Starting phenix.real_space_refine on Fri Mar 15 18:01:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/03_2024/7cwt_30487_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/03_2024/7cwt_30487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/03_2024/7cwt_30487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/03_2024/7cwt_30487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/03_2024/7cwt_30487_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/03_2024/7cwt_30487_trim.pdb" } resolution = 3.7 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= 0.002 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: 5 Type Number sf(0) Gaussians S 165 5.16 5 C 22606 2.51 5 N 5941 2.21 5 O 6926 1.98 5 H 34386 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 466": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1019": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 466": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1019": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 1019": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 70024 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 16426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 16426 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 49, 'TRANS': 1015} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 16515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 16515 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 49, 'TRANS': 1021} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 16571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 16571 Classifications: {'peptide': 1074} Link IDs: {'CIS': 1, 'PTRANS': 51, 'TRANS': 1021} Chain breaks: 6 Chain: "D" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1639 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1761 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1648 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1761 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1557 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "I" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1761 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1648 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1557 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1809 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 112} Chain: "M" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1557 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1809 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 112} Chain: "P" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1809 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 112} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 22.22, per 1000 atoms: 0.32 Number of scatterers: 70024 At special positions: 0 Unit cell: (214.24, 212.16, 221.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 165 16.00 O 6926 8.00 N 5941 7.00 C 22606 6.00 H 34386 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.09 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 91 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.42 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 91 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 97 " distance=2.04 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 Links applied NAG-ASN " NAG A1201 " - " ASN A 616 " " NAG A1202 " - " ASN A1074 " " NAG A1203 " - " ASN A 801 " " NAG A1204 " - " ASN A1098 " " NAG A1205 " - " ASN A 717 " " NAG B1201 " - " ASN B 616 " " NAG B1202 " - " ASN B 801 " " NAG B1203 " - " ASN B1098 " " NAG C1201 " - " ASN C 717 " " NAG C1202 " - " ASN C 801 " " NAG C1203 " - " ASN C1074 " " NAG C1204 " - " ASN C 343 " " NAG C1205 " - " ASN C 658 " " NAG C1206 " - " ASN C 616 " Time building additional restraints: 41.88 Conformation dependent library (CDL) restraints added in 5.2 seconds 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8444 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 83 sheets defined 17.9% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.651A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.642A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.502A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.519A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.612A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.543A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.038A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.999A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.867A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.547A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.546A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.518A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.612A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.542A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.039A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.748A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.627A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.074A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.519A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.642A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.776A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 4.023A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.519A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.613A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.598A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.038A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 80 through 84 removed outlier: 4.334A pdb=" N GLU H 84 " --> pdb=" O THR H 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 33 Processing helix chain 'N' and resid 29 through 33 Processing helix chain 'P' and resid 29 through 33 