Starting phenix.real_space_refine on Fri Mar 22 01:40:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud4_20733/03_2024/6ud4_20733_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud4_20733/03_2024/6ud4_20733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud4_20733/03_2024/6ud4_20733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud4_20733/03_2024/6ud4_20733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud4_20733/03_2024/6ud4_20733_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ud4_20733/03_2024/6ud4_20733_trim_updated.pdb" } resolution = 3.3 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 10673 2.51 5 N 2519 2.21 5 O 2844 1.98 5 F 12 1.80 5 H 15470 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 523": "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 PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 491": "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 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 796": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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" Residue "C TYR 421": "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 PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 523": "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 PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 491": "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 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 796": "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-5265/modules/chem_data/mon_lib" Total number of atoms: 31642 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5658 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 5731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5731 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 57 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: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2112 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 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: "G" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2121 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 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: "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: 86 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 5731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 5731 Classifications: {'peptide': 378} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 366} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 57 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: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'CLR': 1, 'OLC': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 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} 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} Time building chain proxies: 13.88, per 1000 atoms: 0.44 Number of scatterers: 31642 At special positions: 0 Unit cell: (118.326, 101.27, 147.108, 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 2844 8.00 N 2519 7.00 C 10673 6.00 H 15470 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: 24.29 Conformation dependent library (CDL) restraints added in 3.1 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: 80 helices and 14 sheets defined 56.8% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 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 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 546 removed outlier: 4.068A pdb=" N CYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 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 675 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 755 removed outlier: 4.139A pdb=" N LEU A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 4.177A 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: 3.821A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 483 through 487 Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.660A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 626 removed outlier: 3.693A 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 Processing helix chain 'B' and resid 743 through 756 removed outlier: 3.914A 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: 3.701A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 36 removed outlier: 