Starting phenix.real_space_refine on Tue Feb 20 14:07:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd2_33133/02_2024/7xd2_33133_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd2_33133/02_2024/7xd2_33133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd2_33133/02_2024/7xd2_33133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd2_33133/02_2024/7xd2_33133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd2_33133/02_2024/7xd2_33133_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd2_33133/02_2024/7xd2_33133_neut.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.070 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: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 17746 2.51 5 N 4757 2.21 5 O 5462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "I ARG 31": "NH1" <-> "NH2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I ARG 64": "NH1" <-> "NH2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "I ARG 95": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28084 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 7969 Classifications: {'peptide': 1056} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 149 Chain: "B" Number of atoms: 7943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 7943 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 52, 'TRANS': 995} Chain breaks: 7 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 120 Chain: "C" Number of atoms: 7462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7462 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 50, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 137 Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 831 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 733 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 831 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 742 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 96} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 831 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "L" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 742 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 96} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 14.81, per 1000 atoms: 0.53 Number of scatterers: 28084 At special positions: 0 Unit cell: (153.26, 151.32, 226.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 119 16.00 O 5462 8.00 N 4757 7.00 C 17746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.15 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 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=1.54 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=1.96 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.07 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.98 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 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 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.15 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.88 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=1.98 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.96 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.15 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.90 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=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=1.48 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 93 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 93 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 93 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.31 Conformation dependent library (CDL) restraints added in 5.0 seconds 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6952 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 62 sheets defined 20.1% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.777A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.438A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.226A pdb=" N THR A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 4.090A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 774 removed outlier: 3.743A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 783 removed outlier: 3.524A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 869 through 884 removed outlier: 3.680A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.558A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.298A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.682A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.141A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) 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 983 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.871A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 344 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.778A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.438A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 