Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 18:05:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/04_2023/7cwt_30487_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/04_2023/7cwt_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_30487/04_2023/7cwt_30487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/04_2023/7cwt_30487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/04_2023/7cwt_30487_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwt_30487/04_2023/7cwt_30487_trim.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 chiralities: 6 Time building chain proxies: 25.70, per 1000 atoms: 0.37 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: 45.23 Conformation dependent library (CDL) restraints added in 4.4 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: 2.06 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: 30.54 Time building geometry restraints manager: 47.67 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: 27805 25.07 - 50.14: 704 50.14 - 75.22: 155 75.22 - 100.29: 45 100.29 - 125.36: 3 Dihedral angle restraints: 28712 sinusoidal: 12940 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 28709 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: 1.470 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: 0.770 Extract box with map and model: 11.400 Check model and map are aligned: 0.750 Set scattering table: 0.460 Process input model: 174.570 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.380 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: 0.020 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.330 ------------------------------------------------------------------------------- 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 : 11.082 125.360 12915 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 % 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 *********************** 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 : 4.120 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 outliers start: 56 outliers final: 18 residues processed: 723 average time/residue: 1.0157 time to fit residues: 1140.5298 Evaluate side-chains 371 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 353 time to evaluate : 4.068 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 18 average time/residue: 0.8529 time to fit residues: 31.0780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 381 optimal weight: 5.9990 chunk 342 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 354 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 410 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1101 HIS B 271 GLN B 764 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN ** B1005 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** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5119 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 36436 Z= 0.329 Angle : 0.756 15.010 49542 Z= 0.400 Chirality : 0.048 0.583 5610 Planarity : 0.005 0.055 6394 Dihedral : 6.769 45.268 4926 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.47 % Favored : 94.18 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.61 (0.11), residues: 4518 helix: -1.24 (0.18), residues: 694 sheet: -1.43 (0.15), residues: 996 loop : -2.05 (0.10), residues: 2828 *********************** 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 481 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 401 time to evaluate : 4.048 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 outliers start: 80 outliers final: 44 residues processed: 457 average time/residue: 0.9574 time to fit residues: 703.2202 Evaluate side-chains 336 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 292 time to evaluate : 4.082 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 5 residues processed: 44 average time/residue: 0.6629 time to fit residues: 58.8962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 228 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 341 optimal weight: 30.0000 chunk 279 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 411 optimal weight: 20.0000 chunk 444 optimal weight: 0.9990 chunk 366 optimal weight: 30.0000 chunk 407 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 329 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 804 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 949 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 282 ASN C 580 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** 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: 0.5288 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 36436 Z= 0.274 Angle : 0.648 12.191 49542 Z= 0.342 Chirality : 0.045 0.262 5610 Planarity : 0.004 0.066 6394 Dihedral : 5.862 32.997 4926 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.80 % Favored : 92.83 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -2.32 (0.12), residues: 4518 helix: -0.45 (0.19), residues: 704 sheet: -1.35 (0.15), residues: 1122 loop : -1.99 (0.11), residues: 2692 *********************** 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 374 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 309 time to evaluate : 4.060 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 outliers start: 65 outliers final: 35 residues processed: 359 average time/residue: 0.9467 time to fit residues: 547.0407 Evaluate side-chains 296 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 261 time to evaluate : 4.110 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 5 residues processed: 35 average time/residue: 0.7015 time to fit residues: 49.0848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 213 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 412 optimal weight: 30.0000 chunk 436 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 391 