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.273A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.016A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.402A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.843A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.846A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.516A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.166A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.918A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.274A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.016A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.403A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.843A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.846A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 355 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.845A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.166A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.660A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.095A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.673A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 318 removed outlier: 3.840A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.685A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.576A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.703A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.169A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.769A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'D' and resid 9 through 12 removed outlier: 5.955A pdb=" N LEU D 10 " --> pdb=" O GLU D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 47 through 52 removed outlier: 5.997A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.544A pdb=" N VAL E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AG1, first strand: chain 'F' and resid 9 through 12 removed outlier: 5.956A pdb=" N LEU F 10 " --> pdb=" O GLU F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'F' and resid 47 through 52 removed outlier: 5.998A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.544A pdb=" N VAL G 12 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.544A pdb=" N VAL G 12 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR G 109 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP H 86 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR H 91 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL H 100 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 20 through 23 Processing sheet with id=AG9, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AH1, first strand: chain 'I' and resid 18 through 19 removed outlier: 3.879A pdb=" N THR I 69 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 45 through 50 removed outlier: 5.309A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AH4, first strand: chain 'J' and resid 9 through 12 removed outlier: 5.956A pdb=" N LEU J 10 " --> pdb=" O GLU J 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'J' and resid 47 through 52 removed outlier: 5.994A pdb=" N TRP J 38 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.689A pdb=" N ASP K 86 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR K 50 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR K 91 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL K 100 " --> pdb=" O THR K 91 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 20 through 23 Processing sheet with id=AH9, first strand: chain 'L' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN L 3 " --> pdb=" O SER L 26 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 22 through 23 removed outlier: 3.600A pdb=" N ALA L 80 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 46 through 49 Processing sheet with id=AI3, first strand: chain 'M' and resid 9 through 12 removed outlier: 3.689A pdb=" N ASP M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 9 through 12 removed outlier: 3.735A pdb=" N THR M 91 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL M 100 " --> pdb=" O THR M 91 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 20 through 23 Processing sheet with id=AI6, first strand: chain 'N' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN N 3 " --> pdb=" O SER N 26 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.600A pdb=" N ALA N 80 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 46 through 49 Processing sheet with id=AI9, first strand: chain 'P' and resid 3 through 4 removed outlier: 3.836A pdb=" N GLN P 3 " --> pdb=" O SER P 26 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'P' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA P 80 " --> pdb=" O CYS P 23 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'P' and resid 46 through 49 1194 hydrogen bonds defined for protein. 3162 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: 32.83 Time building geometry restraints manager: 44.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 34370 1.01 - 1.22: 39 1.22 - 1.42: 15520 1.42 - 1.63: 20674 1.63 - 1.83: 219 Bond restraints: 70822 Sorted by residual: bond pdb=" CA VAL C 382 " pdb=" HA VAL C 382 " ideal model delta sigma weight residual 0.970 0.807 0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CA GLN J 103 " pdb=" C GLN J 103 " ideal model delta sigma weight residual 1.523 1.421 0.102 1.34e-02 5.57e+03 5.81e+01 bond pdb=" C GLN J 103 " pdb=" N GLY J 104 " ideal model delta sigma weight residual 1.331 1.247 0.084 1.46e-02 4.69e+03 3.31e+01 bond pdb=" CA CYS C 617 " pdb=" CB CYS C 617 " ideal model delta sigma weight residual 1.530 1.436 0.095 1.69e-02 3.50e+03 3.13e+01 bond pdb=" N GLN J 103 " pdb=" CA GLN J 103 " ideal model delta sigma weight residual 1.457 1.515 -0.058 1.29e-02 6.01e+03 1.99e+01 ... (remaining 70817 not shown) Histogram of bond angle deviations from ideal: 94.68 - 102.67: 186 102.67 - 110.66: 68597 110.66 - 118.65: 26875 118.65 - 126.64: 31260 126.64 - 134.63: 446 Bond angle restraints: 127364 Sorted by residual: angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 113.20 102.84 10.36 9.60e-01 1.09e+00 1.17e+02 angle pdb=" O CYS C 379 " pdb=" C CYS C 379 " pdb=" N TYR C 380 " ideal model delta sigma weight residual 123.14 111.24 11.90 