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 755 removed outlier: 3.551A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 773 Processing helix chain 'B' and resid 775 through 783 removed outlier: 3.517A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.588A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.825A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.815A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.697A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.129A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.671A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.013A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.777A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.437A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 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: 3.657A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (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 760 through 774 Processing helix chain 'C' and resid 776 through 783 Processing helix chain 'C' and resid 818 through 827 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.523A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.819A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.673A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.677A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 946 No H-bonds generated for 'chain 'C' and resid 944 through 946' Processing helix chain 'C' and resid 947 through 964 removed outlier: 3.822A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 953 " --> pdb=" O GLN C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.001A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.195A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.119A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.787A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.503A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.614A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 327 removed outlier: 3.830A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.284A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.284A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N PHE A 392 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A 518 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.042A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 720 removed outlier: 3.678A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.952A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.918A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.813A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.208A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 126 through 127 removed outlier: 3.644A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.284A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N PHE B 392 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU B 518 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.284A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 542 removed outlier: 5.305A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.869A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 721 removed outlier: 6.750A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 721 removed outlier: 6.750A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.533A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.631A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.507A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.570A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE2, first strand: chain 'C' and resid 189 through 190 removed outlier: 3.580A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.608A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.284A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N PHE C 392 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU C 518 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.284A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.131A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 714 removed outlier: 3.637A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 717 through 720 Processing sheet with id=AF2, first strand: chain 'C' and resid 717 through 720 removed outlier: 3.659A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.853A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 66 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 55 through 57 removed outlier: 4.991A pdb=" N CYS D 45 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG D 36 " --> pdb=" O CYS D 45 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 6 through 7 removed outlier: 3.579A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.564A pdb=" N TYR J 36 " --> pdb=" O TYR J 87 