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 239 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 969 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 762 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 239 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 36436 Z= 0.336 Angle : 0.666 12.656 49542 Z= 0.352 Chirality : 0.046 0.510 5610 Planarity : 0.005 0.047 6394 Dihedral : 5.855 32.866 4926 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.35 % Favored : 92.30 % Rotamer Outliers : 1.76 % 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: -2.42 (0.12), residues: 4518 helix: -0.57 (0.19), residues: 691 sheet: -1.32 (0.16), residues: 1025 loop : -2.08 (0.11), residues: 2802 *********************** 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 342 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 273 time to evaluate : 4.172 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 outliers start: 69 outliers final: 35 residues processed: 327 average time/residue: 0.9138 time to fit residues: 487.2221 Evaluate side-chains 279 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 244 time to evaluate : 4.090 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 9 residues processed: 35 average time/residue: 0.6905 time to fit residues: 48.6364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 363 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 325 optimal weight: 30.0000 chunk 180 optimal weight: 4.9990 chunk 372 optimal weight: 40.0000 chunk 302 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 223 optimal weight: 0.9980 chunk 392 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 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: 0.5630 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.114 36436 Z= 0.409 Angle : 0.716 12.355 49542 Z= 0.385 Chirality : 0.047 0.376 5610 Planarity : 0.005 0.056 6394 Dihedral : 6.106 30.358 4926 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.31 % Favored : 89.35 % Rotamer Outliers : 1.86 % 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: -2.83 (0.11), residues: 4518 helix: -0.98 (0.18), residues: 691 sheet: -1.54 (0.16), residues: 1030 loop : -2.35 (0.11), residues: 2797 *********************** 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 342 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 269 time to evaluate : 4.090 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 outliers start: 73 outliers final: 42 residues processed: 324 average time/residue: 0.9415 time to fit residues: 496.4727 Evaluate side-chains 279 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 237 time to evaluate : 4.056 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 10 residues processed: 42 average time/residue: 0.6659 time to fit residues: 56.0689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 86 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 437 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 229 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 969 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN ** 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 ** C 804 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 39 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.104 36436 Z= 0.287 Angle : 0.611 14.112 49542 Z= 0.324 Chirality : 0.044 0.275 5610 Planarity : 0.004 0.055 6394 Dihedral : 5.727 30.706 4926 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.81 % Favored : 90.88 % Rotamer Outliers : 1.38 % 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: -2.71 (0.12), residues: 4518 helix: -0.73 (0.19), residues: 713 sheet: -1.41 (0.16), residues: 996 loop : -2.34 (0.11), residues: 2809 *********************** 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 313 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 259 time to evaluate : 4.168 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 outliers start: 54 outliers final: 30 residues processed: 298 average time/residue: 0.9350 time to fit residues: 460.5283 Evaluate side-chains 273 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 4.149 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 30 average time/residue: 0.6892 time to fit residues: 42.4974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 319 optimal weight: 3.9990 chunk 247 optimal weight: 0.5980 chunk 368 optimal weight: 30.0000 chunk 244 optimal weight: 5.9990 chunk 435 optimal weight: 8.9990 chunk 272 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN A1002 GLN ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 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 ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 36436 Z= 0.278 Angle : 0.597 12.134 49542 Z= 0.316 Chirality : 0.044 0.283 5610 Planarity : 0.004 0.056 6394 Dihedral : 5.535 28.816 4926 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.74 % Favored : 89.95 % Rotamer Outliers : 0.87 % 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: -2.65 (0.12), residues: 4518 helix: -0.59 (0.19), residues: 713 sheet: -1.39 (0.16), residues: 1000 loop : -2.33 (0.11), residues: 2805 *********************** 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 289 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 255 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 283 average time/residue: 0.9338 time to fit residues: 429.3099 Evaluate side-chains 259 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 4.088 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 22 average time/residue: 0.6770 time to fit residues: 32.1186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 269 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 260 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 276 optimal weight: 6.9990 chunk 296 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 