Starting phenix.real_space_refine on Fri Feb 16 20:00:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/02_2024/8ss9_40748_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/02_2024/8ss9_40748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/02_2024/8ss9_40748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/02_2024/8ss9_40748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/02_2024/8ss9_40748_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss9_40748/02_2024/8ss9_40748_updated.pdb" } resolution = 2.72 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= 0.005 sd= 0.179 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: 7 Type Number sf(0) Gaussians P 14 5.49 5 S 104 5.16 5 Na 2 4.78 5 C 10718 2.51 5 N 2540 2.21 5 O 2929 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 926": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 926": "NH1" <-> "NH2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16319 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4639 Classifications: {'peptide': 592} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 574} Chain breaks: 4 Chain: "B" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3134 Classifications: {'peptide': 401} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 387} Chain breaks: 2 Chain: "C" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4639 Classifications: {'peptide': 592} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 574} Chain breaks: 4 Chain: "D" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3134 Classifications: {'peptide': 401} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 387} Chain breaks: 2 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 230 Unusual residues: {' NA': 1, '6ZP': 1, 'CLR': 1, 'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 150 Unusual residues: {' NA': 1, '6ZP': 1, 'PCW': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Unusual residues: {'6ZP': 1, 'CLR': 1, 'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 149 Unusual residues: {'6ZP': 1, 'PCW': 3, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 8.62, per 1000 atoms: 0.53 Number of scatterers: 16319 At special positions: 0 Unit cell: (117.475, 132.275, 134.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 104 16.00 P 14 15.00 Na 2 11.00 F 12 9.00 O 2929 8.00 N 2540 7.00 C 10718 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 A 890 " - pdb=" SG CYS A 900 " 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 C 890 " - pdb=" SG CYS C 900 " 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: 6.12 Conformation dependent library (CDL) restraints added in 2.5 seconds 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 16 sheets defined 50.4% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.830A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 463 through 468 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 545 removed outlier: 3.608A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.761A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 628 removed outlier: 3.863A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 654 through 660 removed outlier: 3.789A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.779A pdb=" N SER A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.734A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 removed outlier: 3.534A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 793 through 819 removed outlier: 3.548A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 857 removed outlier: 3.503A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 920 through 951 removed outlier: 3.717A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Proline residue: A 930 - end of helix removed outlier: 3.704A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 941 " --> pdb=" O PHE A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 989 removed outlier: 3.623A pdb=" N ILE A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 984 " --> pdb=" O TYR A 980 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1033 removed outlier: 3.727A pdb=" N ALA A1010 " --> pdb=" O SER A1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.539A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (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 515 through 518 Processing helix chain 'B' and resid 523 through 544 Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.710A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 625 removed outlier: 3.583A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 removed outlier: 3.528A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 686 through 696 removed outlier: 3.572A pdb=" N SER B 696 " --> pdb=" O ARG B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.538A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 756 removed outlier: 3.611A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 793 through 815 removed outlier: 3.887A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.830A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 