1.30e+00 5.92e-01 8.38e+01 angle pdb=" N CYS B 301 " pdb=" CA CYS B 301 " pdb=" C CYS B 301 " ideal model delta sigma weight residual 113.23 102.35 10.88 1.24e+00 6.50e-01 7.70e+01 angle pdb=" N CYS A 301 " pdb=" CA CYS A 301 " pdb=" C CYS A 301 " ideal model delta sigma weight residual 113.23 102.36 10.87 1.24e+00 6.50e-01 7.69e+01 angle pdb=" N TYR C 380 " pdb=" CA TYR C 380 " pdb=" C TYR C 380 " ideal model delta sigma weight residual 111.40 101.75 9.65 1.22e+00 6.72e-01 6.26e+01 ... (remaining 127359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 32555 25.07 - 50.14: 1256 50.14 - 75.22: 321 75.22 - 100.29: 45 100.29 - 125.36: 3 Dihedral angle restraints: 34180 sinusoidal: 18408 harmonic: 15772 Sorted by residual: dihedral pdb=" CA ALA A 123 " pdb=" C ALA A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 54.64 125.36 0 5.00e+00 4.00e-02 6.29e+02 dihedral pdb=" CA ALA B 123 " pdb=" C ALA B 123 " pdb=" N THR B 124 " pdb=" CA THR B 124 " ideal model delta harmonic sigma weight residual 180.00 54.67 125.33 0 5.00e+00 4.00e-02 6.28e+02 dihedral pdb=" CA GLY I 105 " pdb=" C GLY I 105 " pdb=" N THR I 106 " pdb=" CA THR I 106 " ideal model delta harmonic sigma weight residual -180.00 -61.17 -118.83 0 5.00e+00 4.00e-02 5.65e+02 ... (remaining 34177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.810: 5608 0.810 - 1.621: 0 1.621 - 2.431: 0 2.431 - 3.241: 0 3.241 - 4.052: 2 Chirality restraints: 5610 Sorted by residual: chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 1.65 -4.05 2.00e-01 2.50e+01 4.10e+02 chirality pdb=" C1 NAG C1206 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1206 " pdb=" O5 NAG C1206 " both_signs ideal model delta sigma weight residual False -2.40 1.59 -3.99 2.00e-01 2.50e+01 3.98e+02 chirality pdb=" CA PHE C 559 " pdb=" N PHE C 559 " pdb=" C PHE C 559 " pdb=" CB PHE C 559 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 ... (remaining 5607 not shown) Planarity restraints: 10742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1201 " 0.322 2.00e-02 2.50e+03 2.78e-01 9.67e+02 pdb=" C7 NAG A1201 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A1201 " 0.024 2.00e-02 2.50e+03 pdb=" N2 NAG A1201 " -0.482 2.00e-02 2.50e+03 pdb=" O7 NAG A1201 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1202 " 0.307 2.00e-02 2.50e+03 2.69e-01 9.06e+02 pdb=" C7 NAG B1202 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG B1202 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG B1202 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG B1202 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1205 " 0.310 2.00e-02 2.50e+03 2.69e-01 9.02e+02 pdb=" C7 NAG C1205 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG C1205 " 0.021 2.00e-02 2.50e+03 pdb=" N2 NAG C1205 " -0.467 2.00e-02 2.50e+03 pdb=" O7 NAG C1205 " 0.204 2.00e-02 2.50e+03 ... (remaining 10739 not shown) Histogram of nonbonded interaction distances: 0.40 - 1.24: 38 1.24 - 2.08: 3116 2.08 - 2.92: 185446 2.92 - 3.76: 296030 3.76 - 4.60: 512143 Warning: very small nonbonded interaction distances. Nonbonded interactions: 996773 Sorted by model distance: nonbonded pdb="HD11 LEU A 276 " pdb=" HE1 PHE A 306 " model vdw 0.395 2.270 nonbonded pdb="HD11 LEU B 276 " pdb=" HE1 PHE B 306 " model vdw 0.396 2.270 nonbonded pdb="HD21 LEU C 48 " pdb=" HE2 PHE C 306 " model vdw 0.453 2.270 nonbonded pdb="HD21 LEU C 48 " pdb=" CE2 PHE C 306 " model vdw 0.591 2.970 nonbonded pdb=" HE1 PHE A 392 " pdb=" CD2 LEU A 517 " model vdw 0.636 2.750 ... (remaining 996768 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 14 through 342 or (resid 343 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD22)) or resid 344 through 364 or (resid 365 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2 or name CE1 or name CE2 or name CZ or name OH or name HA or name HB2 or \ name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HH )) or (resid \ 366 and (name N or name CA or name C or name O or name CB or name OG or name HA \ or name HB2 or name HB3 or name HG )) or resid 367 through 387 or (resid 388 an \ d (name N or name CA or name C or name O or name CB or name CG or name OD1 or na \ me ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or resid 389 \ through 392 or (resid 393 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name H or name HA or name HB or name HG21 or name HG2 \ 2 or name HG23)) or resid 394 through 429 or (resid 430 and (name N or name CA o \ r name C or name O or name CB or name OG1 or name CG2 or name H or name HA or na \ me HB or name HG21 or name HG22 or name HG23)) or resid 431 through 656 or (resi \ d 657 and (name N or name CA or name C or name O or name CB or name CG or name O \ D1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or (r \ esid 658 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or \ resid 659 through 982 or (resid 983 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 o \ r name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH21 or name HH22)) or resid 984 through 1147 or \ resid 1201 through 1203)) selection = (chain 'B' and (resid 14 through 327 or (resid 335 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 336 through 342 or (resid 343 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or nam \ e H or name HA or name HB2 or name HB3 or name HD22)) or resid 344 through 392 o \ r (resid 393 and (name N or name CA or name C or name O or name CB or name OG1 o \ r name CG2 or name H or name HA or name HB or name HG21 or name HG22 or name HG2 \ 3)) or resid 394 through 429 or (resid 430 and (name N or name CA or name C or n \ ame O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name \ HG21 or name HG22 or name HG23)) or resid 431 through 525 or (resid 532 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) or resid 533 th \ rough 656 or (resid 657 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or \ name HD22)) or (resid 658 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 \ or name HD21)) or