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR J 87 " --> pdb=" O TYR J 36 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.852A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR E 66 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 55 through 57 removed outlier: 4.991A pdb=" N CYS E 45 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG E 36 " --> pdb=" O CYS E 45 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.579A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.564A pdb=" N TYR H 36 " --> pdb=" O TYR H 87 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR H 87 " --> pdb=" O TYR H 36 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 6 through 7 removed outlier: 3.853A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR I 66 " --> pdb=" O GLN I 79 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 55 through 57 removed outlier: 4.991A pdb=" N CYS I 45 " --> pdb=" O ARG I 36 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG I 36 " --> pdb=" O CYS I 45 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.579A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.564A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 1021 hydrogen bonds defined for protein. 2790 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: 12.66 Time building geometry restraints manager: 11.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4701 1.29 - 1.43: 7717 1.43 - 1.56: 16135 1.56 - 1.70: 0 1.70 - 1.83: 148 Bond restraints: 28701 Sorted by residual: bond pdb=" C PRO A 792 " pdb=" O PRO A 792 " ideal model delta sigma weight residual 1.246 1.187 0.058 8.50e-03 1.38e+04 4.72e+01 bond pdb=" CA SER A1021 " pdb=" CB SER A1021 " ideal model delta sigma weight residual 1.528 1.425 0.103 1.59e-02 3.96e+03 4.21e+01 bond pdb=" CA SER A 816 " pdb=" CB SER A 816 " ideal model delta sigma weight residual 1.527 1.434 0.093 1.44e-02 4.82e+03 4.15e+01 bond pdb=" C PRO C 715 " pdb=" O PRO C 715 " ideal model delta sigma weight residual 1.233 1.154 0.079 1.23e-02 6.61e+03 4.10e+01 bond pdb=" C PRO A 715 " pdb=" O PRO A 715 " ideal model delta sigma weight residual 1.233 1.158 0.075 1.19e-02 7.06e+03 3.93e+01 ... (remaining 28696 not shown) Histogram of bond angle deviations from ideal: 86.82 - 96.41: 5 96.41 - 106.00: 1154 106.00 - 115.59: 16131 115.59 - 125.18: 21422 125.18 - 134.77: 402 Bond angle restraints: 39114 Sorted by residual: angle pdb=" C ASN A 856 " pdb=" CA ASN A 856 " pdb=" CB ASN A 856 " ideal model delta sigma weight residual 111.23 86.82 24.41 1.68e+00 3.54e-01 2.11e+02 angle pdb=" N SER A 943 " pdb=" CA SER A 943 " pdb=" C SER A 943 " ideal model delta sigma weight residual 112.92 98.37 14.55 1.23e+00 6.61e-01 1.40e+02 angle pdb=" C TYR B1067 " pdb=" CA TYR B1067 " pdb=" CB TYR B1067 " ideal model delta sigma weight residual 110.22 92.53 17.69 1.67e+00 3.59e-01 1.12e+02 angle pdb=" N PRO B 812 " pdb=" CA PRO B 812 " pdb=" C PRO B 812 " ideal model delta sigma weight residual 113.47 99.55 13.92 1.43e+00 4.89e-01 9.48e+01 angle pdb=" N PHE B 759 " pdb=" CA PHE B 759 " pdb=" C PHE B 759 " ideal model delta sigma weight residual 112.72 101.89 10.83 1.14e+00 7.69e-01 9.02e+01 ... (remaining 39109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 15416 17.63 - 35.26: 1258 35.26 - 52.88: 295 52.88 - 70.51: 44 70.51 - 88.14: 15 Dihedral angle restraints: 17028 sinusoidal: 6201 harmonic: 10827 Sorted by residual: dihedral pdb=" C ASN A 856 " pdb=" N ASN A 856 " pdb=" CA ASN A 856 " pdb=" CB ASN A 856 " ideal model delta harmonic sigma weight residual -122.60 -96.82 -25.78 0 2.50e+00 1.60e-01 1.06e+02 dihedral pdb=" C TYR B1067 " pdb=" N TYR B1067 " pdb=" CA TYR B1067 " pdb=" CB TYR B1067 " ideal model delta harmonic sigma weight residual -122.60 -98.52 -24.08 0 2.50e+00 1.60e-01 9.27e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -168.48 82.48 1 1.00e+01 1.00e-02 8.34e+01 ... (remaining 17025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 3078 0.144 - 0.288: 1220 0.288 - 0.431: 130 0.431 - 0.575: 16 0.575 - 0.719: 2 Chirality restraints: 4446 Sorted by residual: chirality pdb=" CA CYS A 590 " pdb=" N CYS A 590 " pdb=" C CYS A 590 " pdb=" CB CYS A 590 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" CA CYS C 760 " pdb=" N CYS C 760 " pdb=" C CYS C 760 " pdb=" CB CYS C 760 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.16e+00 ... (remaining 4443 not shown) Planarity restraints: 5131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 622 " 0.023 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C VAL B 622 " -0.084 2.00e-02 2.50e+03 pdb=" O VAL B 622 " 0.033 2.00e-02 2.50e+03 pdb=" N ALA B 623 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 322 " 0.021 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C PRO B 322 " -0.075 2.00e-02 2.50e+03 pdb=" O PRO B 322 " 0.029 