463 through 468 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 545 removed outlier: 3.608A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.761A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 628 removed outlier: 3.863A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 654 through 660 removed outlier: 3.789A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.779A pdb=" N SER C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.734A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 755 removed outlier: 3.533A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 793 through 819 removed outlier: 3.548A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 857 removed outlier: 3.503A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 874 No H-bonds generated for 'chain 'C' and resid 872 through 874' Processing helix chain 'C' and resid 920 through 951 removed outlier: 3.716A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) Proline residue: C 930 - end of helix removed outlier: 3.703A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 941 " --> pdb=" O PHE C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 989 removed outlier: 3.623A pdb=" N ILE C 967 " --> pdb=" O GLY C 963 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 984 " --> pdb=" O TYR C 980 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1033 removed outlier: 3.727A pdb=" N ALA C1010 " --> pdb=" O SER C1006 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.539A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (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 515 through 518 Processing helix chain 'D' and resid 523 through 544 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.710A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 removed outlier: 3.584A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 removed outlier: 3.528A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 666 through 676 Processing helix chain 'D' and resid 686 through 696 removed outlier: 3.572A pdb=" N SER D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.538A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 756 removed outlier: 3.611A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 793 through 815 removed outlier: 3.888A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS D 815 " --> pdb=" O LEU D 811 " (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: 3.927A 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: 4.163A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 997 through 999 removed outlier: 3.670A pdb=" N TYR A 998 " --> pdb=" O GLY A 867 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 867 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE A 868 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A 878 " --> pdb=" O ILE A 868 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 394 through 396 removed outlier: 6.763A pdb=" N LYS B 439 " --> pdb=" O VAL B 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.736A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.238A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.133A 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: 3.928A 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: 4.163A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 997 through 999 removed outlier: 3.669A pdb=" N TYR C 998 " --> pdb=" O GLY C 867 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY C 867 " --> pdb=" O TYR C 998 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE C 868 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL C 878 " --> pdb=" O ILE C 868 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 394 through 396 removed outlier: 6.763A pdb=" N LYS D 439 " --> pdb=" O VAL D 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= O, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.736A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.238A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2085 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: 4.83 Time building geometry restraints manager: 6.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.17: 8 1.17 - 1.34: 4658 1.34 - 1.51: 5590 1.51 - 1.69: 6210 1.69 - 1.86: 190 Bond restraints: 16656 Sorted by residual: bond pdb=" C14 CLR A1107 " pdb=" C8 CLR A1107 " ideal model delta sigma weight residual 1.519 0.991 0.528 2.00e-02 2.50e+03 6.96e+02 bond pdb=" C14 CLR C1107 " pdb=" C8 CLR C1107 " ideal model delta sigma weight residual 1.519 0.993 0.526 2.00e-02 2.50e+03 6.90e+02 bond pdb=" C11 CLR A1107 " pdb=" C12 CLR A1107 " ideal model delta sigma weight residual 1.531 1.099 0.432 2.00e-02 2.50e+03 4.68e+02 bond pdb=" C11 CLR C1107 " pdb=" C12 CLR C1107 " ideal model delta sigma weight residual 1.531 1.099 0.432 2.00e-02 2.50e+03 4.66e+02 bond pdb=" C7 CLR C1107 " pdb=" C8 CLR C1107 " ideal model delta sigma weight residual 1.525 1.208 0.317 2.00e-02 2.50e+03 2.51e+02 ... (remaining 16651 