Starting phenix.real_space_refine on Wed Feb 21 21:10:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud8_20734/02_2024/6ud8_20734_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud8_20734/02_2024/6ud8_20734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud8_20734/02_2024/6ud8_20734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud8_20734/02_2024/6ud8_20734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud8_20734/02_2024/6ud8_20734_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud8_20734/02_2024/6ud8_20734_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 4 5.49 5 S 120 5.16 5 C 10682 2.51 5 N 2524 2.21 5 O 2838 1.98 5 F 12 1.80 5 H 15482 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 456": "OD1" <-> "OD2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 545": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 37": "OD1" <-> "OD2" Residue "F PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 126": "OD1" <-> "OD2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 456": "OD1" <-> "OD2" Residue "C PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 545": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 32": "OD1" <-> "OD2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 126": "OD1" <-> "OD2" Residue "H PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 31662 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5675 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 5742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5742 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2107 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2147 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 5675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5675 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 5742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5742 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2107 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2147 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'OLC': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'OLC': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'OLC': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'OLC': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.07, per 1000 atoms: 0.44 Number of scatterers: 31662 At special positions: 0 Unit cell: (118.326, 100.204, 146.042, 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 120 16.00 P 4 15.00 F 12 9.00 O 2838 8.00 N 2524 7.00 C 10682 6.00 H 15482 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " 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 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: 25.79 Conformation dependent library (CDL) restraints added in 3.2 seconds 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 10 sheets defined 56.8% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 546 removed outlier: 3.959A pdb=" N CYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 628 Processing helix chain 'A' and resid 637 through 640 No H-bonds generated for 'chain 'A' and resid 637 through 640' Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 686 through 695 removed outlier: 3.694A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 743 through 756 removed outlier: 4.505A pdb=" N LEU A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 793 through 822 removed outlier: 3.719A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 469 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 523 through 543 Processing helix chain 'B' and resid 598 through 626 removed outlier: 3.616A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 667 through 675 Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.562A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 removed outlier: 3.582A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 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 823 removed outlier: 3.631A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 36 removed outlier: 3.611A pdb=" N ALA E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 66 removed outlier: 4.192A pdb=" N ILE E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 84 Processing helix chain 'E' and resid 92 through 106 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 128 through 157 removed outlier: 3.544A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 37 removed outlier: 3.901A pdb=" N ALA F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 67 Processing helix chain 'F' and resid 