resid 659 through 716 or (resid 717 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2 or name H or nam \ e HA or name HB2 or name HB3 or name HD22)) or resid 718 through 1073 or (resid \ 1074 and (name N or name CA or name C or name O or name CB or name CG or name OD \ 1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or res \ id 1075 through 1147 or resid 1201 through 1203)) selection = (chain 'C' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 22 through 327 or (resid \ 335 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name HA or name HB2 or name HB3 or name HG or name HD11 or name \ HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or resid 336 through \ 364 or (resid 365 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or nam \ e HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or \ name HH )) or (resid 366 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 367 through \ 387 or (resid 388 and (name N or name CA or name C or name O or name CB or name \ CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name \ HD22)) or resid 389 through 525 or (resid 532 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 or \ name HB3 or name HD21 or name HD22)) or resid 533 through 982 or (resid 983 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 name HB2 or name \ HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH21 or n \ ame HH22)) or resid 984 through 1097 or (resid 1098 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name H or name H \ A or name HB2 or name HB3 or name HD22)) or resid 1099 through 1147 or resid 120 \ 1 through 1203)) } ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 4 through 112)) selection = (chain 'J' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 4 through 112)) } ncs_group { reference = (chain 'E' and (resid 2 through 93 or (resid 94 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2)) or resid 95 through 119)) selection = (chain 'G' and (resid 2 through 93 or (resid 94 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2)) or resid 95 through 119)) selection = (chain 'I' and (resid 2 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 23 through 119)) } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 0.780 Extract box with map and model: 9.660 Check model and map are aligned: 0.770 Set scattering table: 0.490 Process input model: 173.160 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4709 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 0.102 36436 Z= 0.602 Angle : 1.177 14.690 49542 Z= 0.775 Chirality : 0.109 4.052 5610 Planarity : 0.011 0.278 6394 Dihedral : 11.070 125.360 13209 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 28.32 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.91 % Favored : 92.52 % Rotamer: Outliers : 1.43 % Allowed : 3.01 % Favored : 95.56 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -2.94 (0.10), residues: 4518 helix: -2.40 (0.17), residues: 669 sheet: -1.58 (0.15), residues: 933 loop : -2.04 (0.10), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP A 436 HIS 0.007 0.002 HIS C1048 PHE 0.027 0.003 PHE F 35 TYR 0.035 0.002 TYR C 380 ARG 0.012 0.001 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 803 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue THR 393 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Evaluate side-chains 730 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 674 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 40 ASP cc_start: 0.6385 (m-30) cc_final: 0.5241 (p0) REVERT: A 466 ARG cc_start: -0.0031 (OUTLIER) cc_final: -0.0236 (ptt-90) REVERT: B 239 GLN cc_start: 0.5373 (tt0) cc_final: 0.5069 (tt0) REVERT: C 565 PHE cc_start: 0.5750 (m-10) cc_final: 0.3850 (p90) REVERT: C 1118 ASP cc_start: 0.5985 (m-30) cc_final: 0.5773 (m-30) REVERT: I 83 MET cc_start: 0.2946 (mmm) cc_final: 0.2311 (ptp) REVERT: I 114 THR cc_start: 0.2722 (m) cc_final: 0.2494 (m) REVERT: L 71 MET cc_start: 0.1226 (mtm) cc_final: 0.0667 (mtm) REVERT: N 71 MET cc_start: -0.0069 (mtm) cc_final: -0.0307 (mtm) REVERT: P 71 MET cc_start: 0.0517 (mtm) cc_final: -0.0778 (tmm) outliers start: 56 outliers final: 18 residues processed: 723 average time/residue: 0.9900 time to fit residues: 1111.6630 Evaluate side-chains 375 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 356 time to evaluate : 4.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 561 PRO Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 72 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 381 optimal weight: 9.9990 chunk 342 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 354 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 215 optimal weight: 0.4980 chunk 263 optimal weight: 3.9990 chunk 410 optimal weight: 20.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1101 HIS A1134 ASN B 271 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 188 ASN C 657 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C1005 GLN C1113 GLN L 40 GLN N 40 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4944 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 36436 Z= 0.246 Angle : 0.687 11.472 49542 Z= 0.366 Chirality : 0.047 0.543 5610 Planarity : 0.005 0.050 6394 Dihedral : 7.489 69.290 5262 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.62 % Favored : 94.05 % Rotamer: Outliers : 1.96 % Allowed : 7.96 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.41 (0.11), residues: 4518 helix: -0.97 (0.18), residues: 695 sheet: -1.41 (0.15), residues: 1001 loop : -1.90 (0.10), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 110 HIS 0.008 0.002 HIS C 69 PHE 0.026 0.002 PHE A 377 TYR 0.015 0.002 TYR C 351 ARG 0.005 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 803 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue THR 393 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 399 time to evaluate : 4.