0.4836 (p0) REVERT: D 425 CYS cc_start: 0.8372 (m) cc_final: 0.8125 (m) REVERT: D 432 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8534 (tp) REVERT: D 479 LEU cc_start: 0.8556 (mt) cc_final: 0.8343 (mt) REVERT: D 503 MET cc_start: 0.8660 (tmm) cc_final: 0.8424 (tmm) REVERT: D 670 MET cc_start: 0.8326 (mtm) cc_final: 0.7931 (mtp) REVERT: D 710 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8198 (mt-10) REVERT: D 763 LYS cc_start: 0.8689 (tttm) cc_final: 0.8335 (tptm) REVERT: D 815 CYS cc_start: 0.7249 (m) cc_final: 0.6909 (t) outliers start: 2 outliers final: 0 residues processed: 470 average time/residue: 0.2596 time to fit residues: 185.1287 Evaluate side-chains 320 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 0.0270 chunk 151 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 181 optimal weight: 0.0000 chunk 196 optimal weight: 0.0070 chunk 162 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 overall best weight: 0.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 508 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 HIS A1186 GLN A1202 HIS ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 HIS D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16094 Z= 0.139 Angle : 0.511 6.358 21754 Z= 0.272 Chirality : 0.039 0.147 2442 Planarity : 0.004 0.039 2678 Dihedral : 5.559 71.350 2178 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.84 (0.18), residues: 1990 helix: 0.32 (0.16), residues: 1048 sheet: -1.40 (0.39), residues: 166 loop : -1.51 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1032 HIS 0.004 0.001 HIS C1181 PHE 0.016 0.001 PHE C1169 TYR 0.021 0.001 TYR A 732 ARG 0.003 0.000 ARG C 715 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 473 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8706 (t) cc_final: 0.8149 (t) REVERT: A 425 CYS cc_start: 0.8648 (m) cc_final: 0.8440 (p) REVERT: A 434 LYS cc_start: 0.8930 (tptt) cc_final: 0.8523 (tmmt) REVERT: A 506 LYS cc_start: 0.7252 (ttmm) cc_final: 0.6791 (ttpt) REVERT: A 537 SER cc_start: 0.9204 (p) cc_final: 0.8875 (t) REVERT: A 585 MET cc_start: 0.8413 (mmt) cc_final: 0.7679 (mmt) REVERT: A 589 CYS cc_start: 0.7138 (t) cc_final: 0.6834 (t) REVERT: A 591 ILE cc_start: 0.8204 (mp) cc_final: 0.7849 (pt) REVERT: A 637 GLU cc_start: 0.8153 (tt0) cc_final: 0.7345 (mp0) REVERT: A 805 LEU cc_start: 0.8690 (mt) cc_final: 0.8327 (tt) REVERT: A 1022 PHE cc_start: 0.8459 (m-10) cc_final: 0.8062 (m-10) REVERT: A 1033 CYS cc_start: 0.7854 (m) cc_final: 0.7650 (m) REVERT: A 1139 LEU cc_start: 0.8875 (tp) cc_final: 0.8517 (tp) REVERT: A 1169 PHE cc_start: 0.8060 (m-80) cc_final: 0.7758 (m-80) REVERT: A 1175 LEU cc_start: 0.9239 (mt) cc_final: 0.8925 (tp) REVERT: A 1211 CYS cc_start: 0.8955 (p) cc_final: 0.8491 (p) REVERT: A 1219 CYS cc_start: 0.8720 (m) cc_final: 0.8169 (m) REVERT: B 407 MET cc_start: 0.8173 (mtp) cc_final: 0.7891 (mtp) REVERT: B 503 MET cc_start: 0.8979 (tmm) cc_final: 0.8723 (tmm) REVERT: B 504 ILE cc_start: 0.9124 (pt) cc_final: 0.8799 (pt) REVERT: B 509 LYS cc_start: 0.7815 (pttm) cc_final: 0.7550 (tppt) REVERT: B 542 LEU cc_start: 0.8480 (mt) cc_final: 0.8240 (mp) REVERT: B 633 ILE cc_start: 0.8694 (pt) cc_final: 0.7945 (pt) REVERT: B 638 ASP cc_start: 0.7237 (m-30) cc_final: 0.6922 (t0) REVERT: B 693 VAL cc_start: 0.8696 (t) cc_final: 0.8495 (t) REVERT: B 721 MET cc_start: 0.8891 (ptt) cc_final: 0.8373 (ppp) REVERT: B 761 LYS cc_start: 0.8606 (mtpp) cc_final: 0.7819 (mtmm) REVERT: C 434 LYS cc_start: 0.8993 (tptt) cc_final: 0.8495 (pttp) REVERT: C 435 HIS cc_start: 0.8677 (t-170) cc_final: 0.8247 (t-90) REVERT: C 476 ILE cc_start: 0.8900 (mp) cc_final: 0.8639 (mp) REVERT: C 585 MET cc_start: 0.8535 (mmt) cc_final: 0.7805 (mmt) REVERT: C 591 ILE cc_start: 0.8119 (mp) cc_final: 0.7833 (pt) REVERT: C 619 ASN cc_start: 0.8413 (t0) cc_final: 0.8027 (t0) REVERT: C 637 GLU cc_start: 0.7966 (tt0) cc_final: 0.7103 (mp0) REVERT: C 705 GLU cc_start: 0.7488 (pm20) cc_final: 0.7045 (mp0) REVERT: C 734 ILE cc_start: 0.9020 (mt) cc_final: 0.8718 (mt) REVERT: C 770 LYS cc_start: 0.6847 (mptt) cc_final: 0.6508 (mppt) REVERT: C 797 TYR cc_start: 0.8291 (m-10) cc_final: 0.8035 (m-10) REVERT: C 1022 PHE cc_start: 0.8510 (m-10) cc_final: 0.8273 (m-10) REVERT: C 1025 THR cc_start: 0.9049 (m) cc_final: 0.8821 (p) REVERT: C 1172 LEU cc_start: 0.9150 (mm) cc_final: 0.8843 (tp) REVERT: C 1182 MET cc_start: 0.8146 (mmt) cc_final: 0.7937 (mmt) REVERT: C 1211 CYS cc_start: 0.8983 (p) cc_final: 0.8556 (p) REVERT: C 1219 CYS cc_start: 0.8828 (m) cc_final: 0.8340 (m) REVERT: C 1224 SER cc_start: 0.8993 (t) cc_final: 0.8713 (p) REVERT: D 408 MET cc_start: 0.7045 (mmm) cc_final: 0.6707 (mmm) REVERT: D 418 ASN cc_start: 0.6501 (m-40) cc_final: 0.5170 (p0) REVERT: D 432 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8435 (tp) REVERT: D 479 LEU cc_start: 0.8593 (mt) cc_final: 0.8166 (mp) REVERT: D 503 MET cc_start: 0.8839 (tmm) cc_final: 0.8480 (tmm) REVERT: D 590 ASP cc_start: 0.7585 (p0) cc_final: 0.7186 (m-30) REVERT: D 591 ILE cc_start: 0.8450 (pt) cc_final: 0.8156 (pt) REVERT: D 789 LEU cc_start: 0.8993 (tp) cc_final: 0.8711 (tp) REVERT: D 807 MET cc_start: 0.8931 (mmm) cc_final: 0.8646 (tpp) REVERT: D 815 CYS cc_start: 0.7151 (m) cc_final: 0.6906 (t) outliers start: 2 outliers final: 0 residues processed: 473 average time/residue: 0.2382 time to fit residues: 173.2253 Evaluate side-chains 338 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 95 optimal weight: 0.0980 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A1163 ASN A1186 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1163 ASN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16094 Z= 0.256 Angle : 0.575 7.434 21754 Z= 0.308 Chirality : 0.042 0.148 2442 Planarity : 0.004 0.039 2678 Dihedral : 5.794 83.125 2178 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.60 (0.18), residues: 1990 helix: 0.56 (0.16), residues: 1050 sheet: -1.51 (0.38), residues: 156 loop : -1.42 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1204 HIS 0.008 0.001 HIS C1181 PHE 0.019 0.002 PHE C1143 TYR 0.023 0.002 TYR A 732 ARG 0.003 0.000 ARG C 675 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 424 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8738 (t) cc_final: 0.8242 (t) REVERT: A 425 CYS cc_start: 0.8699 (m) cc_final: 0.8492 (p) REVERT: A 431 GLU cc_start: 0.8236 (mp0) cc_final: 0.7938 (mp0) REVERT: A 434 LYS cc_start: 0.8912 (tptt) cc_final: 0.8442 (pttp) REVERT: A 537 SER cc_start: 0.9186 (p) cc_final: 0.8901 (t) REVERT: A 585 MET cc_start: 0.8471 (mmt) cc_final: 0.7860 (mmt) REVERT: A 589 CYS cc_start: 0.7374 (t) cc_final: 0.7118 (t) REVERT: A 637 GLU cc_start: 0.8136 (tt0) cc_final: 0.7310 (mp0) REVERT: A 768 TYR cc_start: 0.7575 (m-80) cc_final: 0.7326 (m-80) REVERT: A 805 LEU cc_start: 0.8710 (mt) cc_final: 0.8363 (tt) REVERT: A 1139 LEU cc_start: 0.8813 (tp) cc_final: 0.8456 (tp) REVERT: A 1143 PHE cc_start: 0.8337 (p90) cc_final: 0.8015 (p90) REVERT: A 1169 PHE cc_start: 0.8111 (m-80) cc_final: 0.7765 (m-80) REVERT: A 1219 CYS cc_start: 0.8767 (m) cc_final: 0.8315 (m) REVERT: B 407 MET cc_start: 0.7950 (mtp) cc_final: 0.7718 (mtp) REVERT: B 503 MET cc_start: 0.8942 (tmm) cc_final: 0.8504 (tmm) REVERT: B 504 ILE cc_start: 0.9234 (pt) cc_final: 0.8882 (pt) REVERT: B 509 LYS cc_start: 0.8018 (pttm) cc_final: 0.7715 (tppt) REVERT: B 546 PHE cc_start: 0.6662 (m-10) cc_final: 0.6110 (m-80) REVERT: B 657 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7474 (tp30) REVERT: B 670 MET cc_start: 0.8759 (mtp) cc_final: 0.8536 (ttm) REVERT: B 721 MET cc_start: 0.8844 (ptt) cc_final: 0.8180 (ppp) REVERT: B 761 LYS cc_start: 0.8782 (mtpp) cc_final: 0.7974 (mtmm) REVERT: B 807 MET cc_start: 0.9094 (tpp) cc_final: 0.8679 (mmt) REVERT: C 434 LYS cc_start: 0.8936 (tptt) cc_final: 0.8479 (pttp) REVERT: C 585 MET cc_start: 0.8504 (mmt) cc_final: 0.7857 (mmt) REVERT: C 591 ILE