2.00e-02 2.50e+03 pdb=" N THR B 323 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 589 " -0.020 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C PRO C 589 " 0.074 2.00e-02 2.50e+03 pdb=" O PRO C 589 " -0.028 2.00e-02 2.50e+03 pdb=" N CYS C 590 " -0.025 2.00e-02 2.50e+03 ... (remaining 5128 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 3 2.11 - 2.81: 7447 2.81 - 3.51: 36391 3.51 - 4.20: 63832 4.20 - 4.90: 110219 Nonbonded interactions: 217892 Sorted by model distance: nonbonded pdb=" OE2 GLU B1072 " pdb=" CD2 LEU C 894 " model vdw 1.416 3.460 nonbonded pdb=" CD GLU B1072 " pdb=" CD2 LEU C 894 " model vdw 2.042 3.690 nonbonded pdb=" O ASN A 856 " pdb=" CB ASN A 856 " model vdw 2.069 2.752 nonbonded pdb=" CB PHE A 855 " pdb=" N ASN A 856 " model vdw 2.288 2.816 nonbonded pdb=" O SER C 721 " pdb=" OG SER C 721 " model vdw 2.307 2.440 ... (remaining 217887 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 26 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 41 or (resid 42 through 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 83 or (res \ id 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throu \ gh 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 104 or (resid 105 and (name N or name CA or name C or \ name O or name CB )) or resid 106 through 108 or (resid 117 through 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 120 through 121 or (r \ esid 122 through 123 and (name N or name CA or name C or name O or name CB )) or \ resid 124 or (resid 125 and (name N or name CA or name C or name O or name CB ) \ ) or resid 126 through 129 or resid 139 through 140 or (resid 141 and (name N or \ name CA or name C or name O or name CB )) or resid 142 or (resid 143 through 14 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 153 through \ 157 or (resid 158 and (name N or name CA or name C or name O or name CB )) or re \ sid 169 through 173 or resid 188 or (resid 189 through 191 and (name N or name C \ A or name C or name O or name CB )) or resid 192 or (resid 193 and (name N or na \ me CA or name C or name O or name CB )) or resid 194 or (resid 195 and (name N o \ r name CA or name C or name O or name CB )) or resid 196 through 210 or (resid 2 \ 11 through 212 and (name N or name CA or name C or name O or name CB )) or resid \ 213 through 225 or (resid 226 through 227 and (name N or name CA or name C or n \ ame O or name CB )) or resid 228 through 241 or (resid 242 through 243 and (name \ N or name CA or name C or name O or name CB )) or resid 260 through 309 or (res \ id 310 and (name N or name CA or name C or name O or name CB )) or resid 311 thr \ ough 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 361 or (resid 362 through 364 and (name N or name CA or nam \ e C or name O or name CB )) or resid 365 through 564 or (resid 565 and (name N o \ r name CA or name C or name O or name CB )) or resid 566 through 572 or (resid 5 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 574 through \ 582 or (resid 583 through 584 and (name N or name CA or name C or name O or nam \ e CB )) or resid 585 through 591 or (resid 592 and (name N or name CA or name C \ or name O or name CB )) or resid 593 through 598 or (resid 599 and (name N or na \ me CA or name C or name O or name CB )) or resid 600 through 601 or (resid 602 a \ nd (name N or name CA or name C or name O or name CB )) or resid 603 through 607 \ or (resid 608 through 610 and (name N or name CA or name C or name O or name CB \ )) or resid 611 through 619 or (resid 620 and (name N or name CA or name C or n \ ame O or name CB )) or resid 621 or resid 641 through 645 or (resid 646 through \ 647 and (name N or name CA or name C or name O or name CB )) or resid 648 throug \ h 662 or (resid 663 and (name N or name CA or name C or name O or name CB )) or \ resid 664 through 675 or resid 691 through 704 or (resid 705 through 706 and (na \ me N or name CA or name C or name O or name CB )) or resid 707 through 709 or (r \ esid 710 through 714 and (name N or name CA or name C or name O or name CB )) or \ resid 715 through 744 or (resid 745 and (name N or name CA or name C or name O \ or name CB )) or resid 746 through 747 or (resid 748 and (name N or name CA or n \ ame C or name O or name CB )) or resid 749 through 764 or (resid 765 through 766 \ and (name N or name CA or name C or name O or name CB )) or resid 767 through 7 \ 69 or (resid 770 through 771 and (name N or name CA or name C or name O or name \ CB )) or resid 772 through 826 or (resid 855 and (name N or name CA or name C or \ name O or name CB )) or resid 856 through 857 or (resid 858 and (name N or name \ CA or name C or name O or name CB )) or resid 859 through 867 or (resid 868 and \ (name N or name CA or name C or name O or name CB )) or resid 869 through 903 o \ r (resid 