342 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 148 ASN ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** 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: 0.5640 moved from start: 0.7864 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= 0.289 Angle : 0.599 12.578 49542 Z= 0.317 Chirality : 0.044 0.288 5610 Planarity : 0.004 0.058 6394 Dihedral : 5.500 29.992 4926 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.72 % Favored : 89.97 % Rotamer Outliers : 0.84 % 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: -2.65 (0.12), residues: 4518 helix: -0.52 (0.19), residues: 712 sheet: -1.48 (0.16), residues: 1034 loop : -2.31 (0.11), residues: 2772 *********************** 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 278 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 4.180 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 outliers start: 33 outliers final: 24 residues processed: 273 average time/residue: 0.9724 time to fit residues: 428.7786 Evaluate side-chains 249 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 225 time to evaluate : 4.194 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 24 average time/residue: 0.7624 time to fit residues: 37.4336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 396 optimal weight: 6.9990 chunk 417 optimal weight: 9.9990 chunk 380 optimal weight: 6.9990 chunk 405 optimal weight: 20.0000 chunk 244 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 318 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 366 optimal weight: 40.0000 chunk 383 optimal weight: 20.0000 chunk 404 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 804 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 0.8074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 36436 Z= 0.249 Angle : 0.576 11.830 49542 Z= 0.303 Chirality : 0.043 0.293 5610 Planarity : 0.004 0.052 6394 Dihedral : 5.351 27.831 4926 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.52 % Favored : 90.15 % Rotamer Outliers : 0.51 % 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: -2.56 (0.12), residues: 4518 helix: -0.41 (0.19), residues: 713 sheet: -1.45 (0.15), residues: 1041 loop : -2.25 (0.11), residues: 2764 *********************** 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 257 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 237 time to evaluate : 4.178 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 outliers start: 20 outliers final: 14 residues processed: 251 average time/residue: 0.9531 time to fit residues: 387.4657 Evaluate side-chains 236 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 222 time to evaluate : 4.146 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 14 average time/residue: 0.7382 time to fit residues: 23.2270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 266 optimal weight: 1.9990 chunk 429 optimal weight: 0.0970 chunk 262 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 450 optimal weight: 8.9990 chunk 414 optimal weight: 9.9990 chunk 358 optimal weight: 40.0000 chunk 37 optimal weight: 10.0000 chunk 276 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.8150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 36436 Z= 0.188 Angle : 0.545 11.496 49542 Z= 0.284 Chirality : 0.043 0.310 5610 Planarity : 0.004 0.050 6394 Dihedral : 5.097 27.990 4926 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.28 % Favored : 91.43 % Rotamer Outliers : 0.43 % 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: -2.33 (0.12), residues: 4518 helix: -0.09 (0.19), residues: 707 sheet: -1.33 (0.16), residues: 1038 loop : -2.12 (0.11), residues: 2773 ********************** 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 250 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 233 time to evaluate : 4.627 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 outliers start: 17 outliers final: 14 residues processed: 246 average time/residue: 0.9622 time to fit residues: 382.8002 Evaluate side-chains 235 residues out of total 3934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 4.077 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 14 average time/residue: 0.7152 time to fit residues: 23.1080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 284 optimal weight: 6.9990 chunk 381 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 330 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 359 optimal weight: 0.0970 chunk 150 optimal weight: 10.0000 chunk 368 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 overall best weight: 3.7584 ------------------------------------------------------------------------------- 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN ** 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 = 0.4708 r_free = 0.4708 target = 0.141816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.118025 restraints weight = 354809.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.117650 restraints weight = 424035.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.118397 restraints weight = 312426.220| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.8419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 36436 Z= 0.287 Angle : 0.591 11.678 49542 Z= 0.312 Chirality : 0.044 0.279 5610 Planarity : 0.004 0.052 6394 Dihedral : 5.290 28.022 4926 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.49 % Favored : 89.22 % Rotamer Outliers : 0.33 % 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: -2.50 (0.12), residues: 4518 helix: -0.37 (0.19), residues: 728 sheet: -1.41 (0.15), residues: 1036 loop : -2.22 (0.11), residues: 2754 =============================================================================== Job complete usr+sys time: 10813.05 seconds wall clock time: 189 minutes 44.72 seconds (11384.72 seconds total)