cc_start: 0.8285 (mp) cc_final: 0.7970 (pt) REVERT: C 613 ILE cc_start: 0.9311 (mt) cc_final: 0.8923 (mt) REVERT: C 619 ASN cc_start: 0.8645 (t0) cc_final: 0.8255 (t0) REVERT: C 637 GLU cc_start: 0.8024 (tt0) cc_final: 0.7033 (mp0) REVERT: C 638 ASP cc_start: 0.8222 (p0) cc_final: 0.7974 (p0) REVERT: C 734 ILE cc_start: 0.8903 (mt) cc_final: 0.8538 (mt) REVERT: C 1022 PHE cc_start: 0.8613 (m-10) cc_final: 0.8359 (m-10) REVERT: C 1143 PHE cc_start: 0.8720 (p90) cc_final: 0.8519 (p90) REVERT: C 1172 LEU cc_start: 0.9228 (mm) cc_final: 0.9008 (mm) REVERT: C 1182 MET cc_start: 0.8270 (mmt) cc_final: 0.8055 (mmt) REVERT: C 1211 CYS cc_start: 0.9197 (p) cc_final: 0.8844 (p) REVERT: C 1219 CYS cc_start: 0.8673 (m) cc_final: 0.8268 (m) REVERT: D 408 MET cc_start: 0.6963 (mmm) cc_final: 0.6689 (mmm) REVERT: D 411 ASN cc_start: 0.7640 (t0) cc_final: 0.7381 (t0) REVERT: D 432 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8432 (tp) REVERT: D 479 LEU cc_start: 0.8601 (mt) cc_final: 0.8334 (mt) REVERT: D 503 MET cc_start: 0.8736 (tmm) cc_final: 0.8270 (tmm) REVERT: D 585 MET cc_start: 0.8784 (mmm) cc_final: 0.8559 (mmm) REVERT: D 693 VAL cc_start: 0.8766 (t) cc_final: 0.8546 (t) REVERT: D 765 LYS cc_start: 0.8299 (pttp) cc_final: 0.8006 (tmmt) REVERT: D 815 CYS cc_start: 0.7383 (m) cc_final: 0.7146 (t) outliers start: 3 outliers final: 0 residues processed: 425 average time/residue: 0.2368 time to fit residues: 155.0498 Evaluate side-chains 312 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 619 ASN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS C 508 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1186 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16094 Z= 0.420 Angle : 0.701 8.216 21754 Z= 0.376 Chirality : 0.046 0.171 2442 Planarity : 0.005 0.043 2678 Dihedral : 6.403 83.477 2178 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.18 % Allowed : 4.25 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.97 (0.18), residues: 1990 helix: 0.29 (0.15), residues: 1044 sheet: -1.61 (0.38), residues: 156 loop : -1.66 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1204 HIS 0.014 0.002 HIS C1181 PHE 0.041 0.003 PHE A1022 TYR 0.028 0.003 TYR A 732 ARG 0.007 0.001 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 377 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8291 (mp0) cc_final: 0.7904 (mp0) REVERT: A 434 LYS cc_start: 0.8948 (tptt) cc_final: 0.8564 (tmmt) REVERT: A 537 SER cc_start: 0.9210 (p) cc_final: 0.8864 (t) REVERT: A 585 MET cc_start: 0.8603 (mmt) cc_final: 0.7961 (mmt) REVERT: A 637 GLU cc_start: 0.8342 (tt0) cc_final: 0.7381 (mp0) REVERT: A 768 TYR cc_start: 0.7473 (m-80) cc_final: 0.7225 (m-80) REVERT: A 805 LEU cc_start: 0.8742 (mt) cc_final: 0.8507 (tt) REVERT: A 1020 LEU cc_start: 0.8632 (tp) cc_final: 0.8424 (tp) REVERT: A 1022 PHE cc_start: 0.8344 (m-80) cc_final: 0.7053 (m-80) REVERT: A 1139 LEU cc_start: 0.8870 (tp) cc_final: 0.8486 (tp) REVERT: A 1169 PHE cc_start: 0.8112 (m-80) cc_final: 0.7834 (m-80) REVERT: A 1219 CYS cc_start: 0.8824 (m) cc_final: 0.8397 (m) REVERT: B 503 MET cc_start: 0.8852 (tmm) cc_final: 0.8354 (tmm) REVERT: B 504 ILE cc_start: 0.9214 (pt) cc_final: 0.8851 (pt) REVERT: B 509 LYS cc_start: 0.8056 (pttm) cc_final: 0.7711 (tppt) REVERT: B 546 PHE cc_start: 0.7023 (m-10) cc_final: 0.6576 (m-80) REVERT: B 657 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7997 (mm-30) REVERT: B 693 VAL cc_start: 0.8818 (t) cc_final: 0.8480 (p) REVERT: B 721 MET cc_start: 0.8819 (ptt) cc_final: 0.8032 (ppp) REVERT: B 761 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8146 (mtmm) REVERT: B 807 MET cc_start: 0.9073 (tpp) cc_final: 0.8773 (mmt) REVERT: C 434 LYS cc_start: 0.8965 (tptt) cc_final: 0.8592 (tmmt) REVERT: C 541 PHE cc_start: 0.9055 (t80) cc_final: 0.8850 (t80) REVERT: C 585 MET cc_start: 0.8583 (mmt) cc_final: 0.7864 (mmt) REVERT: C 619 ASN cc_start: 0.8732 (t0) cc_final: 0.8457 (t0) REVERT: C 