Starting phenix.real_space_refine on Fri Mar 22 04:57:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peq_20330/03_2024/6peq_20330_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peq_20330/03_2024/6peq_20330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peq_20330/03_2024/6peq_20330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peq_20330/03_2024/6peq_20330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peq_20330/03_2024/6peq_20330_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peq_20330/03_2024/6peq_20330_trim_updated.pdb" } resolution = 2.97 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 10874 2.51 5 N 2490 2.21 5 O 2826 1.98 5 F 12 1.80 5 H 15197 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 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A 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 PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B 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 TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 545": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 608": "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 ASP 760": "OD1" <-> "OD2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 22": "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 "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H 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 "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 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C 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 PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D 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 TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 545": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 608": "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 ASP 760": "OD1" <-> "OD2" Residue "D PHE 814": "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: 31523 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 5559 Classifications: {'peptide': 380} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 5558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5558 Classifications: {'peptide': 376} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 364} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "E" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2118 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2185 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: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2129 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2185 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: 5559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 5559 Classifications: {'peptide': 380} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 5558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5558 Classifications: {'peptide': 376} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 364} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Unusual residues: {'OLC': 1, 'PAM': 3, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {'OLC': 2, 'PAM': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {'OLC': 2, 'PAM': 3, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 156 Unusual residues: {'OLC': 3, 'PAM': 3, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 13.24, per 1000 atoms: 0.42 Number of scatterers: 31523 At special positions: 0 Unit cell: (118.326, 99.138, 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 2826 8.00 N 2490 7.00 C 10874 6.00 H 15197 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.31 Conformation dependent library (CDL) restraints added in 3.5 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: 3820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 12 sheets defined 58.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.21 Creating SS restraints... Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 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: 3.798A 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 641 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 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: 3.685A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.782A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 626 removed outlier: 3.628A 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 665 through 675 Processing helix chain 'B' and resid 686 through 694 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 743 through 756 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 Processing helix chain 'E' and resid 6 through 36 removed outlier: 3.662A pdb=" N ALA E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 66 removed outlier: 4.210A pdb=" N ILE E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 84 Processing helix chain 'E' and resid 88 through 106 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 128 through 157 removed outlier: 3.617A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 37 Processing helix chain 'F' and resid 49 through 67 Processing helix chain 'F' and resid 69 through 84 Processing helix chain 'F' and resid 91 through 107 Proline residue: F 96 - end of helix removed outlier: 3.853A pdb=" N TYR F 105 " --> pdb=" O HIS F 101 