3.772A pdb=" N ALA E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 66 removed outlier: 4.036A pdb=" N ILE E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) removed outlier: 3.627A 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 88 through 106 removed outlier: 4.302A pdb=" N LEU E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 129 through 157 removed outlier: 3.710A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 37 removed outlier: 3.707A 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: 4.023A pdb=" N TYR F 105 " --> pdb=" O HIS F 101 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 157 removed outlier: 4.648A pdb=" N LYS F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 36 removed outlier: 3.772A pdb=" N ALA G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 66 removed outlier: 4.036A pdb=" N ILE G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 3.627A 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 88 through 106 removed outlier: 4.303A pdb=" N LEU G 93 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN G 94 " --> pdb=" O THR G 90 " (cutoff:3.500A) Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 129 through 157 removed outlier: 3.710A pdb=" N PHE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 37 removed outlier: 3.706A 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: 4.024A pdb=" N TYR H 105 " --> pdb=" O HIS H 101 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE H 106 " --> pdb=" O PHE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 157 removed outlier: 4.648A pdb=" N LYS H 133 " --> pdb=" O SER H 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 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 546 removed outlier: 4.069A pdb=" N CYS C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 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 675 Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 755 removed outlier: 4.171A pdb=" N LEU C 748 " --> pdb=" O ASN C 744 " (cutoff:3.500A) removed outlier: 4.192A 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: 3.831A pdb=" N ALA C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 487 Processing helix chain 'D' and resid 523 through 545 removed outlier: 3.660A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 626 removed outlier: 3.693A 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 Processing helix chain 'D' and resid 743 through 756 removed outlier: 3.915A 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: 3.702A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (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: 3.614A 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: 6.643A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 451 through 453 Processing sheet with id= E, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= F, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.599A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.698A pdb=" N LEU B 704 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= I, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.618A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 500 through 503 removed outlier: 6.639A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 451 through 453 Processing sheet with id= L, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= M, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.599A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.699A pdb=" N LEU D 704 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2502 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: 11.48 Time building geometry restraints manager: 25.55 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: 15418 1.04 - 1.25: 2170 1.25 - 1.45: 5164 1.45 - 1.65: 9106 1.65 - 1.86: 184 Bond restraints: 32042 Sorted by residual: bond pdb=" CAT ZK1 A 901 " pdb=" OAA ZK1 A 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" CAT ZK1 C 901 " pdb=" OAA ZK1 C 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" CAU ZK1 B 901 " pdb=" OAB ZK1 B 901 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.28e+01 bond pdb=" CAU ZK1 D 901 " pdb=" OAB ZK1 D 901 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" CAU ZK1 C 901 " pdb=" OAB ZK1 C 901 