637 GLU cc_start: 0.8213 (tt0) cc_final: 0.7337 (mp0) REVERT: C 638 ASP cc_start: 0.8184 (p0) cc_final: 0.7941 (p0) REVERT: C 705 GLU cc_start: 0.7028 (pm20) cc_final: 0.6730 (pm20) REVERT: C 708 MET cc_start: 0.8060 (mtm) cc_final: 0.7717 (mtt) REVERT: C 734 ILE cc_start: 0.8945 (mt) cc_final: 0.8617 (mt) REVERT: C 1022 PHE cc_start: 0.8762 (m-10) cc_final: 0.8497 (m-10) REVERT: C 1169 PHE cc_start: 0.8176 (m-80) cc_final: 0.7640 (m-80) REVERT: C 1211 CYS cc_start: 0.9273 (p) cc_final: 0.9002 (p) REVERT: C 1219 CYS cc_start: 0.8638 (m) cc_final: 0.8281 (m) REVERT: D 432 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8455 (tp) REVERT: D 503 MET cc_start: 0.8749 (tmm) cc_final: 0.8238 (tmm) REVERT: D 642 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8309 (mp10) REVERT: D 693 VAL cc_start: 0.8807 (t) cc_final: 0.8569 (p) REVERT: D 765 LYS cc_start: 0.8428 (pttp) cc_final: 0.8173 (tmmt) REVERT: D 815 CYS cc_start: 0.7476 (m) cc_final: 0.7135 (t) outliers start: 3 outliers final: 0 residues processed: 379 average time/residue: 0.2374 time to fit residues: 139.8325 Evaluate side-chains 296 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 295 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16094 Z= 0.183 Angle : 0.553 7.839 21754 Z= 0.292 Chirality : 0.041 0.172 2442 Planarity : 0.004 0.043 2678 Dihedral : 5.893 80.720 2178 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.43 (0.18), residues: 1990 helix: 0.79 (0.16), residues: 1040 sheet: -1.25 (0.40), residues: 146 loop : -1.50 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1204 HIS 0.008 0.001 HIS C1181 PHE 0.043 0.001 PHE A1022 TYR 0.021 0.002 TYR B 732 ARG 0.006 0.000 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 407 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8829 (t) cc_final: 0.8381 (t) REVERT: A 425 CYS cc_start: 0.8568 (m) cc_final: 0.8361 (p) REVERT: A 431 GLU cc_start: 0.8296 (mp0) cc_final: 0.7889 (mp0) REVERT: A 434 LYS cc_start: 0.8917 (tptt) cc_final: 0.8484 (pttp) REVERT: A 537 SER cc_start: 0.9173 (p) cc_final: 0.8847 (t) REVERT: A 585 MET cc_start: 0.8541 (mmt) cc_final: 0.7779 (mmt) REVERT: A 637 GLU cc_start: 0.8340 (tt0) cc_final: 0.7476 (mp0) REVERT: A 768 TYR cc_start: 0.7455 (m-80) cc_final: 0.7224 (m-80) REVERT: A 812 ILE cc_start: 0.7769 (tp) cc_final: 0.7464 (mt) REVERT: A 1139 LEU cc_start: 0.8880 (tp) cc_final: 0.8653 (tp) REVERT: A 1143 PHE cc_start: 0.8146 (p90) cc_final: 0.7917 (p90) REVERT: A 1219 CYS cc_start: 0.8831 (m) cc_final: 0.8301 (m) REVERT: B 479 LEU cc_start: 0.8760 (tp) cc_final: 0.8291 (mt) REVERT: B 503 MET cc_start: 0.8912 (tmm) cc_final: 0.8389 (tmm) REVERT: B 504 ILE cc_start: 0.9161 (pt) cc_final: 0.8787 (pt) REVERT: B 509 LYS cc_start: 0.8001 (pttm) cc_final: 0.7642 (tppt) REVERT: B 543 VAL cc_start: 0.8395 (t) cc_final: 0.8152 (m) REVERT: B 546 PHE cc_start: 0.6888 (m-10) cc_final: 0.6151 (m-80) REVERT: B 721 MET cc_start: 0.8834 (ptt) cc_final: 0.8234 (ppp) REVERT: B 761 LYS cc_start: 0.8936 (mtpp) cc_final: 0.8094 (mtmm) REVERT: B 764 ASN cc_start: 0.9092 (t0) cc_final: 0.8891 (t0) REVERT: C 406 VAL cc_start: 0.8791 (t) cc_final: 0.8519 (t) REVERT: C 434 LYS cc_start: 0.8917 (tptt) cc_final: 0.8624 (tmmt) REVERT: C 435 HIS cc_start: 0.8728 (t-170) cc_final: 0.8258 (t-90) REVERT: C 486 GLU cc_start: 0.8337 (tp30) cc_final: 0.8086 (tp30) REVERT: C 585 MET cc_start: 0.8463 (mmt) cc_final: 0.7679 (mmt) REVERT: C 619 ASN cc_start: 0.8651 (t0) cc_final: 0.8344 (t0) REVERT: C 637 GLU cc_start: 0.8086 (tt0) cc_final: 0.7251 (mp0) REVERT: C 638 ASP cc_start: 0.8007 (p0) cc_final: 0.7729 (p0) REVERT: C 734 ILE cc_start: 0.8898 (mt) cc_final: 0.8567 (mt) REVERT: C 769 ASP cc_start: 0.8113 (m-30) cc_final: 0.7869 (m-30) REVERT: C 1022 PHE cc_start: 0.8655 (m-10) cc_final: 0.8336 (m-10) REVERT: C 1169 PHE cc_start: 0.8271 (m-80) cc_final: 0.7975 (m-80) REVERT: C 1182 MET cc_start: 0.8193 (mmt) cc_final: 0.7607 (mmp) REVERT: C 1219 