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 157 removed outlier: 5.462A pdb=" N GLN F 132 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 36 removed outlier: 3.662A pdb=" N ALA G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 66 removed outlier: 4.209A pdb=" N ILE G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 84 Processing helix chain 'G' and resid 88 through 106 Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 128 through 157 removed outlier: 3.617A pdb=" N PHE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 37 Processing helix chain 'H' and resid 49 through 67 Processing helix chain 'H' and resid 69 through 84 Processing helix chain 'H' and resid 91 through 107 Proline residue: H 96 - end of helix removed outlier: 3.854A pdb=" N TYR H 105 " --> pdb=" O HIS H 101 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE H 106 " --> pdb=" O PHE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 157 removed outlier: 5.462A pdb=" N GLN H 132 " --> pdb=" O SER H 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 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: 3.798A 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 641 Processing helix chain 'C' and resid 654 through 660 Processing helix chain 'C' and resid 665 through 676 Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 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: 3.685A pdb=" N ALA C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 523 through 545 removed outlier: 3.782A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 626 removed outlier: 3.629A 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 665 through 675 Processing helix chain 'D' and resid 686 through 694 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 743 through 756 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 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: 3.741A 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: 6.477A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.487A 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 496 through 498 removed outlier: 3.589A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.070A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= H, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.741A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 500 through 503 removed outlier: 6.477A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 451 through 453 Processing sheet with id= K, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.590A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.069A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 874 hydrogen bonds defined for protein. 2436 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: 11.13 Time building geometry restraints manager: 26.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15145 1.03 - 1.24: 2065 1.24 - 1.45: 5171 1.45 - 1.65: 9340 1.65 - 1.86: 184 Bond restraints: 31905 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 8.38e+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 8.34e+01 bond pdb=" CAU ZK1 D 901 " pdb=" OAB ZK1 D 901 " ideal model delta sigma weight residual 1.215 1.398 -0.183 2.00e-02 2.50e+03 8.33e+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 8.29e+01 bond pdb=" CAT ZK1 D 901 " pdb=" OAA ZK1 D 901 " ideal model delta sigma weight residual 1.214 1.396 -0.182 2.00e-02 2.50e+03 8.29e+01 ... (remaining 31900 not shown) Histogram of bond angle deviations from ideal: 72.20 - 84.56: 6 84.56 - 96.92: 0 96.92 - 109.28: 19541 109.28 - 121.64: 31869 121.64 - 134.00: 5589 Bond angle restraints: 57005 Sorted by residual: angle pdb=" CB ALA H 19 " pdb=" CA ALA H 19 " pdb=" HA ALA H 19 " ideal model delta sigma weight residual 109.00 72.20 36.80 3.00e+00 1.11e-01 1.51e+02 angle pdb=" N ALA H 19 " pdb=" CA ALA H 19 " pdb=" HA ALA H 19 " ideal model delta sigma weight residual 110.00 73.86 36.14 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C ALA H 19 " pdb=" CA ALA H 19 " pdb=" HA ALA H 19 " ideal model delta sigma weight residual 109.00 73.60 35.40 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB LEU H 16 " pdb=" CG LEU H 16 " pdb=" HG LEU H 16 " ideal model delta sigma weight residual 109.00 78.43 30.57 3.00e+00 1.11e-01 1.04e+02 angle pdb=" CD2 LEU H 16 " pdb=" CG LEU H 16 " pdb=" HG LEU H 16 " ideal model delta sigma weight residual 108.00 77.93 30.07 3.00e+00 1.11e-01 1.00e+02 ... (remaining 57000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 15090 35.43 - 70.86: 451 70.86 - 106.30: 10 106.30 - 141.73: 12 141.73 - 177.16: 9 Dihedral angle restraints: 15572 sinusoidal: 8186 harmonic: 7386 Sorted by residual: dihedral pdb=" O23 OLC B 902 " pdb=" C22 OLC B 902 " pdb=" C24 OLC B 902 " pdb=" O25 OLC B 902 " ideal model delta sinusoidal sigma weight residual 60.48 -116.68 177.16 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 OLC B 902 " pdb=" C22 OLC B 902 " pdb=" C24 OLC B 902 " pdb=" O25 OLC B 902 " ideal model delta sinusoidal sigma weight residual -174.20 2.59 -176.79 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O20 OLC A 902 " pdb=" C21 OLC A 902 " pdb=" C22 OLC A 902 " pdb=" O23 OLC A 902 " ideal model delta sinusoidal sigma weight residual 302.77 126.49 176.28 