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.24e+01 ... (remaining 32037 not shown) Histogram of bond angle deviations from ideal: 81.02 - 91.61: 6 91.61 - 102.20: 67 102.20 - 112.80: 36601 112.80 - 123.39: 18170 123.39 - 133.98: 2692 Bond angle restraints: 57536 Sorted by residual: angle pdb=" CG2 THR C 784 " pdb=" CB THR C 784 " pdb=" HB THR C 784 " ideal model delta sigma weight residual 108.00 81.02 26.98 3.00e+00 1.11e-01 8.09e+01 angle pdb=" CG2 THR A 784 " pdb=" CB THR A 784 " pdb=" HB THR A 784 " ideal model delta sigma weight residual 108.00 81.07 26.93 3.00e+00 1.11e-01 8.06e+01 angle pdb=" OG1 THR C 784 " pdb=" CB THR C 784 " pdb=" HB THR C 784 " ideal model delta sigma weight residual 109.00 82.73 26.27 3.00e+00 1.11e-01 7.67e+01 angle pdb=" OG1 THR A 784 " pdb=" CB THR A 784 " pdb=" HB THR A 784 " ideal model delta sigma weight residual 109.00 82.76 26.24 3.00e+00 1.11e-01 7.65e+01 angle pdb=" CA THR A 784 " pdb=" CB THR A 784 " pdb=" HB THR A 784 " ideal model delta sigma weight residual 109.00 83.45 25.55 3.00e+00 1.11e-01 7.25e+01 ... (remaining 57531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.45: 14999 32.45 - 64.89: 458 64.89 - 97.34: 10 97.34 - 129.78: 11 129.78 - 162.23: 1 Dihedral angle restraints: 15479 sinusoidal: 8106 harmonic: 7373 Sorted by residual: dihedral pdb=" C21 OLC B 902 " pdb=" C1 OLC B 902 " pdb=" O20 OLC B 902 " pdb=" O19 OLC B 902 " ideal model delta sinusoidal sigma weight residual -1.92 160.31 -162.23 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" NAX ZK1 D 901 " pdb=" CAK ZK1 D 901 " pdb=" CAM ZK1 D 901 " pdb=" OAQ ZK1 D 901 " ideal model delta sinusoidal sigma weight residual -57.16 64.38 -121.54 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" O20 OLC B 902 " pdb=" C21 OLC B 902 " pdb=" C22 OLC B 902 " pdb=" O23 OLC B 902 " ideal model delta sinusoidal sigma weight residual -57.23 -175.56 118.33 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 15476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 2536 0.276 - 0.552: 4 0.552 - 0.828: 0 0.828 - 1.103: 0 1.103 - 1.379: 2 Chirality restraints: 2542 Sorted by residual: chirality pdb=" CB THR A 784 " pdb=" CA THR A 784 " pdb=" OG1 THR A 784 " pdb=" CG2 THR A 784 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.76e+01 chirality pdb=" CB THR C 784 " pdb=" CA THR C 784 " pdb=" OG1 THR C 784 " pdb=" CG2 THR C 784 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.74e+01 chirality pdb=" C22 OLC D 902 " pdb=" C21 OLC D 902 " pdb=" C24 OLC D 902 " pdb=" O23 OLC D 902 " both_signs ideal model delta sigma weight residual False -2.31 -2.80 0.49 2.00e-01 2.50e+01 6.03e+00 ... (remaining 2539 not shown) Planarity restraints: 4654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLC D 902 " -0.341 2.00e-02 2.50e+03 2.46e-01 6.05e+02 pdb=" C11 OLC D 902 " 0.113 2.00e-02 2.50e+03 pdb=" C8 OLC D 902 " -0.094 2.00e-02 2.50e+03 pdb=" C9 OLC D 902 " 0.322 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC A 902 " -0.323 2.00e-02 2.50e+03 2.41e-01 5.82e+02 pdb=" C11 OLC A 902 " 0.100 2.00e-02 2.50e+03 pdb=" C8 OLC A 902 " -0.105 2.00e-02 2.50e+03 pdb=" C9 OLC A 902 " 0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC B 902 " 0.181 2.00e-02 2.50e+03 1.96e-01 3.85e+02 pdb=" C11 OLC B 902 " -0.192 2.00e-02 2.50e+03 pdb=" C8 OLC B 902 " -0.200 2.00e-02 2.50e+03 pdb=" C9 OLC B 902 " 0.211 2.00e-02 2.50e+03 ... (remaining 4651 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 873 2.13 - 2.75: 57646 2.75 - 3.37: 89469 3.37 - 3.98: 109511 3.98 - 4.60: 174534 Nonbonded interactions: 432033 Sorted by model distance: nonbonded pdb=" O ALA D 433 " pdb=" H GLY D 437 " model vdw 1.513 1.850 nonbonded pdb=" O ALA B 433 " pdb=" H GLY B 437 " model vdw 1.513 1.850 nonbonded pdb="HH22 ARG B 545 " pdb=" O LYS G 66 " model vdw 1.534 1.850 nonbonded pdb="HH12 ARG B 485 " pdb=" OAA ZK1 B 901 " model vdw 1.556 1.850 nonbonded pdb=" HZ1 LYS D 505 " pdb=" O ARG D 694 " model vdw 1.587 1.850 ... (remaining 432028 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 824 or res \ id 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 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 396 through 417 or (resid 418 through 419 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 420 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 