904 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 05 through 913 or (resid 914 through 916 and (name N or name CA or name C or nam \ e O or name CB )) or resid 917 through 922 or (resid 923 through 924 and (name N \ or name CA or name C or name O or name CB )) or resid 925 through 938 or (resid \ 939 and (name N or name CA or name C or name O or name CB )) or resid 940 or (r \ esid 941 through 942 and (name N or name CA or name C or name O or name CB )) or \ resid 943 through 961 or (resid 962 and (name N or name CA or name C or name O \ or name CB )) or resid 963 through 996 or (resid 997 and (name N or name CA or n \ ame C or name O or name CB )) or resid 998 through 1001 or (resid 1002 and (name \ N or name CA or name C or name O or name CB )) or resid 1003 through 1016 or (r \ esid 1017 through 1018 and (name N or name CA or name C or name O or name CB )) \ or resid 1019 through 1071 or (resid 1072 through 1073 and (name N or name CA or \ name C or name O or name CB )) or resid 1074 through 1103 or (resid 1104 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1105 through 1126 or \ (resid 1127 through 1129 and (name N or name CA or name C or name O or name CB \ )) or resid 1130 through 1131 or (resid 1132 and (name N or name CA or name C or \ name O or name CB )) or resid 1133 through 1140 or (resid 1141 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1142 through 1144)) selection = (chain 'B' and (resid 26 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 41 or (resid 42 through 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 50 or (res \ id 51 and (name N or name CA or name C or name O or name CB )) or resid 52 throu \ gh 68 or resid 76 through 95 or (resid 96 through 97 and (name N or name CA or n \ ame C or name O or name CB )) or resid 98 through 100 or (resid 101 and (name N \ or name CA or name C or name O or name CB )) or resid 102 through 107 or (resid \ 108 and (name N or name CA or name C or name O or name CB )) or (resid 117 throu \ gh 119 and (name N or name CA or name C or name O or name CB )) or resid 120 thr \ ough 121 or (resid 122 through 123 and (name N or name CA or name C or name O or \ name CB )) or resid 124 through 129 or resid 139 through 140 or (resid 141 and \ (name N or name CA or name C or name O or name CB )) or resid 142 or (resid 143 \ through 145 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 3 through 155 or (resid 156 and (name N or name CA or name C or name O or name C \ B )) or resid 157 through 158 or resid 169 or (resid 170 and (name N or name CA \ or name C or name O or name CB )) or resid 171 through 173 or resid 188 or (resi \ d 189 through 191 and (name N or name CA or name C or name O or name CB )) or re \ sid 192 or (resid 193 and (name N or name CA or name C or name O or name CB )) o \ r resid 194 through 200 or (resid 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 210 or (resid 211 through 212 and (name N or \ name CA or name C or name O or name CB )) or resid 213 through 226 or (resid 22 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 228 through \ 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) or re \ sid 232 through 233 or (resid 234 and (name N or name CA or name C or name O or \ name CB )) or resid 235 through 236 or (resid 237 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 through 241 or (resid 242 th \ rough 243 and (name N or name CA or name C or name O or name CB )) or resid 260 \ through 311 or (resid 312 and (name N or name CA or name C or name O or name CB \ )) or resid 313 through 318 or (resid 319 and (name N or name CA or name C or na \ me O or name CB )) or resid 320 through 325 or (resid 326 and (name N or name CA \ or name C or name O or name CB )) or resid 327 through 331 or (resid 332 and (n \ ame N or name CA or name C or name O or name CB )) or resid 333 through 543 or ( \ resid 544 and (name N or name CA or name C or name O or name CB )) or resid 545 \ through 552 or (resid 553 and (name N or name CA or name C or name O or name CB \ )) or resid 554 through 572 or (resid 573 and (name N or name CA or name C or na \ me O or name CB )) or resid 574 through 577 or (resid 578 and (name N or name CA \ or name C or name O or name CB )) or resid 579 through 582 or (resid 583 throug \ h 584 and (name N or name CA or name C or name O or name CB )) or resid 585 thro \ ugh 597 or (resid 598 through 599 and (name N or name CA or name C or name O or \ name CB )) or resid 600 through 601 or (resid 602 and (name N or name CA or name \ C or name O or name CB )) or resid 603 through 609 or (resid 610 and (name N or \ name CA or name C or name O or name CB )) or resid 611 through 621 or resid 641 \ through 645 or (resid 646 through 647 and (name N or name CA or name C or name \ O or name CB )) or resid 648 