69 through 84 Processing helix chain 'F' and resid 91 through 107 Proline residue: F 96 - end of helix removed outlier: 3.809A pdb=" N TYR F 105 " --> pdb=" O HIS F 101 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 156 removed outlier: 4.236A pdb=" N GLN F 132 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 420 No H-bonds generated for 'chain 'C' and resid 418 through 420' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 483 through 487 Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 546 removed outlier: 3.958A pdb=" N CYS C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 628 Processing helix chain 'C' and resid 637 through 640 No H-bonds generated for 'chain 'C' and resid 637 through 640' Processing helix chain 'C' and resid 654 through 659 Processing helix chain 'C' and resid 665 through 676 Processing helix chain 'C' and resid 686 through 695 removed outlier: 3.695A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 743 through 756 removed outlier: 4.505A pdb=" N LEU C 748 " --> pdb=" O ASN C 744 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 793 through 822 removed outlier: 3.719A pdb=" N ALA C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 463 through 469 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 523 through 543 Processing helix chain 'D' and resid 598 through 626 removed outlier: 3.615A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 667 through 675 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.562A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 755 removed outlier: 3.581A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 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 823 removed outlier: 3.630A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 36 removed outlier: 3.611A pdb=" N ALA G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 66 removed outlier: 4.191A pdb=" N ILE G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 84 Processing helix chain 'G' and resid 92 through 106 Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 128 through 157 removed outlier: 3.545A pdb=" N PHE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 37 removed outlier: 3.901A pdb=" N ALA H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 67 Processing helix chain 'H' and resid 69 through 84 Processing helix chain 'H' and resid 91 through 107 Proline residue: H 96 - end of helix removed outlier: 3.809A pdb=" N TYR H 105 " --> pdb=" O HIS H 101 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE H 106 " --> pdb=" O PHE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 156 removed outlier: 4.236A pdb=" N GLN H 132 " --> pdb=" O SER H 129 " (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: 3.670A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 500 through 503 removed outlier: 6.682A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 496 through 498 Processing sheet with id= E, first strand: chain 'B' and resid 500 through 503 Processing sheet with id= F, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= G, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.670A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 500 through 503 removed outlier: 6.681A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 496 through 498 Processing sheet with id= J, first strand: chain 'D' and resid 500 through 503 832 hydrogen bonds defined for protein. 2316 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: 11.31 Time building geometry restraints manager: 26.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15430 1.04 - 1.25: 2172 1.25 - 1.45: 5169 1.45 - 1.65: 9107 1.65 - 1.86: 184 Bond restraints: 32062 Sorted by residual: bond pdb=" CAT ZK1 A 902 " pdb=" OAA ZK1 A 902 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" CAU ZK1 C 902 " pdb=" OAB ZK1 C 902 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.33e+01 bond pdb=" CAT ZK1 C 902 " pdb=" OAA ZK1 C 902 " ideal model delta sigma weight residual 1.214 1.396 -0.182 2.00e-02 2.50e+03 8.33e+01 bond pdb=" CAU ZK1 B 902 " pdb=" OAB ZK1 B 902 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.30e+01 bond pdb=" CAU ZK1 A 902 " pdb=" OAB ZK1 A 902 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.29e+01 ... (remaining 32057 not shown) Histogram of bond angle deviations from ideal: 58.60 - 73.67: 4 73.67 - 88.75: 6 88.75 - 103.83: 176 103.83 - 118.91: 42832 118.91 - 133.98: 14554 Bond angle restraints: 57572 Sorted by residual: angle pdb=" C VAL A 445 " pdb=" N GLY A 