not shown) Histogram of bond angle deviations from ideal: 84.38 - 102.69: 87 102.69 - 121.00: 17734 121.00 - 139.31: 4611 139.31 - 157.62: 0 157.62 - 175.93: 4 Bond angle restraints: 22436 Sorted by residual: angle pdb=" C12 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C18 CLR A1107 " ideal model delta sigma weight residual 111.01 84.38 26.63 3.00e+00 1.11e-01 7.88e+01 angle pdb=" C12 CLR C1107 " pdb=" C13 CLR C1107 " pdb=" C18 CLR C1107 " ideal model delta sigma weight residual 111.01 84.88 26.13 3.00e+00 1.11e-01 7.59e+01 angle pdb=" C14 CLR C1107 " pdb=" C13 CLR C1107 " pdb=" C18 CLR C1107 " ideal model delta sigma weight residual 112.24 90.51 21.73 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C14 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C18 CLR A1107 " ideal model delta sigma weight residual 112.24 91.23 21.01 3.00e+00 1.11e-01 4.91e+01 angle pdb=" C12 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C17 CLR A1107 " ideal model delta sigma weight residual 116.52 133.32 -16.80 3.00e+00 1.11e-01 3.13e+01 ... (remaining 22431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 9713 35.94 - 71.89: 258 71.89 - 107.83: 49 107.83 - 143.77: 5 143.77 - 179.71: 17 Dihedral angle restraints: 10042 sinusoidal: 4348 harmonic: 5694 Sorted by residual: dihedral pdb=" CA GLN C 508 " pdb=" C GLN C 508 " pdb=" N LYS C 509 " pdb=" CA LYS C 509 " ideal model delta harmonic sigma weight residual 180.00 142.34 37.66 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA GLN A 508 " pdb=" C GLN A 508 " pdb=" N LYS A 509 " pdb=" CA LYS A 509 " ideal model delta harmonic sigma weight residual 180.00 142.46 37.54 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA CYS A 589 " pdb=" C CYS A 589 " pdb=" N ASP A 590 " pdb=" CA ASP A 590 " ideal model delta harmonic sigma weight residual 180.00 145.43 34.57 0 5.00e+00 4.00e-02 4.78e+01 ... (remaining 10039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 2434 1.020 - 2.041: 2 2.041 - 3.061: 2 3.061 - 4.081: 0 4.081 - 5.102: 4 Chirality restraints: 2442 Sorted by residual: chirality pdb=" C17 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C16 CLR A1107 " pdb=" C20 CLR A1107 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.10 2.00e-01 2.50e+01 6.51e+02 chirality pdb=" C17 CLR C1107 " pdb=" C13 CLR C1107 " pdb=" C16 CLR C1107 " pdb=" C20 CLR C1107 " both_signs ideal model delta sigma weight residual False 2.55 -2.51 5.06 2.00e-01 2.50e+01 6.40e+02 chirality pdb=" C9 CLR C1107 " pdb=" C10 CLR C1107 " pdb=" C11 CLR C1107 " pdb=" C8 CLR C1107 " both_signs ideal model delta sigma weight residual False -2.45 2.40 -4.84 2.00e-01 2.50e+01 5.87e+02 ... (remaining 2439 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 6ZP C1101 " 0.036 2.00e-02 2.50e+03 3.20e-02 2.30e+01 pdb=" C03 6ZP C1101 " 0.030 2.00e-02 2.50e+03 pdb=" C04 6ZP C1101 " 0.028 2.00e-02 2.50e+03 pdb=" C05 6ZP C1101 " 0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP C1101 " -0.031 2.00e-02 2.50e+03 pdb=" C07 6ZP C1101 " -0.023 2.00e-02 2.50e+03 pdb=" C08 6ZP C1101 " -0.004 2.00e-02 2.50e+03 pdb=" C09 6ZP C1101 " 0.025 2.00e-02 2.50e+03 pdb=" N01 6ZP C1101 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP A1101 " -0.035 2.00e-02 2.50e+03 3.08e-02 2.14e+01 pdb=" C03 6ZP A1101 " -0.028 2.00e-02 2.50e+03 pdb=" C04 6ZP A1101 " -0.027 2.00e-02 2.50e+03 pdb=" C05 6ZP A1101 " -0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP A1101 " 0.030 2.00e-02 2.50e+03 pdb=" C07 6ZP A1101 " 0.022 2.00e-02 2.50e+03 pdb=" C08 6ZP A1101 " 0.004 2.00e-02 2.50e+03 pdb=" C09 6ZP A1101 " -0.025 2.00e-02 2.50e+03 pdb=" N01 6ZP A1101 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP B1101 " -0.022 2.00e-02 2.50e+03 1.81e-02 7.36e+00 pdb=" C03 6ZP B1101 " -0.016 2.00e-02 2.50e+03 pdb=" C04 6ZP B1101 " -0.013 2.00e-02 2.50e+03 pdb=" C05 6ZP B1101 " -0.003 2.00e-02 2.50e+03 pdb=" C06 6ZP B1101 " 0.019 2.00e-02 2.50e+03 pdb=" C07 6ZP B1101 " 0.014 2.00e-02 2.50e+03 pdb=" C08 6ZP B1101 " -0.006 2.00e-02 2.50e+03 pdb=" C09 6ZP B1101 " -0.011 2.00e-02 2.50e+03 pdb=" N01 6ZP B1101 " 0.037 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5082 2.84 - 3.36: 14662 3.36 - 3.87: 27024 3.87 - 4.39: 32558 4.39 - 4.90: 54079 Nonbonded interactions: 133405 Sorted by model distance: nonbonded pdb=" OH TYR D 533 " pdb=" O LEU D 577 " model vdw 2.329 2.440 nonbonded pdb=" OH TYR B 533 " pdb=" O LEU B 577 " model vdw 2.329 2.440 nonbonded pdb=" OE1 GLN A 586 " pdb=" O HOH A1201 " model vdw 2.353 2.440 nonbonded pdb=" OE1 GLN C 586 " pdb=" O HOH C1201 " model vdw 2.355 2.440 nonbonded pdb=" OE1 GLN D 586 " pdb=" O HOH D1201 " model vdw 2.359 2.440 ... (remaining 133400 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' and (resid 392 through 1034 or resid 1101 through 1107)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 392 through 817 or resid 1101 through 1105)) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.610 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 43.190 