through 675 or resid 691 through 701 or (resid 702 \ and (name N or name CA or name C or name O or name CB )) or resid 703 through 72 \ 3 or (resid 724 and (name N or name CA or name C or name O or name CB )) or resi \ d 725 through 744 or (resid 745 and (name N or name CA or name C or name O or na \ me CB )) or resid 746 through 747 or (resid 748 and (name N or name CA or name C \ or name O or name CB )) or resid 749 through 784 or (resid 785 and (name N or n \ ame CA or name C or name O or name CB )) or resid 786 through 790 or (resid 791 \ and (name N or name CA or name C or name O or name CB )) or resid 792 through 80 \ 3 or (resid 804 and (name N or name CA or name C or name O or name CB )) or resi \ d 805 through 813 or (resid 814 and (name N or name CA or name C or name O or na \ me CB )) or resid 815 through 816 or (resid 817 and (name N or name CA or name C \ or name O or name CB )) or resid 818 through 821 or (resid 822 and (name N or n \ ame CA or name C or name O or name CB )) or resid 823 through 826 or resid 855 t \ hrough 857 or (resid 858 and (name N or name CA or name C or name O or name CB ) \ ) or resid 859 through 894 or (resid 895 and (name N or name CA or name C or nam \ e O or name CB )) or resid 896 through 901 or (resid 902 through 904 and (name N \ or name CA or name C or name O or name CB )) or resid 905 through 913 or (resid \ 914 through 916 and (name N or name CA or name C or name O or name CB )) or res \ id 917 through 920 or (resid 921 and (name N or name CA or name C or name O or n \ ame CB )) or resid 922 or (resid 923 through 924 and (name N or name CA or name \ C or name O or name CB )) or resid 925 through 934 or (resid 935 and (name N or \ name CA or name C or name O or name CB )) or resid 936 through 940 or (resid 941 \ through 942 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 43 through 972 or (resid 973 and (name N or name CA or name C or name O or name \ CB )) or resid 974 through 983 or (resid 984 and (name N or name CA or name C or \ name O or name CB )) or resid 985 through 1028 or (resid 1029 and (name N or na \ me CA or name C or name O or name CB )) or resid 1030 through 1033 or (resid 103 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 1035 through \ 1060 or (resid 1061 and (name N or name CA or name C or name O or name CB )) or \ resid 1062 through 1071 or (resid 1072 through 1073 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1074 through 1076 or (resid 1077 through \ 1078 and (name N or name CA or name C or name O or name CB )) or resid 1079 thro \ ugh 1091 or (resid 1092 and (name N or name CA or name C or name O or name CB )) \ or resid 1093 through 1106 or (resid 1107 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1108 through 1127 or (resid 1128 through 1129 and ( \ name N or name CA or name C or name O or name CB )) or resid 1130 through 1144)) \ selection = (chain 'C' and (resid 26 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 50 or (resid 51 and (name N or nam \ e CA or name C or name O or name CB )) or resid 52 through 83 or (resid 84 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 through 96 or (r \ esid 97 and (name N or name CA or name C or name O or name CB )) or resid 98 thr \ ough 100 or (resid 101 and (name N or name CA or name C or name O or name CB )) \ or resid 102 through 104 or (resid 105 and (name N or name CA or name C or name \ O or name CB )) or resid 106 through 107 or (resid 108 through 119 and (name N o \ r name CA or name C or name O or name CB )) or resid 120 through 124 or (resid 1 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 126 through \ 144 or (resid 145 and (name N or name CA or name C or name O or name CB )) or r \ esid 153 through 155 or (resid 156 and (name N or name CA or name C or name O or \ name CB )) or resid 157 through 169 or (resid 170 and (name N or name CA or nam \ e C or name O or name CB )) or resid 171 through 173 or resid 188 through 194 or \ (resid 195 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 6 through 200 or (resid 201 and (name N or name CA or name C or name O or name C \ B )) or resid 202 through 211 or (resid 212 and (name N or name CA or name C or \ name O or name CB )) or resid 213 through 225 or (resid 226 through 227 and (nam \ e N or name CA or name C or name O or name CB )) or resid 228 through 230 or (re \ sid 231 and (name N or name CA or name C or name O or name CB )) or resid 232 th \ rough 233 or (resid 234 and (name N or name CA or name C or name O or name CB )) \ or resid 235 through 236 or (resid 237 through 238 and (name N or name CA or na \ me C or name O or name CB )) or resid 239 through 309 or (resid 310 and (name N \ or name CA or name C or name O or name CB )) or resid 311 through 325 or (resid \ 326 and (name N or name CA or name