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 177 MET cc_start: 0.5870 (tpt) cc_final: 0.5123 (mtt) REVERT: A 616 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7663 (t0) REVERT: B 53 ASP cc_start: 0.3873 (OUTLIER) cc_final: 0.3612 (t70) REVERT: B 203 ILE cc_start: 0.6540 (mt) cc_final: 0.6100 (pt) REVERT: B 408 ARG cc_start: 0.3460 (ttp80) cc_final: 0.2898 (mtt90) REVERT: B 779 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6706 (mp10) REVERT: C 192 PHE cc_start: 0.6216 (m-80) cc_final: 0.5998 (m-80) REVERT: C 422 ASN cc_start: 0.0502 (OUTLIER) cc_final: 0.0120 (p0) REVERT: C 754 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8277 (tt) REVERT: C 774 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7354 (mm-40) REVERT: C 796 ASP cc_start: 0.2440 (p0) cc_final: 0.2091 (p0) REVERT: I 72 ARG cc_start: -0.0608 (OUTLIER) cc_final: -0.1349 (ptt90) REVERT: I 83 MET cc_start: 0.3865 (mmm) cc_final: 0.2579 (ptp) REVERT: N 71 MET cc_start: 0.0254 (mtm) cc_final: -0.0433 (mtm) REVERT: P 60 MET cc_start: -0.1210 (ttm) cc_final: -0.2182 (ttp) REVERT: P 71 MET cc_start: 0.0637 (mtm) cc_final: -0.0885 (tmm) outliers start: 77 outliers final: 38 residues processed: 452 average time/residue: 0.9593 time to fit residues: 699.8933 Evaluate side-chains 355 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 311 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 72 ARG Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 228 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 341 optimal weight: 50.0000 chunk 279 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 411 optimal weight: 20.0000 chunk 444 optimal weight: 10.0000 chunk 366 optimal weight: 30.0000 chunk 407 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 329 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1101 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 853 GLN B 949 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 69 HIS C 282 ASN C 804 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5184 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36436 Z= 0.260 Angle : 0.639 10.755 49542 Z= 0.340 Chirality : 0.045 0.329 5610 Planarity : 0.004 0.063 6394 Dihedral : 6.471 58.436 5233 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.40 % Favored : 93.23 % Rotamer: Outliers : 2.07 % Allowed : 9.54 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.12 (0.12), residues: 4518 helix: -0.23 (0.19), residues: 693 sheet: -1.25 (0.15), residues: 1103 loop : -1.85 (0.11), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 110 HIS 0.008 0.002 HIS B1048 PHE 0.026 0.002 PHE C 817 TYR 0.021 0.002 TYR J 31 ARG 0.005 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 803 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue THR 393 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 334 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 101 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.6100 (tp) REVERT: A 177 MET cc_start: 0.6027 (tpt) cc_final: 0.5723 (mtt) REVERT: B 779 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: C 220 PHE cc_start: 0.5299 (p90) cc_final: 0.5002 (p90) REVERT: C 422 ASN cc_start: 0.0993 (OUTLIER) cc_final: 0.0590 (p0) REVERT: C 754 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8400 (tt) REVERT: I 83 MET cc_start: 0.4108 (mmm) cc_final: 0.2881 (ptp) REVERT: L 65 PHE cc_start: -0.0317 (OUTLIER) cc_final: -0.0534 (m-80) REVERT: N 5 LEU cc_start: 0.4400 (tt) cc_final: 0.3908 (mt) REVERT: N 71 MET cc_start: -0.0114 (mtm) cc_final: -0.0866 (mtm) REVERT: P 2 VAL cc_start: 0.1141 (OUTLIER) cc_final: 0.0865 (m) REVERT: P 71 MET cc_start: 0.1500 (mtm) cc_final: 0.0034 (ttp) outliers start: 81 outliers final: 50 residues processed: 389 average time/residue: 0.9190 time to fit residues: 581.1240 Evaluate side-chains 331 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 275 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 35 PHE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain P residue 2 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 406 optimal weight: 20.0000 chunk 309 optimal weight: 4.9990 chunk 213 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 412 optimal weight: 20.0000 chunk 436 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 391 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A 969 ASN A1101 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 764 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 69 HIS ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 36436 Z= 0.394 Angle : 0.714 15.212 49542 Z= 0.383 Chirality : 0.048 0.374 5610 Planarity : 0.005 0.075 6394 Dihedral : 6.888 54.349 5229 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.72 % Favored : 91.88 % Rotamer: Outliers : 3.04 % Allowed : 9.59 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.49 (0.12), residues: 4518 helix: -0.76 (0.19), residues: 685 sheet: -1.32 (0.16), residues: 1037 loop : -2.10 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 110 HIS 0.010 0.002 HIS C1058 PHE 0.031 0.003 PHE C1042 TYR 0.025 0.002 TYR A 170 ARG 0.007 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 803 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue THR 393 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Evaluate side-chains 400 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 281 time to evaluate : 4.