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.014 0.528 16656 Z= 0.818 Angle : 1.360 26.627 22436 Z= 0.647 Chirality : 0.232 5.102 2442 Planarity : 0.007 0.063 2694 Dihedral : 17.975 179.713 6392 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.89 % Favored : 95.80 % Rotamer: Outliers : 0.36 % Allowed : 4.77 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -4.92 (0.13), residues: 1954 helix: -3.58 (0.09), residues: 1078 sheet: -2.07 (0.32), residues: 182 loop : -2.68 (0.19), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 861 HIS 0.003 0.001 HIS C 883 PHE 0.019 0.002 PHE D 667 TYR 0.030 0.002 TYR D 702 ARG 0.009 0.001 ARG C 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 323 time to evaluate : 1.818 Fit side-chains REVERT: A 697 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7773 (mptt) REVERT: B 594 ARG cc_start: 0.6371 (mtt90) cc_final: 0.5361 (mmm-85) REVERT: B 708 MET cc_start: 0.7829 (mmp) cc_final: 0.7497 (mmm) REVERT: C 435 HIS cc_start: 0.7645 (m90) cc_final: 0.7261 (t70) REVERT: C 569 ASN cc_start: 0.2051 (OUTLIER) cc_final: 0.1831 (t0) REVERT: C 594 ARG cc_start: 0.5929 (tpt-90) cc_final: 0.4611 (tmm160) REVERT: C 637 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6691 (mt-10) REVERT: C 865 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6135 (mt-10) REVERT: D 431 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 585 MET cc_start: 0.5263 (mpt) cc_final: 0.4956 (mmt) REVERT: D 663 LYS cc_start: 0.7610 (mttp) cc_final: 0.7357 (mttp) REVERT: D 708 MET cc_start: 0.7775 (mmp) cc_final: 0.7435 (mmm) outliers start: 6 outliers final: 0 residues processed: 329 average time/residue: 1.3694 time to fit residues: 495.8019 Evaluate side-chains 194 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 569 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 0.0060 chunk 94 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 575 ASN A 587 GLN A 726 ASN A 747 ASN A 947 ASN A 990 ASN B 392 GLN B 747 ASN B 756 GLN C 412 HIS C 587 GLN C 726 ASN C 747 ASN C 947 ASN D 392 GLN D 587 GLN D 756 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16656 Z= 0.195 Angle : 0.825 34.950 22436 Z= 0.361 Chirality : 0.060 1.540 2442 Planarity : 0.005 0.054 2694 Dihedral : 19.742 177.727 2802 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 2.92 % Allowed : 11.32 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.17), residues: 1954 helix: -0.53 (0.14), residues: 1070 sheet: -1.78 (0.35), residues: 178 loop : -2.22 (0.20), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 766 HIS 0.009 0.001 HIS C 412 PHE 0.015 0.002 PHE B 579 TYR 0.016 0.001 TYR A1001 ARG 0.006 0.001 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 220 time to evaluate : 1.739 Fit side-chains REVERT: A 408 MET cc_start: 0.7647 (mmm) cc_final: 0.7096 (mmm) REVERT: A 697 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7878 (mptt) REVERT: A 924 MET cc_start: 0.4453 (mmm) cc_final: 0.4190 (mmm) REVERT: A 966 PHE cc_start: 0.7212 (m-80) cc_final: 0.6950 (m-80) REVERT: B 435 HIS cc_start: 0.7810 (m-70) cc_final: 0.6612 (t-90) REVERT: B 594 ARG cc_start: 0.6377 (mtt90) cc_final: 0.5631 (mmm160) REVERT: C 393 LYS cc_start: 0.7640 (mtmt) cc_final: 0.7173 (mttt) REVERT: C 408 MET cc_start: 0.7157 (mtp) cc_final: 0.6938 (mmt) REVERT: C 435 HIS cc_start: 0.7598 (m90) cc_final: 0.7326 (t70) REVERT: C 738 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7761 (tttp) REVERT: C 834 ARG cc_start: 0.6499 (ptm160) cc_final: 0.5817 (mtm180) REVERT: C 865 GLU cc_start: 0.6448 (mt-10) cc_final: 0.6076 (mt-10) REVERT: C 880 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.5227 (ptt) REVERT: C 924 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.5841 (mmm) REVERT: D 435 HIS cc_start: 0.7742 (m-70) cc_final: 0.6617 (t-90) REVERT: D 587 GLN cc_start: 0.6600 (mm-40) cc_final: 0.5752 (mp10) outliers start: 49 outliers final: 16 residues processed: 252 average time/residue: 1.1896 time to fit residues: 335.2280 Evaluate side-chains 205 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 149 optimal weight: 20.0000 chunk 122 optimal weight: 0.0970 chunk 49 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 194 optimal weight: 0.0170 chunk 160 optimal weight: 0.0170 chunk 178 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS B 392 GLN B 747 ASN D 392 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16656 Z= 0.149 Angle : 0.741 34.460 22436 Z= 0.321 Chirality : 0.060 1.585 2442 Planarity : 0.004 0.055 2694 Dihedral : 19.040 179.944 2800 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.16 % Allowed : 12.75 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 1954 helix: 0.98 (0.16), residues: 1068 sheet: -1.57 (0.35), residues: 190 loop : -1.98 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 766 HIS 0.023 0.002 HIS A 412 PHE 0.020 0.001 PHE C 541 TYR 0.021 0.001 TYR C1001 ARG 0.007 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 191 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7965 (mmm) cc_final: 0.7308 (mmm) REVERT: A 650 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7818 (tt) REVERT: A 697 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8053 (mptt) REVERT: A 966 PHE cc_start: 0.7116 (m-80) cc_final: 0.6796 (m-80) REVERT: B 435 HIS cc_start: 0.7704 (m-70) cc_final: 0.6589 (t-90) REVERT: B 594 ARG cc_start: 0.6332 (mtt90) cc_final: 0.5405 (mmm-85) REVERT: B 708 MET cc_start: 0.7880 (mmp) cc_final: 0.7560 (mmm) REVERT: C 393 LYS cc_start: 0.7663 (mtmt) cc_final: 0.7183 (mttt) REVERT: C 411 ASN cc_start: 0.6523 (OUTLIER) cc_final: 0.6141 (p0) REVERT: C 435 HIS cc_start: 0.7728 (m90) cc_final: 0.7396 (t70) REVERT: C 785 SER cc_start: 0.6676 (m) cc_final: 0.6454 (p) REVERT: C 865 GLU cc_start: 0.6405 (mt-10) cc_final: 0.6012 (mt-10) REVERT: C 880 MET cc_start: 0.5495 (ptp) cc_final: 0.5209 (ptt) REVERT: C 924 MET cc_start: 0.6336 (mmt) cc_final: 0.5892 (mmm) REVERT: D 435 HIS cc_start: 0.7624 (m-70) cc_final: 0.6590 (t-90) REVERT: D 527 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6209 (mmm) REVERT: D 587 GLN cc_start: 0.6572 (mm-40) cc_final: 0.5843 (mp10) REVERT: D 684 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7380 (mpp80) REVERT: D 708 MET cc_start: 0.7868 (mmp) cc_final: 0.7551 (mmm) REVERT: D 748 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8490 (mt) outliers start: 53 outliers final: 19 residues processed: 227 average time/residue: 1.1156 time to fit residues: 284.6893 Evaluate side-chains 198 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 748 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 191 optimal weight: 0.2980 chunk 94 optimal weight: 0.3980 chunk 171 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS B 392 GLN B 709 ASN C 990 ASN D 392 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16656 Z= 0.180 Angle : 0.743 34.341 22436 Z= 0.321 Chirality : 0.061 1.600 2442 Planarity : 0.004 0.060 2694 Dihedral : 18.701 178.555 2800 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.52 % Allowed : 13.59 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 1954 helix: 1.53 (0.16), residues: 1070 sheet: -1.39 (0.36), residues: 190 loop : -1.81 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 766 HIS 0.010 0.001 HIS A 412 PHE 0.020 0.001 PHE A 960 TYR 0.022 0.001 TYR C1001 ARG 0.007 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 174 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7972 (mmm) cc_final: 0.7429 (mmm) REVERT: A 650 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8011 (tt) REVERT: A 697 LYS cc_start: 0.8274 (mtmm) cc_final: 0.8070 (mptt) REVERT: A 966 PHE cc_start: 0.7037 (m-80) cc_final: 0.6779 (m-80) REVERT: B 435 HIS cc_start: 0.7673 (m-70) cc_final: 0.6516 (t-90) REVERT: B 594 ARG cc_start: 0.6427 (mtt90) cc_final: 0.5480 (mmm-85) REVERT: C 393 LYS cc_start: 0.7736 (mtmt) cc_final: 0.7163 (mttt) REVERT: C 411 ASN cc_start: 0.6533 (OUTLIER) cc_final: 0.6167 (p0) REVERT: C 435 HIS cc_start: 0.7754 (m90) cc_final: 0.7399 (t-90) REVERT: C 486 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: C 509 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.5918 (tttm) REVERT: C 684 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6998 (ptp90) REVERT: C 865 GLU cc_start: 0.6400 (mt-10) cc_final: 0.5990 (mt-10) REVERT: C 880 MET cc_start: 0.5604 (ptp) cc_final: 0.5343 (ptt) REVERT: C 884 SER cc_start: 0.6594 (OUTLIER) cc_final: 0.6301 (m) REVERT: C 924 MET cc_start: 0.6314 (mmt) cc_final: 0.5902 (mmm) REVERT: D 435 HIS cc_start: 0.7704 (m-70) cc_final: 0.6561 (t-90) REVERT: D 442 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7819 (mp) REVERT: D 503 MET cc_start: 0.9263 (ttp) cc_final: 0.9059 (ttm) REVERT: D 527 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6251 (mmm) REVERT: D 587 GLN cc_start: 0.6665 (mm-40) cc_final: 0.6176 (mp10) REVERT: D 684 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7426 (mpp80) outliers start: 59 outliers final: 25 residues processed: 215 average time/residue: 1.1890 time to fit residues: 286.6688 Evaluate side-chains 201 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.0570 chunk 108 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 163 optimal weight: 0.2980 chunk 132 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 GLN D 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16656 Z= 0.152 Angle : 0.720 33.990 22436 Z= 0.308 Chirality : 0.061 1.622 2442 Planarity : 0.004 0.056 2694 Dihedral : 18.483 179.598 2800 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.52 % Allowed : 14.00 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1954 helix: 1.87 (0.16), residues: 1068 sheet: -1.29 (0.37), residues: 192 loop : -1.71 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 578 HIS 0.009 0.001 HIS A 412 PHE 0.019 0.001 PHE A 960 TYR 0.030 0.001 TYR C1032 ARG 0.008 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 174 time to evaluate : 1.845 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.7986 (mmm) cc_final: 