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 15569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 2532 0.147 - 0.293: 8 0.293 - 0.440: 0 0.440 - 0.586: 8 0.586 - 0.733: 2 Chirality restraints: 2550 Sorted by residual: chirality pdb=" CG LEU H 16 " pdb=" CB LEU H 16 " pdb=" CD1 LEU H 16 " pdb=" CD2 LEU H 16 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU F 16 " pdb=" CB LEU F 16 " pdb=" CD1 LEU F 16 " pdb=" CD2 LEU F 16 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C22 OLC B 902 " pdb=" C21 OLC B 902 " pdb=" C24 OLC B 902 " pdb=" O23 OLC B 902 " both_signs ideal model delta sigma weight residual False -2.31 -2.81 0.50 2.00e-01 2.50e+01 6.29e+00 ... (remaining 2547 not shown) Planarity restraints: 4660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PAM A 904 " 0.347 2.00e-02 2.50e+03 2.53e-01 6.38e+02 pdb=" C11 PAM A 904 " -0.110 2.00e-02 2.50e+03 pdb=" C8 PAM A 904 " 0.100 2.00e-02 2.50e+03 pdb=" C9 PAM A 904 " -0.336 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM A 903 " 0.338 2.00e-02 2.50e+03 2.46e-01 6.04e+02 pdb=" C11 PAM A 903 " -0.111 2.00e-02 2.50e+03 pdb=" C8 PAM A 903 " 0.098 2.00e-02 2.50e+03 pdb=" C9 PAM A 903 " -0.325 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM C 904 " -0.327 2.00e-02 2.50e+03 2.39e-01 5.73e+02 pdb=" C11 PAM C 904 " 0.107 2.00e-02 2.50e+03 pdb=" C8 PAM C 904 " -0.098 2.00e-02 2.50e+03 pdb=" C9 PAM C 904 " 0.318 2.00e-02 2.50e+03 ... (remaining 4657 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1423 2.18 - 2.79: 62208 2.79 - 3.39: 86042 3.39 - 4.00: 108924 4.00 - 4.60: 172478 Nonbonded interactions: 431075 Sorted by model distance: nonbonded pdb=" O ALA B 433 " pdb=" H GLY B 437 " model vdw 1.575 1.850 nonbonded pdb=" O ALA D 433 " pdb=" H GLY D 437 " model vdw 1.576 1.850 nonbonded pdb=" H SER B 654 " pdb=" OAD ZK1 B 901 " model vdw 1.594 1.850 nonbonded pdb=" H SER D 654 " pdb=" OAD ZK1 D 901 " model vdw 1.604 1.850 nonbonded pdb=" O PRO A 520 " pdb="HD21 ASN A 619 " model vdw 1.609 1.850 ... (remaining 431070 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 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 435 through 453 or (r \ esid 454 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 455 or (resid 456 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 457 through 633 or (resid 634 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 63 \ 5 through 642 or (resid 643 through 644 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 645 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 re \ sid 676 through 715 or (resid 716 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 717 through 741 or (resid 742 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 74 \ 3 through 751 or (resid 752 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 753 through 754 or (resid 755 through 756 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 757 through 760 or (resid 761 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 762 through 768 or (resid 769 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 77 \ 0 through 774 or (resid 784 and (name N or name CA or name C or name O or name C \ B or name HA )) or (resid 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 or \ resid 905)) selection = (chain 'B' and ((resid 394 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2)) or resid 395 through 505 or (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 or \ (resid 508 through 509 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 510 through 637 or (resid 638 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 639 through 6 \ 50 or (resid 651 through 652 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 653 through 655 or (resid 656 through 657 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 658 through 659 or (resid 660 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name H or name HA )) or resid 661 through 662 or (resid 663 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 664 through 6 \ 94 or (resid 695 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 696 through 743 or (resid 744 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 745 through 759 or \ (resid 760 through 761 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 762 through 763 or (resid 764 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 765 through 7 \ 71 or (resid 772 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 773 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 thr \ ough 902 or resid 905)) selection = (chain 'C' and (resid 394 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 435 through 453 or (r \ esid 454 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 455 or (resid 456 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 457 through 633 or (resid 634 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 63 \ 5 through 642 or (resid 643 through 644 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 645 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 re \ sid 676 through 715 or (resid 716 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 717 through 741 or (resid 742 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 74 \ 3 through 751 or (resid 752 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 753 