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 177 MET cc_start: 0.6350 (tpt) cc_final: 0.5992 (mtt) REVERT: A 314 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6799 (mp10) REVERT: B 239 GLN cc_start: 0.6376 (tt0) cc_final: 0.6150 (tt0) REVERT: B 779 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: B 1067 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7521 (t80) REVERT: C 335 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6692 (mm) REVERT: C 1067 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8121 (t80) REVERT: I 83 MET cc_start: 0.4501 (mmm) cc_final: 0.3112 (ptp) REVERT: L 65 PHE cc_start: -0.0041 (OUTLIER) cc_final: -0.0292 (m-80) REVERT: N 71 MET cc_start: 0.0011 (mtm) cc_final: -0.0780 (mtm) REVERT: P 2 VAL cc_start: 0.1149 (OUTLIER) cc_final: 0.0828 (m) REVERT: P 71 MET cc_start: 0.1566 (mtm) cc_final: -0.0060 (ttp) outliers start: 119 outliers final: 70 residues processed: 377 average time/residue: 0.9078 time to fit residues: 556.5473 Evaluate side-chains 316 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 239 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 65 PHE Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain P residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 363 optimal weight: 30.0000 chunk 248 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 chunk 180 optimal weight: 0.5980 chunk 372 optimal weight: 50.0000 chunk 302 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 223 optimal weight: 9.9990 chunk 392 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 overall best weight: 7.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1002 GLN A1011 GLN A1058 HIS A1101 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 239 GLN C 271 GLN C 519 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5658 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.140 36436 Z= 0.480 Angle : 0.762 16.147 49542 Z= 0.414 Chirality : 0.049 0.399 5610 Planarity : 0.006 0.063 6394 Dihedral : 7.535 77.195 5229 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.54 % Favored : 89.13 % Rotamer: Outliers : 3.22 % Allowed : 11.43 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.96 (0.11), residues: 4518 helix: -1.33 (0.18), residues: 704 sheet: -1.60 (0.16), residues: 1020 loop : -2.38 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G 110 HIS 0.010 0.002 HIS C1058 PHE 0.031 0.003 PHE B 888 TYR 0.029 0.002 TYR B 313 ARG 0.009 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 803 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue THR 393 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 265 time to evaluate : 5.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ASP cc_start: 0.4973 (OUTLIER) cc_final: 0.4594 (m-30) REVERT: B 239 GLN cc_start: 0.6556 (tt0) cc_final: 0.6277 (tt0) REVERT: B 779 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7084 (mp10) REVERT: B 1067 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7622 (t80) REVERT: B 1101 HIS cc_start: 0.5679 (OUTLIER) cc_final: 0.5362 (m170) REVERT: C 148 ASN cc_start: 0.3426 (OUTLIER) cc_final: 0.3134 (m-40) REVERT: C 177 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6554 (ppp) REVERT: C 204 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: C 417 LYS cc_start: 0.6039 (mmmt) cc_final: 0.5810 (ttpp) REVERT: C 427 ASP cc_start: 0.2663 (OUTLIER) cc_final: 0.1626 (p0) REVERT: C 661 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: C 1067 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8073 (t80) REVERT: K 105 THR cc_start: 0.0079 (OUTLIER) cc_final: -0.0133 (p) REVERT: L 71 MET cc_start: 0.1269 (ttm) cc_final: 0.1057 (ttm) REVERT: N 49 MET cc_start: 0.3967 (tpp) cc_final: 0.3480 (tpp) REVERT: N 71 MET cc_start: -0.0011 (mtm) cc_final: -0.1005 (mtm) REVERT: P 2 VAL cc_start: 0.1050 (OUTLIER) cc_final: 0.0836 (m) REVERT: P 32 GLU cc_start: 0.1714 (OUTLIER) cc_final: 0.1244 (pt0) REVERT: P 71 MET cc_start: 0.1580 (mtm) cc_final: -0.0719 (tmm) outliers start: 126 outliers final: 82 residues processed: 366 average time/residue: 0.8964 time to fit residues: 537.5112 Evaluate side-chains 324 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 229 time to evaluate : 4.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 32 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 146 optimal weight: 20.0000 chunk 393 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 437 optimal weight: 0.9990 chunk 363 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 229 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 532 ASN A 564 GLN A 969 ASN A1002 GLN A1058 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 0.7191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 36436 Z= 0.306 Angle : 0.634 13.272 49542 Z= 0.338 Chirality : 0.045 0.329 5610 Planarity : 0.005 0.059 6394 Dihedral : 6.895 66.001 5226 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.68 % Favored : 91.01 % Rotamer: Outliers : 2.70 % Allowed : 12.58 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.87 (0.11), residues: 4518 helix: -0.97 (0.18), residues: 707 sheet: -1.56 (0.16), residues: 986 loop : -2.40 (0.11), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 110 HIS 0.028 0.002 HIS A1058 PHE 0.018 0.002 PHE B 823 TYR 0.017 0.002 TYR E 95 ARG 0.004 0.000 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 803 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue THR 393 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Evaluate side-chains 362 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 256 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 177 MET cc_start: 0.6436 (tpt) cc_final: 0.6227 (mtt) REVERT: A 207 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7684 (t70) REVERT: B 53 ASP cc_start: 0.4938 (OUTLIER) cc_final: 0.4471 (m-30) REVERT: B 195 LYS cc_start: 0.5430 (ptmt) cc_final: 0.5094 (ptmt) REVERT: B 214 ARG cc_start: 0.5519 (mtm110) cc_final: 0.5183 (mmt180) REVERT: B 239 GLN cc_start: 0.6439 (tt0) cc_final: 0.6200 (tt0) REVERT: B 779 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: B 1067 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7512 (t80) REVERT: B 1101 HIS cc_start: 0.5645 (OUTLIER) cc_final: 0.5271 (m170) REVERT: C 177 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.5885 (ppp) REVERT: K 105 THR cc_start: 0.0066 (OUTLIER) cc_final: -0.0152 (p) REVERT: L 71 MET cc_start: 0.1284 (ttm) cc_final: 0.1062 (ttm) REVERT: N 49 MET cc_start: 0.3556 (tpp) cc_final: 0.3168 (tpp) REVERT: N 71 MET cc_start: -0.0175 (mtm) cc_final: -0.0804 (mtm) REVERT: P 2 VAL cc_start: 0.1212 (OUTLIER) cc_final: 0.0989 (m) REVERT: P 71 MET cc_start: 0.1832 (mtm) cc_final: 0.0003 (ttp) outliers start: 