446 " pdb=" H GLY A 446 " ideal model delta sigma weight residual 125.18 68.75 56.43 3.00e+00 1.11e-01 3.54e+02 angle pdb=" C VAL C 445 " pdb=" N GLY C 446 " pdb=" H GLY C 446 " ideal model delta sigma weight residual 125.18 68.75 56.43 3.00e+00 1.11e-01 3.54e+02 angle pdb=" CA GLY C 446 " pdb=" N GLY C 446 " pdb=" H GLY C 446 " ideal model delta sigma weight residual 114.88 58.60 56.28 3.00e+00 1.11e-01 3.52e+02 angle pdb=" CA GLY A 446 " pdb=" N GLY A 446 " pdb=" H GLY A 446 " ideal model delta sigma weight residual 114.88 58.61 56.27 3.00e+00 1.11e-01 3.52e+02 angle pdb=" CB LEU G 16 " pdb=" CG LEU G 16 " pdb=" HG LEU G 16 " ideal model delta sigma weight residual 109.00 84.70 24.30 3.00e+00 1.11e-01 6.56e+01 ... (remaining 57567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 15088 35.89 - 71.78: 374 71.78 - 107.68: 5 107.68 - 143.57: 9 143.57 - 179.46: 6 Dihedral angle restraints: 15482 sinusoidal: 8114 harmonic: 7368 Sorted by residual: dihedral pdb=" O20 OLC D 901 " pdb=" C21 OLC D 901 " pdb=" C22 OLC D 901 " pdb=" O23 OLC D 901 " ideal model delta sinusoidal sigma weight residual 302.77 123.31 179.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O20 OLC B 901 " pdb=" C21 OLC B 901 " pdb=" C22 OLC B 901 " pdb=" O23 OLC B 901 " ideal model delta sinusoidal sigma weight residual 302.77 123.32 179.45 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C24 OLC B 901 " pdb=" C21 OLC B 901 " pdb=" C22 OLC B 901 " pdb=" O20 OLC B 901 " ideal model delta sinusoidal sigma weight residual -177.22 -3.71 -173.51 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 15479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 2538 0.343 - 0.687: 2 0.687 - 1.030: 0 1.030 - 1.373: 0 1.373 - 1.716: 4 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CG LEU E 16 " pdb=" CB LEU E 16 " pdb=" CD1 LEU E 16 " pdb=" CD2 LEU E 16 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 chirality pdb=" CG LEU G 16 " pdb=" CB LEU G 16 " pdb=" CD1 LEU G 16 " pdb=" CD2 LEU G 16 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.35e+01 chirality pdb=" C22 OLC C 901 " pdb=" C21 OLC C 901 " pdb=" C24 OLC C 901 " pdb=" O23 OLC C 901 " both_signs ideal model delta sigma weight residual False -2.31 -0.80 -1.51 2.00e-01 2.50e+01 5.72e+01 ... (remaining 2541 not shown) Planarity restraints: 4654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLC D 901 " -0.191 2.00e-02 2.50e+03 1.89e-01 3.59e+02 pdb=" C11 OLC D 901 " 0.190 2.00e-02 2.50e+03 pdb=" C8 OLC D 901 " 0.189 2.00e-02 2.50e+03 pdb=" C9 OLC D 901 " -0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC B 901 " 0.191 2.00e-02 2.50e+03 1.89e-01 3.58e+02 pdb=" C11 OLC B 901 " -0.190 2.00e-02 2.50e+03 pdb=" C8 OLC B 901 " -0.189 2.00e-02 2.50e+03 pdb=" C9 OLC B 901 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC A 901 " 0.155 2.00e-02 2.50e+03 1.55e-01 2.39e+02 pdb=" C11 OLC A 901 " -0.155 2.00e-02 2.50e+03 pdb=" C8 OLC A 901 " -0.154 2.00e-02 2.50e+03 pdb=" C9 OLC A 901 " 0.154 2.00e-02 2.50e+03 ... (remaining 4651 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1125 2.15 - 2.76: 60076 2.76 - 3.37: 88970 3.37 - 3.99: 109444 3.99 - 4.60: 174480 Nonbonded interactions: 434095 Sorted by model distance: nonbonded pdb=" H GLY A 446 " pdb=" HA2 GLY A 446 " model vdw 1.536 1.816 nonbonded pdb=" H GLY C 446 " pdb=" HA2 GLY C 446 " model vdw 1.536 1.816 nonbonded pdb=" H ILE A 500 " pdb=" OD1 ASP A 728 " model vdw 1.557 1.850 nonbonded pdb=" H ILE C 500 " pdb=" OD1 ASP C 728 " model vdw 1.557 1.850 nonbonded pdb="HH12 ARG A 485 " pdb=" OAA ZK1 A 902 " model vdw 1.600 1.850 ... (remaining 434090 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 394 through 598 or (resid 599 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2)) or resid 600 through 674 or (resid 675 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 676 through 704 or \ (resid 705 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 706 through 776 or (resid 784 and (name N or name CA or name \ C or name O or name CB or name HA )) or (resid 785 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 786 through 787 or (re \ sid 788 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 789 through 824 or resid 901 through 902)) selection = (chain 'B' and ((resid 394 and (name CA or name C or name O or name CB or name O \ G1 or name CG2 or name HB or name HG1 or name HG21 or name HG22 or name HG23)) o \ r resid 395 through 446 or (resid 447 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 448 or (resid 449 