through 754 or (resid 755 through 756 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 757 through 760 or (resid 761 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 762 through 768 or (resid 769 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 77 \ 0 through 774 or (resid 784 and (name N or name CA or name C or name O or name C \ B or name HA )) or (resid 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 or \ resid 905)) selection = (chain 'D' and ((resid 394 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2)) or resid 395 through 505 or (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 or \ (resid 508 through 509 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 510 through 637 or (resid 638 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 639 through 6 \ 50 or (resid 651 through 652 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 653 through 655 or (resid 656 through 657 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 658 through 659 or (resid 660 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name H or name HA )) or resid 661 through 662 or (resid 663 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 664 through 6 \ 94 or (resid 695 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 696 through 743 or (resid 744 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 745 through 759 or \ (resid 760 through 761 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 762 through 763 or (resid 764 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 765 through 7 \ 71 or (resid 772 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 773 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 thr \ ough 902 or resid 905)) } ncs_group { reference = (chain 'E' and (resid 2 through 108 or resid 110 through 159)) selection = (chain 'F' and (resid 2 through 37 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (resid \ 51 through 58 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 59 through 103 or (resid 104 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 105 through 108 or resid 125 or (r \ esid 126 and (name N or name CA or name C or name O or name CB or name HA )) or \ resid 127 through 159)) selection = (chain 'G' and (resid 2 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 105 through 108 or resid 110 throug \ h 159)) selection = (chain 'H' and (resid 2 through 37 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (resid \ 51 through 58 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 59 through 103 or (resid 104 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 105 through 108 or resid 125 or (r \ esid 126 and (name N or name CA or name C or name O or name CB or name HA )) or \ resid 127 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: 3.650 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: 0.490 Extract box with map and model: 11.840 Check model and map are aligned: 0.440 Set scattering table: 0.230 Process input model: 98.850 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.009 0.183 16708 Z= 0.588 Angle : 0.742 10.607 22594 Z= 0.320 Chirality : 0.051 0.733 2550 Planarity : 0.016 0.253 2700 Dihedral : 16.466 177.160 6132 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: -3.10 (0.16), residues: 1996 helix: -1.01 (0.13), residues: 1234 sheet: -3.26 (0.36), residues: 168 loop : -3.75 (0.20), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.012 0.001 HIS G 27 PHE 0.011 0.001 PHE C 546 TYR 0.018 0.001 TYR H 148 ARG 0.002 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 351 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 2.564 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 670 MET cc_start: 0.9209 (mtp) cc_final: 0.8987 (mtm) REVERT: B 519 ASP cc_start: 0.8407 (m-30) cc_final: 0.8201 (m-30) REVERT: B 523 TYR cc_start: 0.7057 (m-80) cc_final: 0.6780 (m-80) REVERT: B 713 GLU cc_start: 0.8300 (tt0) cc_final: 0.7949 (tm-30) REVERT: B 726 ASN cc_start: 0.9069 (m-40) cc_final: 0.8788 (m-40) REVERT: E 23 PHE cc_start: 0.6501 (t80) cc_final: 0.6137 (t80) REVERT: E 61 CYS cc_start: 0.7564 (t) cc_final: 0.7344 (t) REVERT: E 133 LYS cc_start: 0.7221 (mttm) cc_final: 0.6506 (pttp) REVERT: F 65 ARG cc_start: 0.7886 (mtm180) cc_final: 0.7079 (mmt180) REVERT: G 133 LYS cc_start: 0.7574 (mttm) cc_final: 0.6984 (ptmm) REVERT: H 65 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7092 (mmt180) REVERT: D 519 ASP cc_start: 0.8409 (m-30) cc_final: 0.8200 (m-30) REVERT: D 523 TYR cc_start: 0.7074 (m-80) cc_final: 0.6724 (m-10) REVERT: D 713 GLU cc_start: 0.8305 (tt0) cc_final: 0.7969 (tm-30) REVERT: D 726 ASN cc_start: 0.9044 (m-40) cc_final: 0.8767 (m-40) outliers start: 0 outliers final: 1 residues processed: 351 average time/residue: 1.8440 time to fit residues: 748.0593 Evaluate side-chains 207 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 80 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 158 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16708 Z= 0.197 Angle : 0.511 10.523 22594 Z= 0.257 Chirality : 0.049 1.688 2550 Planarity : 0.003 0.036 2700 Dihedral : 14.398 166.440 2904 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.52 % Allowed : 12.41 % Favored : 86.08 % 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: -1.43 (0.18), residues: 1996 helix: 0.32 (0.14), residues: 1230 sheet: -2.96 (0.38), residues: 168 loop : -2.97 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.006 0.001 HIS E 27 PHE 0.012 0.001 PHE E 62 TYR 0.010 0.001 TYR F 151 ARG 0.005 0.000 ARG C 675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 237 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 2.566 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 613 ILE cc_start: 0.9018 (pt) cc_final: 0.8771 (mt) REVERT: A 670 MET cc_start: 0.9213 (mtp) cc_final: 0.8972 (mtm) REVERT: B 503 MET cc_start: 0.8632 (ttp) cc_final: 0.8284 (ttp) REVERT: B 523 TYR cc_start: 0.7084 (m-80) cc_final: 0.6715 (m-10) REVERT: B 627 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6933 (tm-30) REVERT: B 708 MET cc_start: 0.7925 (mtp) cc_final: 0.7626 (mtt) REVERT: B 713 GLU cc_start: 0.8300 (tt0) cc_final: 0.7953 (tm-30) REVERT: B 726 ASN cc_start: 0.9103 (m-40) cc_final: 0.8661 (m-40) REVERT: E 11 MET cc_start: 0.9040 (mtt) cc_final: 0.8822 (mtp) REVERT: E 61 CYS cc_start: 0.7632 (t) cc_final: 0.7391 (t) REVERT: E 133 LYS cc_start: 0.7250 (mttm) cc_final: 0.6511 (pttp) REVERT: F 65 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7076 (mmt180) REVERT: G 11 MET cc_start: 0.9015 (mtt) cc_final: 0.8786 (mtp) REVERT: G 133 LYS cc_start: 0.7541 (mttm) cc_final: 0.6968 (ptmm) REVERT: H 65 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7110 (mmt180) REVERT: D 503 MET cc_start: 0.8629 (ttp) cc_final: 0.8309 (ttp) REVERT: D 523 TYR cc_start: 0.7118 (m-80) cc_final: 0.6731 (m-80) REVERT: D 713 GLU cc_start: 0.8297 (tt0) cc_final: 0.7973 (tm-30) REVERT: D 726 ASN cc_start: 0.9097 (m-40) cc_final: 0.8834 (m-40) outliers start: 24 outliers final: 10 residues processed: 223 average time/residue: 1.6408 time to fit residues: 431.6026 Evaluate side-chains 199 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 189 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16708 Z= 0.217 Angle : 0.489 9.896 22594 Z= 0.255 Chirality : 0.049 1.656 2550 Planarity : 0.003 0.029 2700 Dihedral : 12.551 165.038 2902 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.03 % Allowed : 14.37 % Favored : 83.61 % 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: -0.65 (0.19), residues: 1996 helix: 0.89 (0.15), residues: 1244 sheet: -2.65 (0.42), residues: 148 loop : -2.65 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.004 0.001 HIS E 27 PHE 0.010 0.001 PHE C 814 TYR 0.012 0.001 TYR H 151 ARG 0.003 0.000 ARG C 675 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 228 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 2.379 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: A 627 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: A 647 TYR cc_start: 0.8485 (p90) cc_final: 0.8108 (p90) REVERT: A 789 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8568 (tt) REVERT: B 503 MET cc_start: 0.8578 (ttp) cc_final: 0.8274 (ttp) REVERT: B 523 TYR cc_start: 0.7144 (m-80) cc_final: 0.6813 (m-80) REVERT: B 627 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7102 (tm-30) REVERT: B 708 MET cc_start: 0.8021 (mtp) cc_final: 0.7814 (mtt) REVERT: B 713 GLU cc_start: 0.8333 (tt0) cc_final: 0.8031 (tm-30) REVERT: B 726 ASN cc_start: 0.9123 (m-40) cc_final: 0.8831 (m-40) REVERT: E 11 MET cc_start: 0.9040 (mtt) cc_final: 0.8838 (mtp) REVERT: E 61 CYS cc_start: 0.7744 (t) cc_final: 0.7535 (t) REVERT: E 133 LYS cc_start: 0.7293 (mttm) cc_final: 0.6448 (pttp) REVERT: F 65 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7248 (mpt180) REVERT: G 133 LYS cc_start: 0.7386 (mttm) cc_final: 0.6852 (ptmm) REVERT: H 65 ARG cc_start: 0.7943 (mtm180) cc_final: 0.7204 (mpt180) REVERT: H 81 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7503 (ttp) REVERT: C 627 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: C 647 TYR cc_start: 0.8277 (p90) cc_final: 0.7847 (p90) REVERT: C 789 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8577 (tt) REVERT: D 503 MET cc_start: 0.8699 (ttp) cc_final: 0.8440 (ttp) REVERT: D 523 TYR cc_start: 0.7180 (m-80) cc_final: 0.6756 (m-80) REVERT: D 629 MET cc_start: 0.8052 (mmt) cc_final: 0.7842 (tpt) REVERT: D 713 GLU cc_start: 0.8374 (tt0) cc_final: 0.8050 (tm-30) REVERT: D 726 ASN cc_start: 0.9094 (m-40) cc_final: 0.8809 (m-40) outliers start: 32 outliers final: 13 residues processed: 218 average time/residue: 1.6811 time to fit residues: 436.9661 Evaluate side-chains 197 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 195 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16708 Z= 0.177 Angle : 0.475 9.949 22594 Z= 0.245 Chirality : 0.049 1.688 2550 Planarity : 0.003 0.030 2700 Dihedral : 11.590 174.863 2902 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.65 % Allowed : 16.01 % Favored : 82.34 % 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: -0.23 (0.20), residues: 1996 helix: 1.21 (0.15), residues: 1246 sheet: -2.32 (0.42), residues: 158 loop : -2.50 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.003 0.001 HIS E 27 PHE 0.010 0.001 PHE H 106 TYR 0.012 0.001 TYR H 151 ARG 0.002 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 2.654 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: A 627 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: A 647 