106 outliers final: 79 residues processed: 342 average time/residue: 0.8633 time to fit residues: 490.5827 Evaluate side-chains 325 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 238 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 421 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 319 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 368 optimal weight: 40.0000 chunk 244 optimal weight: 0.7980 chunk 435 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1058 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN K 80 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5601 moved from start: 0.7471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 36436 Z= 0.255 Angle : 0.588 12.390 49542 Z= 0.311 Chirality : 0.044 0.273 5610 Planarity : 0.005 0.093 6394 Dihedral : 6.230 55.393 5226 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.21 % Favored : 90.48 % Rotamer: Outliers : 2.65 % Allowed : 13.17 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -2.66 (0.12), residues: 4518 helix: -0.54 (0.19), residues: 715 sheet: -1.44 (0.16), residues: 983 loop : -2.34 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 110 HIS 0.012 0.001 HIS A1058 PHE 0.025 0.002 PHE B 168 TYR 0.017 0.002 TYR B 873 ARG 0.006 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 803 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue THR 393 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Evaluate side-chains 363 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 259 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 207 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7777 (t70) REVERT: A 660 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: A 675 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.6738 (pm20) REVERT: B 53 ASP cc_start: 0.4865 (OUTLIER) cc_final: 0.4429 (m-30) REVERT: B 195 LYS cc_start: 0.5545 (ptmt) cc_final: 0.5188 (ptmt) REVERT: B 214 ARG cc_start: 0.5475 (mtm110) cc_final: 0.5260 (mmt180) REVERT: B 239 GLN cc_start: 0.6485 (tt0) cc_final: 0.6234 (tt0) REVERT: B 779 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: C 177 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.5972 (ppp) REVERT: I 91 THR cc_start: 0.6049 (m) cc_final: 0.5698 (p) REVERT: L 71 MET cc_start: 0.1282 (ttm) cc_final: 0.0901 (ttm) REVERT: N 49 MET cc_start: 0.3620 (tpp) cc_final: 0.3135 (tpp) REVERT: P 2 VAL cc_start: 0.1096 (OUTLIER) cc_final: 0.0873 (m) REVERT: P 71 MET cc_start: 0.1816 (mtm) cc_final: 0.0542 (ttm) outliers start: 104 outliers final: 76 residues processed: 339 average time/residue: 0.8814 time to fit residues: 494.5142 Evaluate side-chains 319 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 236 time to evaluate : 4.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 269 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 260 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 276 optimal weight: 0.0770 chunk 296 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 342 optimal weight: 20.0000 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.7596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 36436 Z= 0.199 Angle : 0.552 12.018 49542 Z= 0.291 Chirality : 0.043 0.241 5610 Planarity : 0.004 0.059 6394 Dihedral : 5.907 55.157 5226 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.70 % Favored : 91.99 % Rotamer: Outliers : 2.12 % Allowed : 13.83 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -2.48 (0.12), residues: 4518 helix: -0.22 (0.19), residues: 712 sheet: -1.43 (0.16), residues: 1012 loop : -2.22 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 110 HIS 0.027 0.002 HIS A1058 PHE 0.020 0.001 PHE B 79 TYR 0.023 0.001 TYR I 95 ARG 0.005 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 803 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue THR 393 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Evaluate side-chains 327 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 244 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 207 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7741 (t70) REVERT: A 660 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: B 18 LEU cc_start: 0.0239 (OUTLIER) cc_final: -0.0205 (pp) REVERT: B 53 ASP cc_start: 0.4998 (OUTLIER) cc_final: 0.4752 (m-30) REVERT: B 195 LYS cc_start: 0.5435 (ptmt) cc_final: 0.5139 (ptmt) REVERT: B 214 ARG cc_start: 0.5431 (mtm110) cc_final: 0.5230 (mmt180) REVERT: B 779 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: C 177 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.5786 (ppp) REVERT: C 427 ASP cc_start: 0.2479 (OUTLIER) cc_final: 0.1468 (p0) REVERT: I 91 THR cc_start: 0.6024 (m) cc_final: 0.5725 (p) REVERT: L 71 MET cc_start: 0.1299 (ttm) cc_final: 0.1062 (ttm) REVERT: N 49 MET cc_start: 0.3589 (tpp) cc_final: 0.3107 (tpp) REVERT: P 2 VAL cc_start: 0.1074 (OUTLIER) cc_final: 0.0847 (m) REVERT: P 32 GLU cc_start: 0.1852 (OUTLIER) cc_final: 0.1385 (pt0) REVERT: P 71 MET cc_start: 0.1534 (mtm) cc_final: 0.0367 (ttm) outliers start: 83 outliers final: 66 residues processed: 311 average time/residue: 0.8660 time to fit residues: 447.4592 Evaluate side-chains 310 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 235 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 32 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 396 optimal weight: 50.0000 chunk 417 optimal weight: 9.9990 chunk 380 optimal weight: 6.9990 chunk 405 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 318 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 366 optimal weight: 7.9990 chunk 383 optimal weight: 30.0000 chunk 404 optimal weight: 30.