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 450 throug \ h 505 or (resid 506 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 507 through 539 or (resid 540 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 541 through 637 \ or (resid 638 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 639 through 696 or (resid 697 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 698 or (resid 699 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 700 through 728 or (resid 729 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 730 through 822 or (resid 823 through 82 \ 4 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 901 through 902)) selection = (chain 'C' and (resid 394 through 598 or (resid 599 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2)) or resid 600 through 674 or (resid 675 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 676 through 704 or \ (resid 705 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 706 through 776 or (resid 784 and (name N or name CA or name \ C or name O or name CB or name HA )) or (resid 785 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 786 through 787 or (re \ sid 788 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 789 through 824 or resid 901 through 902)) selection = (chain 'D' and ((resid 394 and (name CA or name C or name O or name CB or name O \ G1 or name CG2 or name HB or name HG1 or name HG21 or name HG22 or name HG23)) o \ r resid 395 through 446 or (resid 447 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 448 or (resid 449 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 450 throug \ h 505 or (resid 506 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 507 through 539 or (resid 540 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 541 through 637 \ or (resid 638 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 639 through 696 or (resid 697 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 698 or (resid 699 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 700 through 728 or (resid 729 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 730 through 822 or (resid 823 through 82 \ 4 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 901 through 902)) } ncs_group { reference = (chain 'E' and (resid 2 through 108 or (resid 110 through 126 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 127 and (name N or name CA or n \ ame C or name O or name CB or name OG1 or name CG2 or name HA )) or (resid 128 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2 or name H or name HA )) or resid 129 through 159 or resid 201)) selection = (chain 'F' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 32 through 37 or (resid 50 and (name N or name CA or nam \ e C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (re \ sid 51 through 58 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 59 through 86 or (resid 87 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name \ H or name HA )) or resid 88 through 108 or (resid 125 through 126 and (name N or \ name CA or name C or name O or name CB )) or resid 127 through 159 or resid 201 \ )) selection = (chain 'G' and (resid 2 through 108 or (resid 110 through 126 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 127 and (name N or name CA or n \ ame C or name O or name CB or name OG1 or name CG2 or name HA )) or (resid 128 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2 or name H or name HA )) or resid 129 through 159 or resid 201)) selection = (chain 'H' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 32 through 37 or (resid 50 and (name N or name CA or nam \ e C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (re \ sid 51 through 58 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 59 through 86 or (resid 87 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name \ H or name HA )) or resid 88 through 108 or (resid 125 through 126 and (name N or \ name CA or name C or name O or name CB )) or resid 127 through 159 or resid 201 \ )) } 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: 2.340 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: 0.440 Extract box with map and model: 11.320 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 97.700 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.183 16580 Z= 0.529 Angle : 0.644 10.432 22494 Z= 0.301 Chirality : 0.075 1.716 2544 Planarity : 0.007 0.189 2698 Dihedral : 14.526 179.461 6034 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -3.31 (0.16), residues: 1996 helix: -1.15 (0.13), residues: 1216 sheet: -3.04 (0.37), residues: 154 loop : -3.95 (0.19), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 606 HIS 0.004 0.001 HIS H 75 PHE 0.012 0.001 PHE A 546 TYR 0.015 0.001 TYR H 155 ARG 0.001 0.000 ARG B 628 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 713 GLU cc_start: 0.7963 (tt0) cc_final: 0.7648 (tm-30) REVERT: E 133 LYS cc_start: 0.6921 (mttm) cc_final: 0.6201 (ttpp) REVERT: F 81 MET cc_start: 0.7280 (ttm) cc_final: 0.6880 (ttm) REVERT: F 134 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7727 (tt0) REVERT: C 633 ILE cc_start: 0.7233 (pt) cc_final: 0.6884 (pt) REVERT: D 713 GLU cc_start: 0.8017 (tt0) cc_final: 0.7654 (tm-30) REVERT: D 760 ASP cc_start: 0.7329 (p0) cc_final: 0.6933 (p0) REVERT: D 761 LYS cc_start: 0.8820 (tttt) cc_final: 0.8601 (tttt) REVERT: G 133 LYS cc_start: 0.7384 (mttm) cc_final: 0.7041 (tttm) REVERT: H 81 MET cc_start: 0.7574 (ttm) cc_final: 0.7134 (ttm) REVERT: H 138 LYS cc_start: 0.8266 (ttmm) cc_final: 0.8026 (tttt) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.6600 time to fit residues: 341.6999 Evaluate side-chains 225 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 102 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 791 ASN F 94 ASN C 764 ASN C 791 ASN D 791 ASN H 94 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16580 Z= 0.168 Angle : 0.508 10.429 22494 Z= 0.263 Chirality : 0.060 1.716 2544 Planarity : 0.004 0.067 2698 Dihedral : 11.824 176.022 2636 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.55 % Allowed : 9.19 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -1.79 (0.18), residues: 1996 helix: 0.10 (0.14), residues: 1206 sheet: -3.32 (0.38), residues: 138 loop : -3.14 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 606 HIS 0.004 0.001 HIS G 75 PHE 0.013 0.001 PHE A 546 TYR 0.010 0.001 TYR B 673 ARG 0.005 0.000 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 233 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 713 GLU cc_start: 0.8254 (tt0) cc_final: 0.7682 (tm-30) REVERT: B 760 ASP cc_start: 0.7446 (p0) cc_final: 0.7029 (p0) REVERT: B 761 LYS cc_start: 0.8901 (tttt) cc_final: 0.8579 (ttmt) REVERT: E 133 LYS cc_start: 0.6856 (mttm) cc_final: 0.6138 (ttpp) REVERT: F 134 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7653 (tt0) REVERT: F 138 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7614 (mmpt) REVERT: F 148 TYR cc_start: 0.8151 (t80) cc_final: 0.7948 (t80) REVERT: D 713 GLU cc_start: 0.8326 (tt0) cc_final: 0.7699 (tm-30) REVERT: D 760 ASP cc_start: 0.7362 (p0) cc_final: 0.6950 (p0) REVERT: D 761 LYS cc_start: 0.8830 (tttt) cc_final: 0.8627 (tttt) REVERT: G 133 LYS cc_start: 0.7342 (mttm) cc_final: 0.6991 (tttm) REVERT: H 3 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: H 22 PHE cc_start: 0.8230 (t80) cc_final: 0.7860 (t80) REVERT: H 28 ILE cc_start: 0.8138 (mt) cc_final: 0.7919 (mt) REVERT: H 138 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7750 (mmpt) outliers start: 9 outliers final: 5 residues processed: 239 average time/residue: 0.5758 time to fit residues: 209.1460 Evaluate side-chains 211 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 205 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 38 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 756 GLN B 791 ASN C 756 GLN D 756 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16580 Z= 0.354 Angle : 0.599 9.972 22494 Z= 0.321 Chirality : 0.062 1.726 2544 Planarity : 0.004 0.041 2698 Dihedral : 10.068 178.206 2636 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.23 % Allowed : 11.52 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.18), residues: 1996 helix: 0.34 (0.15), residues: 1236 sheet: -2.93 (0.38), residues: 160 loop : -2.73 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 606 HIS 0.011 0.001 HIS G 75 PHE 0.019 0.002 PHE E 62 TYR 0.012 0.001 TYR H 148 ARG 0.007 0.000 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 213 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 713 GLU cc_start: 0.8303 (tt0) cc_final: 0.7844 (tm-30) REVERT: B 760 ASP cc_start: 0.7612 (p0) cc_final: 0.7291 (p0) REVERT: E 133 LYS cc_start: 0.6957 (mttm) cc_final: 0.6336 (tttm) REVERT: F 3 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6924 (m-80) REVERT: F 81 MET cc_start: 0.7680 (ttm) cc_final: 0.6992 (ttm) REVERT: F 138 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7575 (mmpt) REVERT: D 713 GLU cc_start: 0.8399 (tt0) cc_final: 0.7968 (tm-30) REVERT: D 760 ASP cc_start: 