CYS cc_start: 0.8662 (m) cc_final: 0.8079 (m) REVERT: C 1221 MET cc_start: 0.8425 (mmp) cc_final: 0.8053 (mmt) REVERT: D 479 LEU cc_start: 0.8583 (mt) cc_final: 0.8299 (mt) REVERT: D 503 MET cc_start: 0.8757 (tmm) cc_final: 0.8231 (tmm) REVERT: D 693 VAL cc_start: 0.8757 (t) cc_final: 0.8408 (p) outliers start: 1 outliers final: 0 residues processed: 407 average time/residue: 0.2273 time to fit residues: 143.4026 Evaluate side-chains 303 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A1186 GLN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16094 Z= 0.161 Angle : 0.531 7.375 21754 Z= 0.278 Chirality : 0.040 0.204 2442 Planarity : 0.004 0.044 2678 Dihedral : 5.659 75.763 2178 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.06 % Allowed : 1.65 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.19 (0.19), residues: 1990 helix: 0.98 (0.16), residues: 1046 sheet: -1.15 (0.38), residues: 170 loop : -1.39 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1204 HIS 0.008 0.001 HIS C1181 PHE 0.024 0.001 PHE A 541 TYR 0.018 0.001 TYR A 424 ARG 0.006 0.000 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 389 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8310 (mp0) cc_final: 0.7820 (mp0) REVERT: A 434 LYS cc_start: 0.8883 (tptt) cc_final: 0.8581 (tmmt) REVERT: A 537 SER cc_start: 0.9173 (p) cc_final: 0.8894 (t) REVERT: A 580 SER cc_start: 0.9113 (t) cc_final: 0.8881 (t) REVERT: A 585 MET cc_start: 0.8534 (mmt) cc_final: 0.7717 (mmt) REVERT: A 637 GLU cc_start: 0.8314 (tt0) cc_final: 0.7379 (mp0) REVERT: A 647 TYR cc_start: 0.4815 (m-80) cc_final: 0.4595 (m-80) REVERT: A 768 TYR cc_start: 0.7481 (m-80) cc_final: 0.7246 (m-80) REVERT: A 807 MET cc_start: 0.8460 (pmm) cc_final: 0.8202 (pmm) REVERT: A 812 ILE cc_start: 0.7778 (tp) cc_final: 0.7463 (mt) REVERT: A 1022 PHE cc_start: 0.8390 (m-80) cc_final: 0.8107 (m-80) REVERT: A 1139 LEU cc_start: 0.8839 (tp) cc_final: 0.8513 (tp) REVERT: A 1212 LEU cc_start: 0.8379 (tp) cc_final: 0.8163 (tp) REVERT: A 1219 CYS cc_start: 0.8635 (m) cc_final: 0.8069 (m) REVERT: B 407 MET cc_start: 0.7989 (mtp) cc_final: 0.7750 (mtp) REVERT: B 503 MET cc_start: 0.8934 (tmm) cc_final: 0.8447 (tmm) REVERT: B 504 ILE cc_start: 0.9171 (pt) cc_final: 0.8861 (pt) REVERT: B 509 LYS cc_start: 0.8024 (pttm) cc_final: 0.7721 (tppt) REVERT: B 543 VAL cc_start: 0.8414 (t) cc_final: 0.7876 (t) REVERT: B 546 PHE cc_start: 0.6774 (m-10) cc_final: 0.6198 (m-80) REVERT: B 693 VAL cc_start: 0.8744 (t) cc_final: 0.8189 (t) REVERT: B 715 ARG cc_start: 0.7855 (tpt90) cc_final: 0.7601 (tpt90) REVERT: B 721 MET cc_start: 0.8736 (ptt) cc_final: 0.8254 (ppp) REVERT: B 761 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8017 (mtmm) REVERT: C 434 LYS cc_start: 0.8875 (tptt) cc_final: 0.8600 (tmmt) REVERT: C 435 HIS cc_start: 0.8732 (t-170) cc_final: 0.8218 (t-90) REVERT: C 585 MET cc_start: 0.8405 (mmt) cc_final: 0.7687 (mmt) REVERT: C 619 ASN cc_start: 0.8482 (t0) cc_final: 0.8139 (t0) REVERT: C 637 GLU cc_start: 0.8088 (tt0) cc_final: 0.7241 (mp0) REVERT: C 638 ASP cc_start: 0.8028 (p0) cc_final: 0.7737 (p0) REVERT: C 732 TYR cc_start: 0.8421 (m-10) cc_final: 0.8186 (m-10) REVERT: C 734 ILE cc_start: 0.8850 (mt) cc_final: 0.8523 (mt) REVERT: C 770 LYS cc_start: 0.6676 (mptt) cc_final: 0.6172 (mppt) REVERT: C 1022 PHE cc_start: 0.8514 (m-10) cc_final: 0.8208 (m-10) REVERT: C 1122 LYS cc_start: 0.8048 (mttp) cc_final: 0.7539 (mmtp) REVERT: C 1143 PHE cc_start: 0.8152 (p90) cc_final: 0.7759 (p90) REVERT: C 1169 PHE cc_start: 0.8194 (m-80) cc_final: 0.7690 (m-80) REVERT: C 1182 MET cc_start: 0.8177 (mmt) cc_final: 0.7589 (mmt) REVERT: C 1219 CYS cc_start: 0.8665 (m) cc_final: 0.8099 (m) REVERT: C 1221 MET cc_start: 0.8444 (mmp) cc_final: 0.8108 (mmt) REVERT: D 407 MET cc_start: 0.7760 (mtp) cc_final: 0.7497 (mtp) REVERT: D 479 LEU cc_start: 0.8672 (mt) cc_final: 0.8453 (mt) REVERT: D 503 MET cc_start: 0.8836 (tmm) cc_final: 0.8273 (tmm) REVERT: D 