0.7467 (mmm) REVERT: A 416 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7473 (pp20) REVERT: A 435 HIS cc_start: 0.7704 (m90) cc_final: 0.7403 (t70) REVERT: A 635 SER cc_start: 0.8421 (m) cc_final: 0.8195 (p) REVERT: A 650 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7912 (tt) REVERT: A 697 LYS cc_start: 0.8240 (mtmm) cc_final: 0.8003 (mptt) REVERT: A 966 PHE cc_start: 0.7107 (m-80) cc_final: 0.6844 (m-80) REVERT: B 435 HIS cc_start: 0.7596 (m-70) cc_final: 0.6509 (t-90) REVERT: B 503 MET cc_start: 0.9249 (ttp) cc_final: 0.8998 (ttm) REVERT: B 587 GLN cc_start: 0.5691 (OUTLIER) cc_final: 0.4753 (mp10) REVERT: B 594 ARG cc_start: 0.6447 (mtt90) cc_final: 0.5723 (mmm160) REVERT: C 393 LYS cc_start: 0.7780 (mtmt) cc_final: 0.7245 (mttt) REVERT: C 408 MET cc_start: 0.7367 (mmt) cc_final: 0.7006 (mmt) REVERT: C 435 HIS cc_start: 0.7769 (m90) cc_final: 0.7401 (t-90) REVERT: C 486 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: C 509 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.5881 (tttm) REVERT: C 684 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6914 (ptp90) REVERT: C 865 GLU cc_start: 0.6436 (mt-10) cc_final: 0.5977 (mt-10) REVERT: C 884 SER cc_start: 0.6565 (OUTLIER) cc_final: 0.6275 (m) REVERT: C 924 MET cc_start: 0.6250 (mmt) cc_final: 0.5863 (mmm) REVERT: D 435 HIS cc_start: 0.7584 (m-70) cc_final: 0.6482 (t-90) REVERT: D 503 MET cc_start: 0.9250 (ttp) cc_final: 0.9044 (ttm) REVERT: D 527 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6268 (mmm) REVERT: D 587 GLN cc_start: 0.6696 (mm-40) cc_final: 0.6256 (mp10) outliers start: 59 outliers final: 27 residues processed: 217 average time/residue: 1.1701 time to fit residues: 284.4298 Evaluate side-chains 206 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 191 optimal weight: 0.7980 chunk 159 optimal weight: 0.0980 chunk 88 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 GLN D 392 GLN ** 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: 0.7679 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16656 Z= 0.159 Angle : 0.726 33.845 22436 Z= 0.310 Chirality : 0.061 1.632 2442 Planarity : 0.004 0.057 2694 Dihedral : 18.370 179.261 2800 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.10 % Allowed : 15.14 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 1954 helix: 2.04 (0.16), residues: 1066 sheet: -1.18 (0.38), residues: 192 loop : -1.68 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 578 HIS 0.009 0.001 HIS A 412 PHE 0.020 0.001 PHE A 960 TYR 0.023 0.001 TYR C1001 ARG 0.008 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 170 time to evaluate : 1.961 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.7986 (mmm) cc_final: 0.7469 (mmm) REVERT: A 416 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: A 571 PHE cc_start: 0.6134 (m-10) cc_final: 0.5921 (m-80) REVERT: A 635 SER cc_start: 0.8408 (m) cc_final: 0.8186 (p) REVERT: A 697 LYS cc_start: 0.8243 (mtmm) cc_final: 0.8028 (mptt) REVERT: A 966 PHE cc_start: 0.7095 (m-80) cc_final: 0.6825 (m-80) REVERT: B 435 HIS cc_start: 0.7644 (m-70) cc_final: 0.6519 (t-90) REVERT: B 503 MET cc_start: 0.9220 (ttp) cc_final: 0.9008 (ttm) REVERT: B 587 GLN cc_start: 0.5685 (OUTLIER) cc_final: 0.4733 (mp10) REVERT: B 594 ARG cc_start: 0.6428 (mtt90) cc_final: 0.5564 (mmm-85) REVERT: C 393 LYS cc_start: 0.7748 (mtmt) cc_final: 0.7233 (mttt) REVERT: C 411 ASN cc_start: 0.6456 (OUTLIER) cc_final: 0.6150 (p0) REVERT: C 435 HIS cc_start: 0.7819 (m90) cc_final: 0.7464 (t70) REVERT: C 486 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: C 509 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5895 (tttm) REVERT: C 684 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6922 (ptp90) REVERT: C 865 GLU cc_start: 0.6334 (mt-10) cc_final: 0.5973 (tt0) REVERT: C 884 SER cc_start: 0.6512 (OUTLIER) cc_final: 0.6265 (m) REVERT: C 924 MET cc_start: 0.6240 (mmt) cc_final: 0.5879 (mmm) REVERT: D 435 HIS cc_start: 0.7643 (m-70) cc_final: 0.6493 (t-90) REVERT: D 503 MET cc_start: 0.9302 (ttp) cc_final: 0.9088 (ttm) REVERT: D 527 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.6256 (mmm) REVERT: D 587 GLN cc_start: 0.6699 (mm-40) cc_final: 0.6307 (mp10) outliers start: 52 outliers final: 23 residues processed: 205 average time/residue: 1.2230 time to fit residues: 280.6068 Evaluate side-chains 197 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 GLN C 412 HIS C 587 GLN D 392 GLN D 709 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16656 Z= 0.348 Angle : 0.805 34.158 22436 Z= 0.357 Chirality : 0.064 1.617 2442 Planarity : 0.005 0.061 2694 Dihedral : 18.544 178.993 2800 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.34 % Allowed : 15.14 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1954 helix: 1.54 (0.16), residues: 1086 sheet: -1.25 (0.35), residues: 200 loop : -1.88 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 606 HIS 0.010 0.002 HIS A 412 PHE 0.020 0.002 PHE A 960 TYR 0.022 0.002 TYR A1001 ARG 0.006 0.001 ARG C 