423 through 433 or (resid 434 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 435 through 505 o \ r (resid 506 and (name N or name CA or name C or name O or name CB or name 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 (res \ id 638 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 639 through 660 or (resid 661 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 662 through 822 or (resid 823 \ through 824 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 660 or (resid 661 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 662 through 674 or \ (resid 675 and (name N or name CA or name C or name O or name CB or name H or n \ ame 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 name HA )) or resid 706 through 776 or (resi \ d 784 and (name N or name CA or name C or name O or name CB or name HA )) or (re \ sid 785 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 786 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 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 396 through 417 or (resid 418 through 419 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 420 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 423 through 433 or (resid 434 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 435 through 505 o \ r (resid 506 and (name N or name CA or name C or name O or name CB or name 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 (res \ id 638 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 639 through 660 or (resid 661 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 662 through 822 or (resid 823 \ through 824 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 and (name N or name CA or name \ C or name O or name CB )) or (resid 126 and (name N or name CA or name C or nam \ e O or name CB or name CG or name OD1 or name OD2)) or (resid 127 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name HA )) or \ (resid 128 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 H or name HA )) or resid 129 through 159)) 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 159)) selection = (chain 'G' 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 108 or (resid 110 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 126 and (name N or name CA or name C or \ name O or name CB or name CG or name OD1 or name OD2)) or (resid 127 and (name N \ or name CA or name C or name O or name CB or name OG1 or name CG2 or name HA )) \ or (resid 128 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 H or name HA )) or resid 129 through 159)) 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 159)) } 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: 2.280 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: 0.430 Extract box with map and model: 11.230 Check model and map are aligned: 0.540 Set scattering table: 0.300 Process input model: 97.070 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 16572 Z= 0.508 Angle : 0.629 11.312 22483 Z= 0.298 Chirality : 0.057 1.379 2542 Planarity : 0.008 0.246 2697 Dihedral : 14.044 162.228 6029 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.12 % Allowed : 2.08 % Favored : 97.80 % 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: -3.11 (0.16), residues: 1996 helix: -0.98 (0.13), residues: 1226 sheet: -3.01 (0.42), residues: 120 loop : -3.92 (0.18), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 606 HIS 0.003 0.001 HIS E 75 PHE 0.012 0.001 PHE H 22 TYR 0.013 0.001 TYR H 155 ARG 0.002 0.000 ARG E 59 *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 309 time to evaluate : 2.581 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: 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 760 ASP cc_start: 0.8275 (p0) cc_final: 0.8056 (p0) REVERT: E 88 TRP cc_start: 0.5486 (m100) cc_final: 0.5023 (m100) REVERT: E 147 PHE cc_start: 0.7127 (m-10) cc_final: 0.6662 (t80) REVERT: F 22 PHE cc_start: 0.5900 (OUTLIER) cc_final: 0.5603 (t80) REVERT: F 66 LYS cc_start: 0.6676 (mtpt) cc_final: 0.6238 (mmtp) REVERT: G 33 GLU cc_start: 0.6167 (tt0) cc_final: 0.5579 (tm-30) REVERT: G 88 TRP cc_start: 0.5567 (m100) cc_final: 0.5070 (m100) REVERT: G 147 PHE cc_start: 0.7460 (m-10) cc_final: 0.6774 (t80) REVERT: H 22 PHE cc_start: 0.5979 (OUTLIER) cc_final: 0.5157 (t80) REVERT: H 66 LYS cc_start: 0.7128 (mtpt) cc_final: 0.6540 (mmtp) REVERT: C 764 ASN cc_start: 0.8007 (m-40) cc_final: 0.7757 (m110) REVERT: D 412 HIS cc_start: 0.6977 (p90) cc_final: 0.6739 (p-80) REVERT: D 596 LEU cc_start: 0.8690 (tp) cc_final: 0.8357 (tp) outliers start: 2 outliers final: 0 residues processed: 311 average time/residue: 0.6436 time to fit residues: 288.7365 Evaluate side-chains 184 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain H residue 22 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN E 132 GLN F 94 ASN F 132 GLN C 791 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 16572 Z= 0.216 Angle : 0.517 11.238 22483 Z= 0.270 Chirality : 0.053 1.371 2542 Planarity : 0.004 0.087 2697 Dihedral : 9.181 156.400 2639 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 0.73 % Allowed : 7.41 % Favored : 91.86 % 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: -1.36 (0.18), residues: 1996 helix: 0.34 (0.14), residues: 1246 sheet: -2.26 (0.46), residues: 126 loop : -3.17 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 606 HIS 0.008 0.001 HIS E 107 PHE 0.017 0.001 PHE E 23 TYR 0.020 0.001 TYR F 155 ARG 0.010 0.000 ARG B 661 *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 2.685 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: 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 599 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.7545 (mmt180) REVERT: B 760 ASP cc_start: 0.8351 (p0) cc_final: 0.8135 (p0) REVERT: E 82 PHE cc_start: 0.7290 (m-10) cc_final: 0.7072 (m-10) REVERT: E 147 PHE cc_start: 0.7106 (m-10) cc_final: 0.6686 (t80) REVERT: F 12 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7734 (mp) REVERT: F 22 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5785 (t80) REVERT: F 66 LYS cc_start: 0.6396 (mtpt) cc_final: 0.6137 (mmtp) REVERT: G 33 GLU cc_start: 0.6354 (tt0) cc_final: 0.5741 (tm-30) REVERT: G 147 PHE cc_start: 0.7511 (m-10) cc_final: 0.6830 (t80) REVERT: H 22 PHE cc_start: 0.5759 (OUTLIER) cc_final: 0.5160 (t80) REVERT: H 66 LYS cc_start: 0.7116 (mtpt) cc_final: 0.6473 (mmtp) REVERT: C 599 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.7551 (mmt180) REVERT: D 596 LEU cc_start: 0.8802 (tp) cc_final: 0.8525 (tp) outliers start: 12 outliers final: 5 residues processed: 213 average time/residue: 0.5618 time to fit residues: 181.7941 Evaluate side-chains 184 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain G residue 152 CYS Chi-restraints excluded: chain H residue 22 PHE Chi-restraints excluded: chain C residue 789 LEU 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: 5.9990 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16572 Z= 0.229 Angle : 0.489 11.298 22483 Z= 0.263 Chirality : 0.053 1.387 2542 Planarity : 0.003 0.040 2697 Dihedral : 8.470 103.530 2639 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.10 % Allowed : 7.65 % Favored : 91.24 % 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: -0.55 (0.19), residues: 1996 helix: 0.96 (0.15), residues: 1244 sheet: -1.96 (0.48), residues: 126 loop : -2.79 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 766 HIS 0.005 0.001 HIS G 27 PHE 0.023 0.001 PHE F 62 TYR 0.020 0.001 TYR H 155 ARG 0.005 0.000 ARG B 661 *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 2.656 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8325 (mtt-85) cc_final: 0.7487 (mmp80) REVERT: E 147 PHE cc_start: 0.7259 (m-10) cc_final: 0.6762 (t80) REVERT: F 22 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.5794 (t80) REVERT: F 66 LYS cc_start: 0.6504 (mtpt) cc_final: 0.6213 (mmtp) REVERT: F 155 TYR cc_start: 0.5951 (m-80) cc_final: 0.5740 (m-80) REVERT: G 33 GLU cc_start: 0.6541 (tt0) cc_final: 0.5887 (tm-30) REVERT: G 147 PHE cc_start: 0.7542 (m-10) cc_final: 0.6895 (t80) REVERT: H 66 LYS cc_start: 0.7077 (mtpt) cc_final: 0.6462 (mmtp) REVERT: C 599 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.7525 (mmt180) REVERT: D 596 LEU cc_start: 0.9002 (tp) cc_final: 0.8799 (tp) REVERT: D 726 ASN cc_start: 0.7989 (m-40) cc_final: 0.7512 (m-40) outliers start: 18 outliers final: 8 residues processed: 205 average time/residue: 0.5435 time to fit residues: 170.3715 Evaluate side-chains 188 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16572 Z= 0.307 