TYR cc_start: 0.8266 (p90) cc_final: 0.7826 (p90) REVERT: A 789 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8651 (tt) REVERT: B 523 TYR cc_start: 0.7159 (m-80) cc_final: 0.6754 (m-80) REVERT: B 627 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7179 (tm-30) REVERT: B 708 MET cc_start: 0.8064 (mtp) cc_final: 0.7813 (mtt) REVERT: B 713 GLU cc_start: 0.8335 (tt0) cc_final: 0.8037 (tm-30) REVERT: B 726 ASN cc_start: 0.9127 (m-40) cc_final: 0.8825 (m-40) REVERT: E 61 CYS cc_start: 0.7495 (t) cc_final: 0.7260 (t) REVERT: E 133 LYS cc_start: 0.7314 (mttm) cc_final: 0.6435 (pttp) REVERT: F 65 ARG cc_start: 0.7935 (mtm180) cc_final: 0.7287 (mpt180) REVERT: G 133 LYS cc_start: 0.7430 (mttm) cc_final: 0.6903 (ptmm) REVERT: H 22 PHE cc_start: 0.7622 (t80) cc_final: 0.7314 (t80) REVERT: H 65 ARG cc_start: 0.7902 (mtm180) cc_final: 0.7201 (mpt180) REVERT: C 627 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: C 647 TYR cc_start: 0.8266 (p90) cc_final: 0.7780 (p90) REVERT: C 789 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8652 (tt) REVERT: D 523 TYR cc_start: 0.7174 (m-80) cc_final: 0.6756 (m-80) REVERT: D 627 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7128 (tm-30) REVERT: D 629 MET cc_start: 0.7908 (mmt) cc_final: 0.7572 (tpt) REVERT: D 713 GLU cc_start: 0.8371 (tt0) cc_final: 0.8051 (tm-30) REVERT: D 726 ASN cc_start: 0.9131 (m-40) cc_final: 0.8850 (m-40) outliers start: 26 outliers final: 15 residues processed: 209 average time/residue: 1.6343 time to fit residues: 403.4886 Evaluate side-chains 197 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 178 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16708 Z= 0.205 Angle : 0.471 9.859 22594 Z= 0.246 Chirality : 0.049 1.685 2550 Planarity : 0.003 0.032 2700 Dihedral : 10.687 148.827 2902 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.90 % Allowed : 16.20 % Favored : 81.90 % 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: -0.01 (0.20), residues: 1996 helix: 1.34 (0.15), residues: 1246 sheet: -2.22 (0.42), residues: 158 loop : -2.32 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE H 106 TYR 0.013 0.001 TYR H 151 ARG 0.002 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: A 647 TYR cc_start: 0.8407 (p90) cc_final: 0.7992 (p90) REVERT: A 821 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6406 (pp20) REVERT: B 523 TYR cc_start: 0.7154 (m-80) cc_final: 0.6800 (m-80) REVERT: B 627 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7153 (tm-30) REVERT: B 713 GLU cc_start: 0.8301 (tt0) cc_final: 0.8034 (tm-30) REVERT: B 726 ASN cc_start: 0.9147 (m-40) cc_final: 0.8839 (m-40) REVERT: E 61 CYS cc_start: 0.7515 (t) cc_final: 0.7279 (t) REVERT: E 133 LYS cc_start: 0.7283 (mttm) cc_final: 0.6463 (pttp) REVERT: F 22 PHE cc_start: 0.7631 (t80) cc_final: 0.7296 (t80) REVERT: F 65 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7163 (mpt180) REVERT: G 133 LYS cc_start: 0.7448 (mttm) cc_final: 0.6865 (ptmm) REVERT: H 22 PHE cc_start: 0.7449 (t80) cc_final: 0.7138 (t80) REVERT: H 65 ARG cc_start: 0.7841 (mtm180) cc_final: 0.7135 (mpt180) REVERT: C 627 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: C 647 TYR cc_start: 0.8257 (p90) cc_final: 0.7760 (p90) REVERT: C 789 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8768 (tt) REVERT: C 821 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6453 (pp20) REVERT: D 503 MET cc_start: 0.8658 (ttp) cc_final: 0.8429 (ttp) REVERT: D 523 TYR cc_start: 0.7227 (m-80) cc_final: 0.6799 (m-80) REVERT: D 627 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7176 (tm-30) REVERT: D 713 GLU cc_start: 0.8393 (tt0) cc_final: 0.8073 (tm-30) REVERT: D 726 ASN cc_start: 0.9136 (m-40) cc_final: 0.8827 (m-40) outliers start: 30 outliers final: 20 residues processed: 203 average time/residue: 1.6286 time to fit residues: 390.7556 Evaluate side-chains 199 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16708 Z= 0.313 Angle : 0.517 10.033 22594 Z= 0.275 Chirality : 0.050 1.679 2550 Planarity : 0.003 0.033 2700 Dihedral : 10.813 134.013 2902 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.59 % Allowed : 16.71 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 1996 helix: 1.15 (0.15), residues: 1248 sheet: -2.08 (0.43), residues: 158 loop : -2.23 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.005 0.001 HIS F 75 PHE 0.016 0.001 PHE D 531 TYR 0.012 0.001 TYR F 151 ARG 0.003 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 2.487 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: A 627 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: A 647 TYR cc_start: 0.8515 (p90) cc_final: 0.8102 (p90) REVERT: A 798 ILE cc_start: 0.8717 (pt) cc_final: 0.8482 (mp) REVERT: B 713 GLU cc_start: 0.8353 (tt0) cc_final: 0.8023 (tm-30) REVERT: E 133 LYS cc_start: 0.7264 (mttm) cc_final: 0.6464 (pttp) REVERT: F 22 PHE cc_start: 0.7737 (t80) cc_final: 0.7400 (t80) REVERT: F 65 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7114 (mpt180) REVERT: G 133 LYS cc_start: 0.7491 (mttm) cc_final: 0.6879 (pttp) REVERT: H 22 PHE cc_start: 0.7648 (t80) cc_final: 0.7377 (t80) REVERT: H 65 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7144 (mpt180) REVERT: C 627 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: D 431 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: D 523 TYR cc_start: 0.7307 (m-80) cc_final: 0.6945 (m-80) REVERT: D 713 GLU cc_start: 0.8355 (tt0) cc_final: 0.8046 (tm-30) outliers start: 41 outliers final: 24 residues processed: 203 average time/residue: 1.7013 time to fit residues: 407.2611 Evaluate side-chains 193 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16708 Z= 0.316 Angle : 0.528 9.878 22594 Z= 0.281 Chirality : 0.050 1.682 2550 Planarity : 0.003 0.032 2700 Dihedral : 10.768 126.408 2902 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.22 % Allowed : 17.91 % Favored : 79.87 % 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: -0.06 (0.19), residues: 1996 helix: 1.20 (0.15), residues: 1236 sheet: -1.99 (0.44), residues: 158 loop : -2.11 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 103 HIS 0.005 0.001 HIS H 75 PHE 0.052 0.002 PHE E 106 TYR 0.013 0.001 TYR H 151 ARG 0.006 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 207 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8547 (m-30) cc_final: 0.8283 (m-30) REVERT: A 627 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: A 647 TYR cc_start: 0.8539 (p90) cc_final: 0.8052 (p90) REVERT: B 627 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7246 (tm-30) REVERT: B 713 GLU cc_start: 0.8373 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 726 ASN cc_start: 0.9139 (m-40) cc_final: 0.8810 (m-40) REVERT: E 133 LYS cc_start: 0.7263 (mttm) cc_final: 0.6468 (pttp) REVERT: F 22 PHE cc_start: 0.7661 (t80) cc_final: 0.7352 (t80) REVERT: F 65 ARG cc_start: 0.7853 (mtm180) cc_final: 0.7088 (mpt180) REVERT: G 74 ILE cc_start: 0.8214 (pp) cc_final: 0.7782 (mp) REVERT: G 133 LYS cc_start: 0.7483 (mttm) cc_final: 0.6838 (pttp) REVERT: H 22 PHE cc_start: 0.7676 (t80) cc_final: 0.7410 (t80) REVERT: H 65 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7162 (mpt180) REVERT: C 627 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: C 647 TYR cc_start: 0.8541 (p90) cc_final: 0.8195 (p90) REVERT: D 431 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: D 523 TYR cc_start: 0.7328 (m-80) cc_final: 0.6982 (m-80) REVERT: D 627 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7334 (tm-30) REVERT: D 674 MET cc_start: 0.8192 (mtm) cc_final: 0.7973 (mtm) REVERT: D 713 GLU cc_start: 0.8376 (tt0) cc_final: 0.8019 (tm-30) REVERT: D 726 ASN cc_start: 0.9141 (m-40) cc_final: 0.8813 (m-40) outliers start: 35 outliers final: 22 residues processed: 194 average time/residue: 1.6277 time to fit residues: 373.1618 Evaluate side-chains 189 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16708 Z= 0.302 Angle : 0.533 9.878 22594 Z= 0.282 Chirality : 0.050 1.671 2550 Planarity : 0.003 0.033 2700 Dihedral : 10.751 116.431 2902 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.28 % Allowed : 18.04 % Favored : 79.68 % 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: 0.02 (0.19), residues: 1996 helix: 1.23 (0.15), residues: 1238 sheet: -1.93 (0.44), residues: 158 loop : -2.02 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 136 HIS 0.005 0.001 HIS G 75 PHE 0.017 0.001 PHE D 531 TYR 0.018 0.001 TYR F 142 ARG 0.006 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 202 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8550 (m-30) cc_final: 0.8282 (m-30) REVERT: A 627 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: B 713 GLU cc_start: 0.8368 (tt0) cc_final: 0.8046 (tm-30) REVERT: B 726 ASN cc_start: 0.9094 (m-40) cc_final: 0.8740 (m-40) REVERT: E 133 LYS cc_start: 0.7305 (mttm) cc_final: 0.6497 (pttp) REVERT: F 22 PHE cc_start: 0.7702 (t80) cc_final: 0.7390 (t80) REVERT: F 65 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7111 (mpt180) REVERT: G 74 ILE cc_start: 0.8220 (pp) cc_final: 0.7867 (mp) REVERT: G 133 LYS cc_start: 0.7508 (mttm) cc_final: 0.6811 (pttp) REVERT: H 22 PHE cc_start: 0.7703 (t80) cc_final: 0.7419 (t80) REVERT: C 627 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: D 408 MET cc_start: 0.5770 (mmm) cc_final: 0.5356 (tpp) REVERT: D 431 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: D 523 TYR cc_start: 0.7360 (m-80) cc_final: 0.6969 (m-80) REVERT: D 674 MET cc_start: 0.8176 (mtm) cc_final: 0.7963 (mtm) REVERT: D 713 GLU cc_start: 0.8376 (tt0) cc_final: 0.7999 (tm-30) REVERT: D 726 ASN cc_start: 0.9098 (m-40) cc_final: 0.8745 (m-40) outliers start: 36 outliers final: 20 residues processed: 189 average time/residue: 1.5672 time to fit residues: 352.0481 Evaluate side-chains 182 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL 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 81 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16708 Z= 0.207 Angle : 0.511 9.945 22594 Z= 0.268 Chirality : 0.049 1.682 2550 Planarity : 0.003 0.033 2700 Dihedral : 10.391 112.879 2902 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.65 % Allowed : 18.80 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1996 helix: 1.43 (0.15), residues: 1240 sheet: -1.85 (0.44), residues: 158 loop : -1.97 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 136 HIS 0.004 0.001 HIS E 75 PHE 0.024 0.001 PHE C 546 TYR 0.016 0.001 TYR F 142 ARG 0.005 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 190 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8522 (m-30) cc_final: 0.8249 (m-30) REVERT: A 627 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: B 713 GLU cc_start: 0.8328 (tt0) cc_final: 0.8011 (tm-30) REVERT: B 726 ASN cc_start: 0.9078 (m-40) cc_final: 0.8712 (m-40) REVERT: E 133 LYS cc_start: 0.7291 (mttm) cc_final: 0.6478 (pttp) REVERT: F 22 PHE cc_start: 0.7662 (t80) cc_final: 0.7371 (t80) REVERT: F 65 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7123 (mpt180) REVERT: G 74 ILE cc_start: 0.8157 (pp) cc_final: 0.7811 (mp) REVERT: G 133 LYS cc_start: 0.7517 (mttm) cc_final: 0.6816 (pttp) REVERT: H 14 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8569 (mp) REVERT: H 22 PHE cc_start: 0.7693 (t80) cc_final: 0.7418 (t80) REVERT: H 148 TYR cc_start: 0.7915 (t80) cc_final: 0.7661 (t80) REVERT: C 627 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: D 431 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: D 523 TYR cc_start: 0.7348 (m-80) cc_final: 0.6951 (m-80) REVERT: D 713 GLU cc_start: 0.8366 (tt0) cc_final: 0.7980 (tm-30) REVERT: D 726 ASN cc_start: 0.9084 (m-40) cc_final: 0.8719 (m-40) outliers start: 26 outliers final: 19 residues processed: 183 average time/residue: 1.6346 time to fit residues: 356.1693 Evaluate side-chains 186 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 798 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16708 Z= 0.253 Angle : 0.528 10.002 22594 Z= 0.277 Chirality : 0.050 1.682 2550 Planarity : 0.003 0.037 2700 Dihedral : 10.356 118.356 2902 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.90 % Allowed : 19.05 % Favored : 79.05 % 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: 0.26 (0.20), residues: 1996 helix: 1.43 (0.15), residues: 1238 sheet: -1.83 (0.44), residues: 158 loop : -1.93 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 136 HIS 0.004 0.001 HIS H 75 PHE 0.024 0.001 PHE C 546 TYR 0.014 0.001 TYR F 10 ARG 0.005 0.000 ARG A 675 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 410 is missing expected H atoms. Skipping. Residue MET 414 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue LYS 441 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 VAL 48 is missing expected H atoms. Skipping. Residue LEU 54 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 506 is missing expected H atoms. Skipping. Residue LYS 509 is missing expected H atoms. Skipping. Residue SER 652 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LYS 663 is missing expected H atoms. Skipping. Residue LYS 695 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 738 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 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 THR 643 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 716 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 742 is missing expected H atoms. Skipping. Residue LYS 752 is missing expected H atoms. Skipping. Residue LYS 761 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 198 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8533 (m-30) cc_final: 0.8255 (m-30) REVERT: A 627 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 674 MET cc_start: 0.8122 (mtp) cc_final: 0.7885 (mtm) REVERT: B 713 GLU cc_start: 0.8368 (tt0) cc_final: 0.8004 (tm-30) REVERT: B 726 ASN cc_start: 0.9093 (m-40) cc_final: 0.8758 (m-40) REVERT: E 71 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: E 133 LYS cc_start: 0.7283 (mttm) cc_final: 0.6457 (pttp) REVERT: F 22 PHE cc_start: 0.7710 (t80) cc_final: 0.7421 (t80) REVERT: F 65 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7161 (mpt180) REVERT: G 133 LYS cc_start: 0.7525 (mttm) cc_final: 0.6821 (pttp) REVERT: G 136 TRP cc_start: 0.6568 (t-100) cc_final: 0.6326 (m100) REVERT: H 22 PHE cc_start: 0.7711 (t80) cc_final: 0.7441 (t80) REVERT: C 627 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: D 431 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: D 523 TYR cc_start: 0.7357 (m-80) cc_final: 0.6962 (m-80) REVERT: D 713 GLU cc_start: 0.8365 (tt0) cc_final: 0.8005 (tm-30) outliers start: 30 outliers final: 19 residues processed: 187 average time/residue: 1.5863 time to fit residues: 352.6052 Evaluate side-chains 184 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 613 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 147 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.119068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.092818 restraints weight = 99214.772| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.98 r_work: 0.3243 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16708 Z= 0.159 Angle : 0.509 10.131 22594 Z= 0.262 Chirality : 0.049 1.682 2550 Planarity : 0.003 0.033 2700 Dihedral : 9.915 117.742 2902 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.58 % Allowed : 19.68 % Favored : 78.73 % 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: 0.52 (0.20), residues: 1996 helix: 1.65 (0.15), residues: 1238 sheet: -1.86 (0.45), residues: 148 loop : -1.83 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 136 HIS 0.003 0.001 HIS G 75 PHE 0.027 0.001 PHE C 546 TYR 0.015 0.001 TYR F 151 ARG 0.004 0.000 ARG A 675 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8564.73 seconds wall clock time: 150 minutes 56.65 seconds (9056.65 seconds total)