693 VAL cc_start: 0.8765 (t) cc_final: 0.8387 (p) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.2352 time to fit residues: 141.1353 Evaluate side-chains 300 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 151 optimal weight: 0.2980 chunk 175 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1186 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16094 Z= 0.196 Angle : 0.553 7.619 21754 Z= 0.289 Chirality : 0.041 0.172 2442 Planarity : 0.004 0.044 2678 Dihedral : 5.591 72.341 2178 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.06 % Allowed : 1.30 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.14 (0.19), residues: 1990 helix: 1.01 (0.16), residues: 1042 sheet: -1.05 (0.40), residues: 152 loop : -1.36 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 766 HIS 0.007 0.001 HIS A1181 PHE 0.023 0.001 PHE C 541 TYR 0.015 0.001 TYR C 424 ARG 0.005 0.000 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 387 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8757 (t) cc_final: 0.8546 (t) REVERT: A 431 GLU cc_start: 0.8321 (mp0) cc_final: 0.7841 (mp0) REVERT: A 434 LYS cc_start: 0.8894 (tptt) cc_final: 0.8609 (tmmt) REVERT: A 537 SER cc_start: 0.9237 (p) cc_final: 0.8906 (t) REVERT: A 585 MET cc_start: 0.8554 (mmt) cc_final: 0.7744 (mmt) REVERT: A 637 GLU cc_start: 0.8311 (tt0) cc_final: 0.7407 (mp0) REVERT: A 812 ILE cc_start: 0.7835 (tp) cc_final: 0.7538 (mt) REVERT: A 1175 LEU cc_start: 0.9300 (mt) cc_final: 0.9035 (tp) REVERT: A 1212 LEU cc_start: 0.8480 (tp) cc_final: 0.8122 (tp) REVERT: A 1219 CYS cc_start: 0.8693 (m) cc_final: 0.8155 (m) REVERT: B 407 MET cc_start: 0.8024 (mtp) cc_final: 0.7769 (mtp) REVERT: B 503 MET cc_start: 0.8918 (tmm) cc_final: 0.8418 (tmm) REVERT: B 504 ILE cc_start: 0.9180 (pt) cc_final: 0.8827 (pt) REVERT: B 509 LYS cc_start: 0.8005 (pttm) cc_final: 0.7692 (tppt) REVERT: B 543 VAL cc_start: 0.8259 (t) cc_final: 0.8048 (m) REVERT: B 546 PHE cc_start: 0.6848 (m-10) cc_final: 0.6081 (m-80) REVERT: B 591 ILE cc_start: 0.8406 (pt) cc_final: 0.8200 (pt) REVERT: B 693 VAL cc_start: 0.8791 (t) cc_final: 0.8245 (t) REVERT: B 715 ARG cc_start: 0.7917 (tpt90) cc_final: 0.7664 (tpt90) REVERT: B 721 MET cc_start: 0.8779 (ptt) cc_final: 0.8229 (ppp) REVERT: B 761 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8018 (mtmm) REVERT: B 764 ASN cc_start: 0.9103 (t0) cc_final: 0.8883 (t0) REVERT: B 807 MET cc_start: 0.9072 (tpp) cc_final: 0.8747 (mmt) REVERT: C 434 LYS cc_start: 0.8860 (tptt) cc_final: 0.8470 (pttp) REVERT: C 585 MET cc_start: 0.8488 (mmt) cc_final: 0.7707 (mmt) REVERT: C 619 ASN cc_start: 0.8547 (t0) cc_final: 0.8190 (t0) REVERT: C 637 GLU cc_start: 0.8151 (tt0) cc_final: 0.7296 (mp0) REVERT: C 638 ASP cc_start: 0.8188 (p0) cc_final: 0.7820 (p0) REVERT: C 719 ASP cc_start: 0.7742 (t0) cc_final: 0.7466 (t70) REVERT: C 734 ILE cc_start: 0.8858 (mt) cc_final: 0.8509 (mt) REVERT: C 770 LYS cc_start: 0.6653 (mptt) cc_final: 0.6422 (mttp) REVERT: C 1122 LYS cc_start: 0.8001 (mttp) cc_final: 0.7735 (mttm) REVERT: C 1169 PHE cc_start: 0.8168 (m-80) cc_final: 0.7683 (m-80) REVERT: C 1182 MET cc_start: 0.8257 (mmt) cc_final: 0.7675 (mmt) REVERT: C 1219 CYS cc_start: 0.8629 (m) cc_final: 0.8123 (m) REVERT: D 407 MET cc_start: 0.7827 (mtp) cc_final: 0.7508 (mtp) REVERT: D 479 LEU cc_start: 0.8629 (mt) cc_final: 0.8376 (mt) REVERT: D 503 MET cc_start: 0.8812 (tmm) cc_final: 0.8244 (tmm) REVERT: D 693 VAL cc_start: 0.8758 (t) cc_final: 0.8397 (p) outliers start: 1 outliers final: 0 residues processed: 387 average time/residue: 0.2489 time to fit residues: 149.2420 Evaluate side-chains 297 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1186 GLN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16094 Z= 0.175 Angle : 0.548 7.487 21754 Z= 0.287 Chirality : 0.040 0.147 2442 Planarity : 0.004 0.043 2678 Dihedral : 5.474 70.551 2178 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.06 % Allowed : 0.77 