Angle : 0.533 11.352 22483 Z= 0.291 Chirality : 0.054 1.393 2542 Planarity : 0.004 0.036 2697 Dihedral : 8.448 107.262 2637 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 1.41 % Allowed : 10.10 % Favored : 88.49 % 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: -0.40 (0.19), residues: 1996 helix: 1.01 (0.15), residues: 1256 sheet: -1.78 (0.47), residues: 138 loop : -2.66 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 606 HIS 0.005 0.001 HIS E 27 PHE 0.017 0.001 PHE H 8 TYR 0.031 0.001 TYR F 148 ARG 0.007 0.000 ARG C 661 *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 2.552 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8390 (mtt-85) cc_final: 0.7624 (mmp80) REVERT: E 80 ILE cc_start: 0.9252 (mm) cc_final: 0.9008 (mt) REVERT: E 147 PHE cc_start: 0.7517 (m-10) cc_final: 0.6790 (t80) REVERT: F 12 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7846 (mp) REVERT: F 22 PHE cc_start: 0.6303 (OUTLIER) cc_final: 0.5809 (t80) REVERT: F 66 LYS cc_start: 0.6623 (mtpt) cc_final: 0.6209 (mmtp) REVERT: F 155 TYR cc_start: 0.6038 (m-80) cc_final: 0.5672 (m-80) REVERT: G 33 GLU cc_start: 0.6570 (tt0) cc_final: 0.5870 (tm-30) REVERT: G 147 PHE cc_start: 0.7688 (m-10) cc_final: 0.6973 (t80) REVERT: H 66 LYS cc_start: 0.7066 (mtpt) cc_final: 0.6385 (mmtp) REVERT: C 408 MET cc_start: 0.6683 (mmm) cc_final: 0.5975 (mmm) REVERT: C 599 ARG cc_start: 0.8455 (mtt-85) cc_final: 0.7613 (mmp80) outliers start: 23 outliers final: 16 residues processed: 209 average time/residue: 0.5679 time to fit residues: 183.4766 Evaluate side-chains 199 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16572 Z= 0.282 Angle : 0.513 11.339 22483 Z= 0.280 Chirality : 0.053 1.389 2542 Planarity : 0.003 0.034 2697 Dihedral : 8.311 105.422 2637 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.96 % Allowed : 11.94 % Favored : 86.10 % 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: -0.12 (0.20), residues: 1996 helix: 1.19 (0.15), residues: 1256 sheet: -1.76 (0.49), residues: 128 loop : -2.45 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 88 HIS 0.005 0.001 HIS G 27 PHE 0.013 0.001 PHE F 106 TYR 0.011 0.001 TYR F 130 ARG 0.005 0.000 ARG C 661 *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 2.581 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.7743 (mmp80) REVERT: B 633 ILE cc_start: 0.8434 (mp) cc_final: 0.8146 (mm) REVERT: E 80 ILE cc_start: 0.9269 (mm) cc_final: 0.9005 (mt) REVERT: E 147 PHE cc_start: 0.7560 (m-10) cc_final: 0.6817 (t80) REVERT: F 22 PHE cc_start: 0.6331 (OUTLIER) cc_final: 0.5784 (t80) REVERT: F 66 LYS cc_start: 0.6624 (mtpt) cc_final: 0.6215 (mmtp) REVERT: F 155 TYR cc_start: 0.5922 (m-80) cc_final: 0.5584 (m-80) REVERT: G 33 GLU cc_start: 0.6656 (tt0) cc_final: 0.5797 (tm-30) REVERT: H 66 LYS cc_start: 0.7024 (mtpt) cc_final: 0.6386 (mmtp) REVERT: C 599 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.7739 (mmp80) REVERT: D 760 ASP cc_start: 0.8496 (p0) cc_final: 0.8293 (p0) outliers start: 32 outliers final: 27 residues processed: 207 average time/residue: 0.5333 time to fit residues: 172.4387 Evaluate side-chains 209 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 193 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16572 Z= 0.174 Angle : 0.466 11.269 22483 Z= 0.251 Chirality : 0.052 1.377 2542 Planarity : 0.003 0.036 2697 Dihedral : 7.803 101.007 2637 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.53 % Allowed : 12.92 % Favored : 85.55 % 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: 0.34 (0.20), residues: 1996 helix: 1.55 (0.15), residues: 1252 sheet: -1.49 (0.52), residues: 116 loop : -2.25 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 103 HIS 0.003 0.001 HIS G 75 PHE 0.011 0.001 PHE E 23 TYR 0.008 0.001 TYR E 149 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 2.546 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8542 (mtt-85) cc_final: 0.7726 (mmp80) REVERT: E 80 ILE cc_start: 0.9264 (mm) cc_final: 0.8994 (mt) REVERT: E 147 PHE cc_start: 0.7552 (m-10) cc_final: 0.6797 (t80) REVERT: F 22 PHE cc_start: 0.6295 (OUTLIER) cc_final: 0.5682 (t80) REVERT: F 66 LYS cc_start: 0.6617 (mtpt) cc_final: 0.6200 (mmtp) REVERT: F 155 TYR cc_start: 0.6061 (m-80) cc_final: 0.5709 (m-10) REVERT: G 33 GLU cc_start: 