0.7662 (p0) cc_final: 0.7400 (p0) REVERT: G 133 LYS cc_start: 0.7444 (mttm) cc_final: 0.7104 (tttm) REVERT: H 3 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7135 (m-80) REVERT: H 22 PHE cc_start: 0.8357 (t80) cc_final: 0.7995 (t80) REVERT: H 28 ILE cc_start: 0.8299 (mt) cc_final: 0.8062 (mt) REVERT: H 138 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7709 (mmpt) outliers start: 20 outliers final: 13 residues processed: 223 average time/residue: 0.6168 time to fit residues: 212.7169 Evaluate side-chains 198 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16580 Z= 0.158 Angle : 0.483 10.192 22494 Z= 0.255 Chirality : 0.060 1.710 2544 Planarity : 0.003 0.040 2698 Dihedral : 9.480 173.235 2636 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.35 % Allowed : 11.58 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -0.63 (0.19), residues: 1996 helix: 0.86 (0.15), residues: 1234 sheet: -2.96 (0.39), residues: 150 loop : -2.37 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.005 0.001 HIS E 75 PHE 0.014 0.001 PHE B 541 TYR 0.007 0.001 TYR B 673 ARG 0.002 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 199 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.6955 (mmt) cc_final: 0.6603 (mmp) REVERT: B 713 GLU cc_start: 0.8275 (tt0) cc_final: 0.7825 (tm-30) REVERT: B 760 ASP cc_start: 0.7514 (p0) cc_final: 0.7194 (p0) REVERT: B 761 LYS cc_start: 0.8910 (tttt) cc_final: 0.8695 (tttt) REVERT: E 133 LYS cc_start: 0.7009 (mttm) cc_final: 0.6261 (ttpp) REVERT: F 3 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: F 33 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7759 (tm-30) REVERT: F 138 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7563 (mmpt) REVERT: D 713 GLU cc_start: 0.8365 (tt0) cc_final: 0.7935 (tm-30) REVERT: D 760 ASP cc_start: 0.7547 (p0) cc_final: 0.7243 (p0) REVERT: G 133 LYS cc_start: 0.7439 (mttm) cc_final: 0.7104 (tttm) REVERT: H 3 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: H 138 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7746 (mmpt) outliers start: 22 outliers final: 13 residues processed: 213 average time/residue: 0.5401 time to fit residues: 179.5997 Evaluate side-chains 203 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16580 Z= 0.423 Angle : 0.601 10.007 22494 Z= 0.327 Chirality : 0.062 1.723 2544 Planarity : 0.004 0.042 2698 Dihedral : 9.473 168.370 2636 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.90 % Allowed : 12.81 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -0.97 (0.19), residues: 1996 helix: 0.53 (0.15), residues: 1242 sheet: -2.96 (0.37), residues: 164 loop : -2.40 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.007 0.002 HIS G 75 PHE 0.019 0.002 PHE H 106 TYR 0.012 0.001 TYR A 424 ARG 0.003 0.001 ARG B 628 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7078 (mmt) cc_final: 0.6740 (mmp) REVERT: B 629 MET cc_start: 0.8075 (mmm) cc_final: 0.7683 (mtp) REVERT: B 713 GLU cc_start: 0.8371 (tt0) cc_final: 0.7949 (tm-30) REVERT: B 760 ASP cc_start: 0.7611 (p0) cc_final: 0.7310 (p0) REVERT: E 133 LYS cc_start: 0.7039 (mttm) cc_final: 0.6430 (tttm) REVERT: F 3 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: F 138 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7565 (mmpt) REVERT: D 713 GLU cc_start: 0.8400 (tt0) cc_final: 0.7948 (tm-30) REVERT: D 760 ASP cc_start: 0.7625 (p0) cc_final: 0.7386 (p0) REVERT: G 133 LYS cc_start: 0.7521 (mttm) cc_final: 0.7152 (tttm) REVERT: H 3 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7056 (m-80) REVERT: H 138 LYS cc_start: 0.8314 (ttmm) cc_final: 0.7816 (mmpt) outliers start: 31 outliers final: 25 residues processed: 211 average time/residue: 0.5669 time to fit residues: 187.4656 Evaluate side-chains 209 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16580 Z= 0.177 Angle : 0.493 10.038 22494 Z= 0.261 Chirality : 0.060 1.707 2544 Planarity : 0.003 0.038 2698 Dihedral : 8.589 153.901 2636 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.41 % Allowed : 14.03 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -0.41 (0.19), residues: 1996 helix: 0.98 (0.15), residues: 1238 sheet: -2.91 (0.39), residues: 150 loop : -2.17 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.005 0.001 HIS E 75 PHE 0.013 0.001 PHE F 106 TYR 0.007 0.001 TYR B 673 ARG 0.002 0.000 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7004 (mmt) cc_final: 0.6709 (mmp) REVERT: A 627 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 705 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7880 (mm-30) REVERT: B 713 GLU cc_start: 0.8366 (tt0) cc_final: 0.7950 (tm-30) REVERT: B 760 ASP cc_start: 0.7503 (p0) cc_final: 0.7220 (p0) REVERT: E 98 LEU cc_start: 0.9236 (tt) cc_final: 0.9006 (mt) REVERT: E 133 LYS cc_start: 0.7079 (mttm) cc_final: 0.6368 (tttm) REVERT: F 3 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: F 59 ARG cc_start: 0.6900 (ttp80) cc_final: 0.6551 (ttp80) REVERT: F 138 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7594 (mmpt) REVERT: D 713 GLU cc_start: 0.8389 (tt0) cc_final: 0.7954 (tm-30) REVERT: D 760 ASP cc_start: 0.7535 (p0) cc_final: 0.7249 (p0) REVERT: G 133 LYS cc_start: 0.7454 (mttm) cc_final: 0.7076 (tttm) REVERT: H 3 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7234 (m-80) REVERT: H 138 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7732 (mmpt) outliers start: 23 outliers final: 18 residues processed: 214 average time/residue: 0.5240 time to fit residues: 177.4547 Evaluate side-chains 207 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 192 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16580 Z= 0.230 Angle : 0.499 9.987 22494 Z= 0.266 Chirality : 0.060 1.706 2544 Planarity : 0.003 0.036 2698 Dihedral : 7.480 131.548 2636 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.72 % Allowed : 14.40 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -0.31 (0.19), residues: 1996 helix: 1.09 (0.15), residues: 1238 sheet: -3.00 (0.37), residues: 154 loop : -2.16 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.008 0.001 HIS E 75 PHE 0.014 0.001 PHE F 106 TYR 0.009 0.001 TYR F 10 ARG 0.002 0.000 ARG F 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7117 (mmt) cc_final: 0.6849 (mmp) REVERT: A 705 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 713 GLU cc_start: 0.8371 (tt0) cc_final: 0.7955 (tm-30) REVERT: B 760 ASP cc_start: 0.7451 (p0) cc_final: 0.7143 (p0) REVERT: E 98 LEU cc_start: 0.9267 (tt) cc_final: 0.8995 (mt) REVERT: E 133 LYS cc_start: 0.7145 (mttm) cc_final: 0.6522 (tttm) REVERT: F 3 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: F 59 ARG cc_start: 0.6927 (ttp80) cc_final: 0.6582 (ttp80) REVERT: F 138 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7599 (mmpt) REVERT: D 713 GLU cc_start: 0.8390 (tt0) cc_final: 0.7958 (tm-30) REVERT: D 760 ASP cc_start: 0.7533 (p0) cc_final: 0.7244 (p0) REVERT: G 133 LYS cc_start: 0.7489 (mttm) cc_final: 0.7103 (tttm) REVERT: G 134 GLU cc_start: 0.6472 (pt0) cc_final: 0.5925 (tt0) REVERT: H 3 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: H 138 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7742 (mmpt) outliers start: 28 outliers final: 23 residues processed: 206 average time/residue: 0.5622 time to fit residues: 186.0781 Evaluate side-chains 211 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16580 Z= 0.216 Angle : 0.488 9.988 22494 Z= 0.262 Chirality : 0.060 1.703 2544 Planarity : 0.003 0.035 2698 Dihedral : 6.563 96.856 2636 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.78 % Allowed : 14.46 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -0.14 (0.19), residues: 1996 helix: 1.21 (0.15), residues: 1238 sheet: -2.88 (0.38), residues: 154 loop : -2.06 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.007 0.001 HIS E 75 PHE 0.014 0.001 PHE F 106 TYR 0.008 0.001 TYR F 10 ARG 0.002 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7810 (mm-30) REVERT: B 713 GLU cc_start: 0.8370 (tt0) cc_final: 0.7953 (tm-30) REVERT: B 760 ASP cc_start: 0.7475 (p0) cc_final: 0.7184 (p0) REVERT: E 133 LYS cc_start: 0.7189 (mttm) cc_final: 0.6453 (tttm) REVERT: F 3 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: F 59 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6596 (ttp80) REVERT: F 138 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7556 (mmpt) REVERT: C 408 MET cc_start: 0.6372 (mmp) cc_final: 0.5790 (mmp) REVERT: C 627 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7864 (mm-30) REVERT: D 713 GLU cc_start: 0.8380 (tt0) cc_final: 0.7955 (tm-30) REVERT: D 760 ASP cc_start: 0.7524 (p0) cc_final: 0.7217 (p0) REVERT: G 133 LYS cc_start: 0.7529 (mttm) cc_final: 0.7149 (tttm) REVERT: H 3 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: H 25 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9095 (mm) REVERT: H 138 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7747 (mmpt) outliers start: 29 outliers final: 22 residues processed: 210 average time/residue: 0.5085 time to fit residues: 169.5088 Evaluate side-chains 213 