628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 176 time to evaluate : 1.791 Fit side-chains REVERT: A 408 MET cc_start: 0.7938 (mmm) cc_final: 0.7415 (mmm) REVERT: A 416 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: A 571 PHE cc_start: 0.6211 (m-10) cc_final: 0.5962 (m-80) REVERT: A 629 MET cc_start: 0.8460 (mtt) cc_final: 0.8184 (mtt) REVERT: A 650 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8082 (tt) REVERT: A 952 ARG cc_start: 0.4910 (mtp180) cc_final: 0.4580 (tmt170) REVERT: B 435 HIS cc_start: 0.7777 (m-70) cc_final: 0.6499 (t-90) REVERT: B 587 GLN cc_start: 0.5993 (OUTLIER) cc_final: 0.4900 (mp10) REVERT: B 594 ARG cc_start: 0.6596 (mtt90) cc_final: 0.5671 (mmm-85) REVERT: C 411 ASN cc_start: 0.6694 (OUTLIER) cc_final: 0.6356 (p0) REVERT: C 486 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7581 (mm-30) REVERT: C 509 LYS cc_start: 0.6383 (OUTLIER) cc_final: 0.5936 (tttm) REVERT: C 629 MET cc_start: 0.8475 (mtt) cc_final: 0.8178 (mtt) REVERT: C 684 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6987 (ptp90) REVERT: C 865 GLU cc_start: 0.6349 (mt-10) cc_final: 0.5979 (tt0) REVERT: C 884 SER cc_start: 0.6750 (OUTLIER) cc_final: 0.6435 (m) REVERT: C 901 PHE cc_start: 0.5953 (m-10) cc_final: 0.5741 (m-10) REVERT: C 924 MET cc_start: 0.6396 (mmt) cc_final: 0.5945 (mmm) REVERT: D 435 HIS cc_start: 0.7788 (m-70) cc_final: 0.6465 (t-90) REVERT: D 594 ARG cc_start: 0.6748 (mtt90) cc_final: 0.5602 (mmm-85) outliers start: 56 outliers final: 22 residues processed: 215 average time/residue: 1.2643 time to fit residues: 302.4642 Evaluate side-chains 197 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 741 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 0.0470 chunk 113 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 GLN D 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16656 Z= 0.200 Angle : 0.750 33.790 22436 Z= 0.324 Chirality : 0.062 1.637 2442 Planarity : 0.004 0.059 2694 Dihedral : 18.372 178.883 2800 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.16 % Allowed : 15.97 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1954 helix: 1.87 (0.16), residues: 1066 sheet: -1.16 (0.35), residues: 200 loop : -1.76 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 606 HIS 0.016 0.002 HIS C 412 PHE 0.022 0.001 PHE A 960 TYR 0.024 0.001 TYR C1001 ARG 0.009 0.001 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 173 time to evaluate : 1.739 Fit side-chains REVERT: A 392 GLN cc_start: 0.5440 (OUTLIER) cc_final: 0.5203 (pp30) REVERT: A 408 MET cc_start: 0.7868 (mmm) cc_final: 0.7335 (mmm) REVERT: A 416 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: A 571 PHE cc_start: 0.6181 (m-10) cc_final: 0.5964 (m-80) REVERT: A 629 MET cc_start: 0.8295 (mtt) cc_final: 0.8008 (mtt) REVERT: A 952 ARG cc_start: 0.4896 (mtp180) cc_final: 0.4561 (tmt170) REVERT: B 435 HIS cc_start: 0.7750 (m-70) cc_final: 0.6496 (t-90) REVERT: B 594 ARG cc_start: 0.6581 (mtt90) cc_final: 0.5670 (mmm-85) REVERT: C 408 MET cc_start: 0.7701 (mmt) cc_final: 0.7287 (mmm) REVERT: C 411 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.6540 (p0) REVERT: C 509 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.5933 (tttm) REVERT: C 585 MET cc_start: 0.6788 (mpt) cc_final: 0.6402 (mpt) REVERT: C 629 MET cc_start: 0.8340 (mtt) cc_final: 0.8049 (mtt) REVERT: C 684 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6990 (ptp90) REVERT: C 865 GLU cc_start: 0.6301 (mt-10) cc_final: 0.6054 (tt0) REVERT: C 884 SER cc_start: 0.6565 (OUTLIER) cc_final: 0.6326 (m) REVERT: C 924 MET cc_start: 0.6299 (mmt) cc_final: 0.5851 (mmm) REVERT: D 435 HIS cc_start: 0.7761 (m-70) cc_final: 0.6459 (t-90) REVERT: D 527 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6433 (mtt) REVERT: D 594 ARG cc_start: 0.6733 (mtt90) cc_final: 0.5577 (mmm-85) outliers start: 53 outliers final: 22 residues processed: 206 average time/residue: 1.2961 time to fit residues: 295.9985 Evaluate side-chains 197 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 392 GLN Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 631 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 166 optimal weight: 0.0770 chunk 177 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 160 optimal weight: 0.3980 chunk 168 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 GLN C 412 HIS D 392 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16656 Z= 0.178 Angle : 0.736 33.599 22436 Z= 0.316 Chirality : 0.062 1.650 2442 Planarity : 0.004 0.058 2694 Dihedral : 18.255 179.594 2800 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.68 % Allowed : 16.87 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1954 helix: 2.03 (0.16), residues: 1066 sheet: -1.14 (0.36), residues: 202 loop : -1.70 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 606 HIS 0.008 0.001 HIS A 412 PHE 0.022 0.001 PHE A 960 TYR 0.024 0.001 TYR A1001 ARG 0.009 0.000 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 170 time to evaluate : 1.819 Fit