0.6728 (tt0) cc_final: 0.5871 (tm-30) REVERT: H 66 LYS cc_start: 0.7048 (mtpt) cc_final: 0.6455 (mmtp) REVERT: C 599 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.7730 (mmp80) REVERT: D 760 ASP cc_start: 0.8441 (p0) cc_final: 0.8216 (p0) outliers start: 25 outliers final: 23 residues processed: 209 average time/residue: 0.5318 time to fit residues: 172.6472 Evaluate side-chains 207 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 120 optimal weight: 0.0470 chunk 117 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16572 Z= 0.160 Angle : 0.456 11.250 22483 Z= 0.245 Chirality : 0.052 1.377 2542 Planarity : 0.003 0.033 2697 Dihedral : 7.673 101.524 2637 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.78 % Allowed : 12.98 % Favored : 85.24 % 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: 0.56 (0.20), residues: 1996 helix: 1.72 (0.15), residues: 1252 sheet: -1.68 (0.50), residues: 128 loop : -2.08 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 103 HIS 0.003 0.001 HIS G 75 PHE 0.011 0.001 PHE E 23 TYR 0.008 0.001 TYR E 149 ARG 0.002 0.000 ARG E 104 *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 2.628 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.7714 (mmp80) REVERT: E 80 ILE cc_start: 0.9228 (mm) cc_final: 0.9004 (mt) REVERT: E 147 PHE cc_start: 0.7530 (m-10) cc_final: 0.6770 (t80) REVERT: F 22 PHE cc_start: 0.6256 (OUTLIER) cc_final: 0.5597 (t80) REVERT: F 66 LYS cc_start: 0.6605 (mtpt) cc_final: 0.6030 (mmmm) REVERT: F 155 TYR cc_start: 0.6134 (m-80) cc_final: 0.5816 (m-10) REVERT: G 33 GLU cc_start: 0.6677 (tt0) cc_final: 0.5787 (tm-30) REVERT: H 66 LYS cc_start: 0.7015 (mtpt) cc_final: 0.6417 (mmtp) REVERT: C 599 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.7696 (mmp80) REVERT: D 760 ASP cc_start: 0.8432 (p0) cc_final: 0.8209 (p0) outliers start: 29 outliers final: 24 residues processed: 210 average time/residue: 0.5275 time to fit residues: 173.2278 Evaluate side-chains 211 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16572 Z= 0.178 Angle : 0.460 11.255 22483 Z= 0.248 Chirality : 0.052 1.377 2542 Planarity : 0.003 0.035 2697 Dihedral : 7.615 102.832 2637 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.65 % Allowed : 12.98 % Favored : 85.36 % 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 (0.20), residues: 1996 helix: 1.77 (0.15), residues: 1256 sheet: -1.42 (0.53), residues: 116 loop : -2.11 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 103 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE E 23 TYR 0.008 0.001 TYR E 151 ARG 0.002 0.000 ARG E 104 *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 2.471 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.7678 (mmp80) REVERT: E 80 ILE cc_start: 0.9266 (mm) cc_final: 0.9039 (mt) REVERT: E 147 PHE cc_start: 0.7515 (m-10) cc_final: 0.6760 (t80) REVERT: F 22 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5504 (t80) REVERT: F 66 LYS cc_start: 0.6605 (mtpt) cc_final: 0.6023 (mmmm) REVERT: F 155 TYR cc_start: 0.6053 (m-80) cc_final: 0.5751 (m-80) REVERT: G 33 GLU cc_start: 0.6688 (tt0) cc_final: 0.5785 (tm-30) REVERT: H 66 LYS cc_start: 0.7017 (mtpt) cc_final: 0.6415 (mmtp) REVERT: C 599 ARG cc_start: 0.8599 (mtt-85) cc_final: 0.7824 (mmp80) REVERT: D 760 ASP cc_start: 0.8437 (p0) cc_final: 0.8194 (p0) outliers start: 27 outliers final: 26 residues processed: 205 average time/residue: 0.5619 time to fit residues: 180.8379 Evaluate side-chains 208 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 189 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16572 Z= 0.233 Angle : 0.488 11.282 22483 Z= 0.264 Chirality : 0.053 1.380 2542 Planarity : 0.003 0.033 2697 Dihedral : 7.734 105.222 2637 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.84 % Allowed : 13.35 % Favored : 84.81 % 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: 0.54 (0.20), residues: 1996 helix: 1.67 (0.15), residues: 1260 sheet: -1.71 (0.47), residues: 138 loop : -2.04 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 103 HIS 0.003 0.001 HIS E 75 PHE 0.011 0.001 PHE F 106 TYR 0.010 0.001 TYR F 130 ARG 0.003 0.000 ARG E 104 *********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 2.795 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: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8591 (mtt-85) cc_final: 0.7843 (mmp80) REVERT: B 596 LEU cc_start: 0.8974 (tp) cc_final: 0.8769 (tp) REVERT: E 80 ILE cc_start: 0.9301 (mm) cc_final: 0.9066 (mt) REVERT: E 147 PHE cc_start: 0.7525 (m-10) cc_final: 0.6705 (t80) REVERT: F 22 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.5154 (t80) REVERT: F 66 LYS cc_start: 0.6783 (mtpt) cc_final: 0.6170 (mmmm) REVERT: F 155 TYR cc_start: 0.6335 (m-80) cc_final: 0.5839 (m-80) REVERT: G 33 GLU cc_start: 0.6692 (tt0) cc_final: 0.5757 (tm-30) REVERT: H 66 LYS cc_start: 0.7061 (mtpt) cc_final: 0.6444 (mmtp) REVERT: C 599 ARG cc_start: 0.8613 (mtt-85) cc_final: 0.7937 (mmt180) REVERT: C 808 LEU cc_start: 0.8463 (tp) cc_final: 0.8249 (tt) REVERT: D 760 ASP cc_start: 0.8457 (p0) cc_final: 0.8227 (p0) outliers start: 30 outliers final: 28 residues processed: 208 average time/residue: 0.5324 time to fit residues: 173.7798 Evaluate side-chains 212 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 683 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16572 Z= 0.210 Angle : 0.484 11.270 22483 Z= 0.259 Chirality : 0.053 1.377 2542 Planarity : 0.003 0.035 2697 Dihedral : 7.596 104.390 2637 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.71 % Allowed : 13.84 % Favored : 84.45 % 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: 0.59 (0.20), residues: 1996 helix: 1.72 (0.15), residues: 1258 sheet: -1.67 (0.47), residues: 138 loop : -2.05 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 88 HIS 0.003 0.001 HIS E 75 PHE 0.012 0.001 PHE B 541 TYR 0.008 0.001 TYR E 149 ARG 0.002 0.000 ARG E 104 ********************** 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 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 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 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 VAL 395 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 434 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 506 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 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 697 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue THR 784 is missing expected H atoms. Skipping. Residue SER 785 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 2.617 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: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.8591 (mtt-85) cc_final: 0.7845 (mmp80) REVERT: B 596 LEU cc_start: 0.8989 (tp) cc_final: 0.8786 (tp) REVERT: E 80 ILE cc_start: 0.9314 (mm) cc_final: 0.9078 (mt) REVERT: E 147 PHE cc_start: 0.7527 (m-10) cc_final: 0.6703 (t80) REVERT: F 66 LYS cc_start: 0.6796 (mtpt) cc_final: 0.6164 (mmmm) REVERT: F 155 TYR cc_start: 0.6334 (m-80) cc_final: 0.5717 (m-80) REVERT: G 33 GLU cc_start: 0.6758 (tt0) cc_final: 0.5768 (tm-30) REVERT: H 66 LYS cc_start: 0.7070 (mtpt) cc_final: 0.6443 (mmtp) REVERT: C 599 ARG cc_start: 0.8614 (mtt-85) cc_final: 0.7857 (mmp80) REVERT: C 808 LEU cc_start: 0.8474 (tp) cc_final: 0.8257 (tt) REVERT: D 760 ASP cc_start: 0.8448 (p0) cc_final: 0.8200 (p0) outliers start: 28 outliers final: 27 residues processed: 204 average time/residue: 0.5315 time to fit residues: 169.4129 Evaluate side-chains 207 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 683 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 158 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.116374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.096240 restraints weight = 124844.713| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.27 r_work: 0.3422 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16572 Z= 0.142 Angle : 0.465 11.239 22483 Z= 0.245 Chirality : 0.052 1.374 2542 Planarity : 0.003 0.049 2697 Dihedral : 7.141 99.810 2635 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.59 % Allowed : 14.08 % Favored : 84.32 % 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: 0.87 (0.20), residues: 1996 helix: 1.94 (0.15), residues: 1250 sheet: -1.56 (0.47), residues: 138 loop : -1.89 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 605 HIS 0.003 0.001 HIS F 75 PHE 0.012 0.001 PHE B 541 TYR 0.009 0.001 TYR E 149 ARG 0.007 0.000 ARG D 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5959.85 seconds wall clock time: 106 minutes 16.07 seconds (6376.07 seconds total)