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.7959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 36436 Z= 0.299 Angle : 0.603 11.881 49542 Z= 0.322 Chirality : 0.044 0.268 5610 Planarity : 0.005 0.056 6394 Dihedral : 6.152 59.834 5226 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.51 % Favored : 89.18 % Rotamer: Outliers : 2.37 % Allowed : 13.96 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -2.63 (0.12), residues: 4518 helix: -0.43 (0.19), residues: 712 sheet: -1.55 (0.15), residues: 1041 loop : -2.28 (0.11), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 36 HIS 0.008 0.002 HIS B 207 PHE 0.020 0.002 PHE A 86 TYR 0.019 0.002 TYR B 313 ARG 0.005 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 803 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue THR 393 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 246 time to evaluate : 4.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 207 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7767 (t70) REVERT: A 660 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.7247 (m-80) REVERT: A 675 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.6861 (pm20) REVERT: B 18 LEU cc_start: 0.0193 (OUTLIER) cc_final: -0.0290 (pp) REVERT: B 53 ASP cc_start: 0.5070 (OUTLIER) cc_final: 0.4776 (m-30) REVERT: B 195 LYS cc_start: 0.6026 (ptmt) cc_final: 0.5687 (ptmt) REVERT: B 214 ARG cc_start: 0.5532 (mtm110) cc_final: 0.5283 (mmt180) REVERT: B 779 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: B 1101 HIS cc_start: 0.5551 (OUTLIER) cc_final: 0.5181 (m170) REVERT: C 177 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6364 (ppp) REVERT: C 427 ASP cc_start: 0.2800 (OUTLIER) cc_final: 0.1698 (p0) REVERT: C 562 PHE cc_start: 0.4985 (OUTLIER) cc_final: 0.4359 (m-80) REVERT: C 661 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: C 957 GLN cc_start: 0.7670 (tp40) cc_final: 0.7453 (tm-30) REVERT: L 71 MET cc_start: 0.1347 (ttm) cc_final: 0.1109 (ttm) REVERT: N 49 MET cc_start: 0.3643 (tpp) cc_final: 0.3179 (tpp) REVERT: N 71 MET cc_start: 0.0398 (mtm) cc_final: -0.0809 (mtm) REVERT: P 2 VAL cc_start: 0.1217 (OUTLIER) cc_final: 0.0981 (m) outliers start: 93 outliers final: 73 residues processed: 317 average time/residue: 0.8646 time to fit residues: 456.0965 Evaluate side-chains 317 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 232 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 266 optimal weight: 2.9990 chunk 429 optimal weight: 0.7980 chunk 262 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 450 optimal weight: 9.9990 chunk 414 optimal weight: 30.0000 chunk 358 optimal weight: 50.0000 chunk 37 optimal weight: 30.0000 chunk 276 optimal weight: 0.8980 chunk 219 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A1002 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 36436 Z= 0.186 Angle : 0.542 11.638 49542 Z= 0.284 Chirality : 0.043 0.236 5610 Planarity : 0.004 0.057 6394 Dihedral : 5.695 58.458 5226 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.61 % Favored : 92.08 % Rotamer: Outliers : 1.94 % Allowed : 14.67 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -2.38 (0.12), residues: 4518 helix: -0.06 (0.19), residues: 712 sheet: -1.42 (0.16), residues: 1030 loop : -2.15 (0.11), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 110 HIS 0.008 0.001 HIS A1048 PHE 0.020 0.001 PHE B 79 TYR 0.016 0.001 TYR I 95 ARG 0.005 0.000 ARG C 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 803 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue THR 393 is missing expected H atoms. Skipping. Residue THR 430 is missing expected H atoms. Skipping. Residue SER 803 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue TYR 94 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Evaluate side-chains 318 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 242 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 207 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7714 (t70) REVERT: A 660 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6938 (m-80) REVERT: B 18 LEU cc_start: 0.0025 (OUTLIER) cc_final: -0.0436 (pp) REVERT: B 195 LYS cc_start: 0.6059 (ptmt) cc_final: 0.5858 (ptmt) REVERT: B 779 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: C 177 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6281 (ppp) REVERT: C 427 ASP cc_start: 0.2515 (OUTLIER) cc_final: 0.1506 (p0) REVERT: C 562 PHE cc_start: 0.4996 (OUTLIER) cc_final: 0.4431 (m-80) REVERT: D 51 ILE cc_start: 0.4968 (OUTLIER) cc_final: 0.3407 (tt) REVERT: L 71 MET cc_start: 0.1346 (ttm) cc_final: 0.1142 (ttm) REVERT: M 49 ILE cc_start: 0.0250 (mm) cc_final: 0.0004 (tp) REVERT: N 49 MET cc_start: 0.3481 (tpp) cc_final: 0.3013 (tpp) REVERT: P 2 VAL cc_start: 0.1192 (OUTLIER) cc_final: 0.0971 (m) outliers start: 76 outliers final: 61 residues processed: 301 average time/residue: 0.8708 time to fit residues: 434.3779 Evaluate side-chains 302 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 284 optimal weight: 5.9990 chunk 381 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 330 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 359 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 368 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.141553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.118239 restraints weight = 356328.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.117991 restraints weight = 414846.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.118861 restraints weight = 285666.475| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.8216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 36436 Z= 0.248 Angle : 0.562 11.409 49542 Z= 0.297 Chirality : 0.043 0.242 5610 Planarity : 0.004 0.064 6394 Dihedral : 5.742 59.237 5226 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.98 % Favored : 89.71 % Rotamer: Outliers : 2.02 % Allowed : 14.70 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -2.41 (0.12), residues: 4518 helix: -0.16 (0.19), residues: 719 sheet: -1.43 (0.16), residues: 1039 loop : -2.15 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 110 HIS 0.006 0.001 HIS B 207 PHE 0.019 0.002 PHE B 79 TYR 0.013 0.001 TYR A1067 ARG 0.008 0.000 ARG C 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11382.88 seconds wall clock time: 199 minutes 20.75 seconds (11960.75 seconds total)