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.08 (0.19), residues: 1990 helix: 1.07 (0.16), residues: 1050 sheet: -1.17 (0.38), residues: 172 loop : -1.35 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1204 HIS 0.007 0.001 HIS A1181 PHE 0.054 0.001 PHE A1022 TYR 0.017 0.001 TYR C 732 ARG 0.005 0.000 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 389 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8315 (mp0) cc_final: 0.7855 (mp0) REVERT: A 434 LYS cc_start: 0.8881 (tptt) cc_final: 0.8621 (tmmt) REVERT: A 497 SER cc_start: 0.7896 (m) cc_final: 0.7592 (t) REVERT: A 537 SER cc_start: 0.9242 (p) cc_final: 0.8891 (t) REVERT: A 585 MET cc_start: 0.8516 (mmt) cc_final: 0.7692 (mmt) REVERT: A 637 GLU cc_start: 0.8134 (tt0) cc_final: 0.7331 (mp0) REVERT: A 647 TYR cc_start: 0.4852 (m-80) cc_final: 0.4611 (m-80) REVERT: A 812 ILE cc_start: 0.7857 (tp) cc_final: 0.7527 (mt) REVERT: A 1034 GLN cc_start: 0.8420 (pm20) cc_final: 0.8191 (pm20) REVERT: A 1175 LEU cc_start: 0.9298 (mt) cc_final: 0.9017 (tp) REVERT: A 1212 LEU cc_start: 0.8472 (tp) cc_final: 0.8184 (tp) REVERT: A 1218 THR cc_start: 0.8864 (m) cc_final: 0.8664 (p) REVERT: B 407 MET cc_start: 0.7964 (mtp) cc_final: 0.7697 (mtp) REVERT: B 479 LEU cc_start: 0.8738 (tp) cc_final: 0.8383 (mt) REVERT: B 503 MET cc_start: 0.8935 (tmm) cc_final: 0.8419 (tmm) REVERT: B 504 ILE cc_start: 0.9166 (pt) cc_final: 0.8827 (pt) REVERT: B 509 LYS cc_start: 0.8042 (pttm) cc_final: 0.7738 (tppt) REVERT: B 543 VAL cc_start: 0.8299 (t) cc_final: 0.8090 (m) REVERT: B 546 PHE cc_start: 0.6732 (m-10) cc_final: 0.6090 (m-80) REVERT: B 585 MET cc_start: 0.8993 (mmm) cc_final: 0.8504 (mmm) REVERT: B 693 VAL cc_start: 0.8804 (t) cc_final: 0.8299 (t) REVERT: B 721 MET cc_start: 0.8749 (ptt) cc_final: 0.8253 (ppp) REVERT: B 761 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8046 (mtmm) REVERT: B 807 MET cc_start: 0.9071 (tpp) cc_final: 0.8769 (mmt) REVERT: C 412 HIS cc_start: 0.7892 (p90) cc_final: 0.7637 (p90) REVERT: C 434 LYS cc_start: 0.8836 (tptt) cc_final: 0.8600 (tmmt) REVERT: C 585 MET cc_start: 0.8468 (mmt) cc_final: 0.7686 (mmt) REVERT: C 619 ASN cc_start: 0.8534 (t0) cc_final: 0.8170 (t0) REVERT: C 637 GLU cc_start: 0.8155 (tt0) cc_final: 0.7288 (mp0) REVERT: C 638 ASP cc_start: 0.8150 (p0) cc_final: 0.7793 (p0) REVERT: C 719 ASP cc_start: 0.7923 (t0) cc_final: 0.7707 (t0) REVERT: C 770 LYS cc_start: 0.6617 (mptt) cc_final: 0.6370 (mttp) REVERT: C 1022 PHE cc_start: 0.8357 (m-10) cc_final: 0.8036 (m-10) REVERT: C 1122 LYS cc_start: 0.8004 (mttp) cc_final: 0.7559 (mmtp) REVERT: C 1135 TYR cc_start: 0.8681 (t80) cc_final: 0.8359 (t80) REVERT: C 1169 PHE cc_start: 0.8103 (m-80) cc_final: 0.7808 (m-80) REVERT: C 1182 MET cc_start: 0.8250 (mmt) cc_final: 0.7673 (mmt) REVERT: C 1219 CYS cc_start: 0.8717 (m) cc_final: 0.8102 (m) REVERT: D 407 MET cc_start: 0.7738 (mtp) cc_final: 0.7493 (mtp) REVERT: D 479 LEU cc_start: 0.8646 (mt) cc_final: 0.8371 (mt) REVERT: D 503 MET cc_start: 0.8822 (tmm) cc_final: 0.8244 (tmm) REVERT: D 543 VAL cc_start: 0.8315 (t) cc_final: 0.7858 (m) REVERT: D 585 MET cc_start: 0.8948 (mmm) cc_final: 0.8597 (mmm) REVERT: D 693 VAL cc_start: 0.8753 (t) cc_final: 0.8376 (p) REVERT: D 807 MET cc_start: 0.8880 (mmm) cc_final: 0.8663 (mmt) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.2403 time to fit residues: 143.3219 Evaluate side-chains 299 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.9980 chunk 90 optimal weight: 0.0030 chunk 132 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 169 optimal weight: 0.1980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1186 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16094 Z= 0.151 Angle : 0.544 7.842 21754 Z= 0.280 Chirality : 0.040 0.138 2442 Planarity : 0.004 0.043 2678 Dihedral : 5.342 73.667 2178 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.06 % Allowed : 0.30 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.00 (0.19), residues: 1990 helix: 1.13 (0.16), residues: 1058 sheet: -1.10 (0.38), residues: 172 loop : -1.34 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1214 HIS 0.006 0.001 HIS A1181 PHE 0.041 0.001 PHE A1022 TYR 0.018 0.001 TYR C 732 ARG 0.002 0.000 ARG A 485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 396 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8375 (mp0) cc_final: 0.8011 (mp0) REVERT: A 434 LYS cc_start: 0.8854 (tptt) cc_final: 0.8539 (pttp) REVERT: A 498 LEU cc_start: 0.7629 (pp) cc_final: 0.7242 (pp) REVERT: A 537 SER cc_start: 0.9165 (p) cc_final: 0.8876 (t) REVERT: A 585 MET cc_start: 0.8491 (mmt) cc_final: 0.7663 (mmt) REVERT: A 637 GLU cc_start: 0.8182 (tt0) cc_final: 0.7234 (mp0) REVERT: A 705 GLU cc_start: 0.7381 (pp20) cc_final: 0.6573 (pp20) REVERT: A 812 ILE cc_start: 0.7870 (tp) cc_final: 0.7537 (mt) REVERT: A 1034 GLN cc_start: 0.8435 (pm20) cc_final: 0.8141 (pm20) REVERT: A 1212 LEU cc_start: 0.8241 (tp) cc_final: 0.8031 (tp) REVERT: A 1218 THR cc_start: 0.8859 (m) cc_final: 0.8633 (p) REVERT: A 1219 CYS cc_start: 0.8645 (m) cc_final: 0.7843 (m) REVERT: B 407 MET cc_start: 0.7950 (mtp) cc_final: 0.7651 (mtp) REVERT: B 503 MET cc_start: 0.9002 (tmm) cc_final: 0.8457 (tmm) REVERT: B 504 ILE cc_start: 0.9143 (pt) cc_final: 0.8827 (pt) REVERT: B 509 LYS cc_start: 0.8027 (pttm) cc_final: 0.7759 (tppt) REVERT: B 543 VAL cc_start: 0.8285 (t) cc_final: 0.8077 (m) REVERT: B 546 PHE cc_start: 0.6730 (m-10) cc_final: 0.6056 (m-80) REVERT: B 585 MET cc_start: 0.8973 (mmm) cc_final: 0.8635 (mmm) REVERT: B 693 VAL cc_start: 0.8788 (t) cc_final: 0.8235 (p) REVERT: B 721 MET cc_start: 0.8708 (ptt) cc_final: 0.8244 (ppp) REVERT: B 761 LYS cc_start: 0.8734 (mtpp) cc_final: 0.7987 (mtmm) REVERT: B 764 ASN cc_start: 0.9095 (t0) cc_final: 0.8881 (t0) REVERT: B 807 MET cc_start: 0.9022 (tpp) cc_final: 0.8732 (mmt) REVERT: C 585 MET cc_start: 0.8499 (mmt) cc_final: 0.7713 (mmt) REVERT: C 619 ASN cc_start: 0.8484 (t0) cc_final: 0.8130 (t0) REVERT: C 637 GLU cc_start: 0.8111 (tt0) cc_final: 0.7276 (mp0) REVERT: C 638 ASP cc_start: 0.8095 (p0) cc_final: 0.7732 (p0) REVERT: C 734 ILE cc_start: 0.8866 (mt) cc_final: 0.8622 (mm) REVERT: C 770 LYS cc_start: 0.6628 (mptt) cc_final: 0.6268 (mttp) REVERT: C 1022 PHE cc_start: 0.8246 (m-10) cc_final: 0.8040 (m-10) REVERT: C 1122 LYS cc_start: 0.7926 (mttp) cc_final: 0.7569 (mmtp) REVERT: C 1169 PHE cc_start: 0.8135 (m-80) cc_final: 0.7795 (m-80) REVERT: C 1172 LEU cc_start: 0.9209 (mm) cc_final: 0.8976 (mm) REVERT: C 1182 MET cc_start: 0.8229 (mmt) cc_final: 0.7650 (mmt) REVERT: C 1219 CYS cc_start: 0.8666 (m) cc_final: 0.8182 (m) REVERT: D 407 MET cc_start: 0.7759 (mtp) cc_final: 0.7538 (mtp) REVERT: D 503 MET cc_start: 0.8888 (tmm) cc_final: 0.8301 (tmm) REVERT: D 693 VAL cc_start: 0.8729 (t) cc_final: 0.8336 (p) outliers start: 1 outliers final: 0 residues processed: 396 average time/residue: 0.2387 time to fit residues: 145.8075 Evaluate side-chains 308 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.101564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.079739 restraints weight = 45522.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.080601 restraints weight = 29842.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081275 restraints weight = 24943.786| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16094 Z= 0.264 Angle : 0.610 9.266 21754 Z= 0.319 Chirality : 0.042 0.142 2442 Planarity : 0.004 0.043 2678 Dihedral : 5.525 72.681 2178 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.14 (0.19), residues: 1990 helix: 0.99 (0.16), residues: 1060 sheet: -1.11 (0.39), residues: 152 loop : -1.37 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1204 HIS 0.008 0.002 HIS A1181 PHE 0.032 0.002 PHE A1022 TYR 0.023 0.002 TYR C 732 ARG 0.004 0.000 ARG A 545 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3753.28 seconds wall clock time: 69 minutes 18.73 seconds (4158.73 seconds total)