side-chains REVERT: A 392 GLN cc_start: 0.5437 (OUTLIER) cc_final: 0.5202 (pp30) REVERT: A 408 MET cc_start: 0.7855 (mmm) cc_final: 0.7360 (mmm) REVERT: A 416 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7492 (pp20) REVERT: A 571 PHE cc_start: 0.6078 (m-10) cc_final: 0.5855 (m-80) REVERT: A 629 MET cc_start: 0.8244 (mtt) cc_final: 0.7960 (mtt) REVERT: A 952 ARG cc_start: 0.4891 (mtp180) cc_final: 0.4554 (tmt170) REVERT: B 435 HIS cc_start: 0.7736 (m-70) cc_final: 0.6520 (t-90) REVERT: B 594 ARG cc_start: 0.6593 (mtt90) cc_final: 0.5711 (mmm-85) REVERT: C 393 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7406 (mttt) REVERT: C 408 MET cc_start: 0.7540 (mmt) cc_final: 0.7224 (mmm) REVERT: C 411 ASN cc_start: 0.6564 (OUTLIER) cc_final: 0.6227 (p0) REVERT: C 509 LYS cc_start: 0.6156 (OUTLIER) cc_final: 0.5941 (tttm) REVERT: C 585 MET cc_start: 0.6854 (mpt) cc_final: 0.6491 (mpt) REVERT: C 629 MET cc_start: 0.8298 (mtt) cc_final: 0.8004 (mtt) REVERT: C 684 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6968 (ptp90) REVERT: C 865 GLU cc_start: 0.6352 (mt-10) cc_final: 0.6076 (tt0) REVERT: C 884 SER cc_start: 0.6567 (OUTLIER) cc_final: 0.6311 (m) REVERT: C 924 MET cc_start: 0.6283 (mmt) cc_final: 0.5888 (mmm) REVERT: D 435 HIS cc_start: 0.7746 (m-70) cc_final: 0.6475 (t-90) REVERT: D 503 MET cc_start: 0.9323 (ttp) cc_final: 0.9083 (ttm) REVERT: D 527 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6393 (mtt) REVERT: D 594 ARG cc_start: 0.6777 (mtt90) cc_final: 0.5634 (mmm-85) outliers start: 45 outliers final: 24 residues processed: 201 average time/residue: 1.2580 time to fit residues: 281.7792 Evaluate side-chains 196 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 748 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 89 optimal weight: 0.0070 chunk 130 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 392 GLN D 392 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16656 Z= 0.212 Angle : 0.749 33.605 22436 Z= 0.325 Chirality : 0.062 1.655 2442 Planarity : 0.004 0.059 2694 Dihedral : 18.213 179.729 2800 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.09 % Allowed : 17.58 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 1954 helix: 2.02 (0.16), residues: 1066 sheet: -1.13 (0.36), residues: 202 loop : -1.67 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 606 HIS 0.011 0.001 HIS C 412 PHE 0.022 0.001 PHE A 960 TYR 0.026 0.001 TYR A1001 ARG 0.008 0.001 ARG B 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.622 Fit side-chains REVERT: A 392 GLN cc_start: 0.5437 (OUTLIER) cc_final: 0.5194 (pp30) REVERT: A 408 MET cc_start: 0.7861 (mmm) cc_final: 0.7361 (mmm) REVERT: A 416 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7494 (pp20) REVERT: A 571 PHE cc_start: 0.6005 (m-10) cc_final: 0.5789 (m-80) REVERT: A 629 MET cc_start: 0.8282 (mtt) cc_final: 0.8031 (mtt) REVERT: A 952 ARG cc_start: 0.4874 (mtp180) cc_final: 0.4542 (tmt170) REVERT: B 435 HIS cc_start: 0.7746 (m-70) cc_final: 0.6520 (t-90) REVERT: B 594 ARG cc_start: 0.6753 (mtt90) cc_final: 0.5864 (mmm-85) REVERT: C 393 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7450 (mttt) REVERT: C 629 MET cc_start: 0.8332 (mtt) cc_final: 0.8050 (mtt) REVERT: C 684 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6970 (ptp90) REVERT: C 865 GLU cc_start: 0.6346 (mt-10) cc_final: 0.6085 (tt0) REVERT: C 884 SER cc_start: 0.6589 (OUTLIER) cc_final: 0.6332 (m) REVERT: C 924 MET cc_start: 0.6177 (mmt) cc_final: 0.5899 (mmm) REVERT: D 435 HIS cc_start: 0.7754 (m-70) cc_final: 0.6482 (t-90) REVERT: D 527 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6425 (mtt) REVERT: D 594 ARG cc_start: 0.6820 (mtt90) cc_final: 0.5659 (mmm-85) outliers start: 35 outliers final: 24 residues processed: 194 average time/residue: 1.3055 time to fit residues: 281.3570 Evaluate side-chains 194 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1032 TYR Chi-restraints excluded: chain D residue 392 GLN Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 783 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS D 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.181822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137262 restraints weight = 17917.577| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.84 r_work: 0.3128 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16656 Z= 0.285 Angle : 0.777 33.712 22436 Z= 0.341 Chirality : 0.064 1.655 2442 Planarity : 0.004 0.061 2694 Dihedral : 18.240 179.518 2800 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.21 % Allowed : 17.40 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1954 helix: 1.86 (0.16), residues: 1066 sheet: -1.24 (0.35), residues: 202 loop : -1.70 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 606 HIS 0.013 0.002 HIS C 412 PHE 0.022 0.002 PHE A 960 TYR 0.026 0.002 TYR C1001 ARG 0.008 0.001 ARG B 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5631.29 seconds wall clock time: 101 minutes 22.04 seconds (6082.04 seconds total)