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16580 Z= 0.296 Angle : 0.527 10.178 22494 Z= 0.286 Chirality : 0.061 1.706 2544 Planarity : 0.003 0.034 2698 Dihedral : 6.245 65.008 2636 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.02 % Allowed : 14.77 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -0.25 (0.19), residues: 1996 helix: 1.08 (0.15), residues: 1242 sheet: -2.94 (0.39), residues: 148 loop : -2.04 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.009 0.001 HIS E 75 PHE 0.017 0.001 PHE F 106 TYR 0.012 0.001 TYR F 10 ARG 0.003 0.000 ARG C 628 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7867 (mm-30) REVERT: B 713 GLU cc_start: 0.8380 (tt0) cc_final: 0.7953 (tm-30) REVERT: B 760 ASP cc_start: 0.7505 (p0) cc_final: 0.7213 (p0) REVERT: E 98 LEU cc_start: 0.9309 (tt) cc_final: 0.8988 (mt) REVERT: E 133 LYS cc_start: 0.7284 (mttm) cc_final: 0.6642 (tttm) REVERT: F 3 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7383 (m-80) REVERT: F 59 ARG cc_start: 0.6979 (ttp80) cc_final: 0.6624 (ttp80) REVERT: F 138 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7562 (mmpt) REVERT: C 408 MET cc_start: 0.6504 (mmp) cc_final: 0.5914 (mmp) REVERT: D 713 GLU cc_start: 0.8388 (tt0) cc_final: 0.8090 (tm-30) REVERT: D 760 ASP cc_start: 0.7582 (p0) cc_final: 0.7290 (p0) REVERT: G 133 LYS cc_start: 0.7553 (mttm) cc_final: 0.7179 (tttm) REVERT: H 3 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: H 138 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7687 (mmpt) outliers start: 33 outliers final: 29 residues processed: 209 average time/residue: 0.5212 time to fit residues: 173.8551 Evaluate side-chains 217 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16580 Z= 0.218 Angle : 0.501 9.999 22494 Z= 0.268 Chirality : 0.060 1.709 2544 Planarity : 0.003 0.034 2698 Dihedral : 5.988 53.382 2636 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.78 % Allowed : 15.26 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -0.07 (0.20), residues: 1996 helix: 1.23 (0.15), residues: 1242 sheet: -2.84 (0.40), residues: 148 loop : -1.97 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.008 0.001 HIS E 75 PHE 0.014 0.001 PHE F 106 TYR 0.013 0.001 TYR D 421 ARG 0.002 0.000 ARG C 628 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LEU 540 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Residue SER 788 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7846 (mm-30) REVERT: B 713 GLU cc_start: 0.8375 (tt0) cc_final: 0.7958 (tm-30) REVERT: B 760 ASP cc_start: 0.7472 (p0) cc_final: 0.7176 (p0) REVERT: E 98 LEU cc_start: 0.9246 (tt) cc_final: 0.8943 (mt) REVERT: E 133 LYS cc_start: 0.7344 (mttm) cc_final: 0.6520 (tttm) REVERT: F 3 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: F 59 ARG cc_start: 0.6967 (ttp80) cc_final: 0.6604 (ttp80) REVERT: F 138 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7552 (mmpt) REVERT: C 408 MET cc_start: 0.6467 (mmp) cc_final: 0.5914 (mmp) REVERT: D 408 MET cc_start: 0.7003 (mmp) cc_final: 0.6542 (mmp) REVERT: D 713 GLU cc_start: 0.8377 (tt0) cc_final: 0.8083 (tm-30) REVERT: D 760 ASP cc_start: 0.7540 (p0) cc_final: 0.7230 (p0) REVERT: G 133 LYS cc_start: 0.7516 (mttm) cc_final: 0.7141 (tttm) REVERT: H 138 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7683 (mmpt) outliers start: 29 outliers final: 27 residues processed: 213 average time/residue: 0.5147 time to fit residues: 174.0436 Evaluate side-chains 220 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 38 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 136 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.108864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086169 restraints weight = 114510.136| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.17 r_work: 0.3244 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16580 Z= 0.171 Angle : 0.481 9.978 22494 Z= 0.255 Chirality : 0.060 1.699 2544 Planarity : 0.003 0.034 2698 Dihedral : 5.634 53.048 2636 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.65 % Allowed : 15.20 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.19 (0.20), residues: 1996 helix: 1.45 (0.15), residues: 1238 sheet: -2.74 (0.38), residues: 154 loop : -1.89 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 103 HIS 0.007 0.001 HIS E 75 PHE 0.011 0.001 PHE H 106 TYR 0.009 0.001 TYR F 10 ARG 0.002 0.000 ARG F 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6400.86 seconds wall clock time: 114 minutes 46.40 seconds (6886.40 seconds total)