C or name O or name CB )) or resid 327 throug \ h 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) or \ resid 333 through 361 or (resid 362 through 364 and (name N or name CA or name C \ or name O or name CB )) or resid 365 through 543 or (resid 544 and (name N or n \ ame CA or name C or name O or name CB )) or resid 545 through 579 or (resid 580 \ and (name N or name CA or name C or name O or name CB )) or resid 581 through 59 \ 1 or (resid 592 and (name N or name CA or name C or name O or name CB )) or resi \ d 593 through 597 or (resid 598 through 599 and (name N or name CA or name C or \ name O or name CB )) or resid 600 through 607 or (resid 608 through 610 and (nam \ e N or name CA or name C or name O or name CB )) or resid 611 through 619 or (re \ sid 620 and (name N or name CA or name C or name O or name CB )) or resid 621 th \ rough 701 or (resid 702 and (name N or name CA or name C or name O or name CB )) \ or resid 703 through 704 or (resid 705 through 706 and (name N or name CA or na \ me C or name O or name CB )) or resid 707 through 709 or (resid 710 through 714 \ and (name N or name CA or name C or name O or name CB )) or resid 715 through 72 \ 3 or (resid 724 and (name N or name CA or name C or name O or name CB )) or resi \ d 725 through 764 or (resid 765 through 766 and (name N or name CA or name C or \ name O or name CB )) or resid 767 through 769 or (resid 770 through 771 and (nam \ e N or name CA or name C or name O or name CB )) or resid 772 through 784 or (re \ sid 785 and (name N or name CA or name C or name O or name CB )) or resid 786 th \ rough 790 or (resid 791 and (name N or name CA or name C or name O or name CB )) \ or resid 792 through 803 or (resid 804 and (name N or name CA or name C or name \ O or name CB )) or resid 805 through 813 or (resid 814 and (name N or name CA o \ r name C or name O or name CB )) or resid 815 through 816 or (resid 817 and (nam \ e N or name CA or name C or name O or name CB )) or resid 818 through 820 or (re \ sid 821 through 822 and (name N or name CA or name C or name O or name CB )) or \ resid 823 through 825 or (resid 826 and (name N or name CA or name C or name O o \ r name CB )) or resid 855 through 867 or (resid 868 and (name N or name CA or na \ me C or name O or name CB )) or resid 869 through 882 or (resid 883 and (name N \ or name CA or name C or name O or name CB )) or resid 884 through 894 or (resid \ 895 and (name N or name CA or name C or name O or name CB )) or resid 896 throug \ h 901 or (resid 902 through 904 and (name N or name CA or name C or name O or na \ me CB )) or resid 905 through 915 or (resid 916 and (name N or name CA or name C \ or name O or name CB )) or resid 917 through 920 or (resid 921 and (name N or n \ ame CA or name C or name O or name CB )) or resid 922 through 934 or (resid 935 \ and (name N or name CA or name C or name O or name CB )) or resid 936 through 93 \ 8 or (resid 939 and (name N or name CA or name C or name O or name CB )) or resi \ d 940 through 946 or (resid 947 and (name N or name CA or name C or name O or na \ me CB )) or resid 948 through 961 or (resid 962 and (name N or name CA or name C \ or name O or name CB )) or resid 963 through 976 or (resid 977 and (name N or n \ ame CA or name C or name O or name CB )) or resid 978 through 982 or (resid 983 \ through 984 and (name N or name CA or name C or name O or name CB )) or resid 98 \ 5 through 996 or (resid 997 and (name N or name CA or name C or name O or name C \ B )) or resid 998 through 1016 or (resid 1017 through 1018 and (name N or name C \ A or name C or name O or name CB )) or resid 1019 through 1049 or (resid 1050 an \ d (name N or name CA or name C or name O or name CB )) or resid 1051 through 106 \ 0 or (resid 1061 and (name N or name CA or name C or name O or name CB )) or res \ id 1062 through 1072 or (resid 1073 and (name N or name CA or name C or name O o \ r name CB )) or resid 1074 through 1076 or (resid 1077 through 1078 and (name N \ or name CA or name C or name O or name CB )) or resid 1079 through 1103 or (resi \ d 1104 and (name N or name CA or name C or name O or name CB )) or resid 1105 th \ rough 1126 or (resid 1127 through 1129 and (name N or name CA or name C or name \ O or name CB )) or resid 1130 through 1144)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'H' and resid 1 through 104) selection = chain 'J' selection = (chain 'L' and resid 1 through 104) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.020 Extract box with map and model: 8.560 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 74.490 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 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 : 0.014 0.103 28701 Z= 0.956 Angle : 1.961 24.407 39114 Z= 1.448 Chirality : 0.140 0.719 4446 Planarity : 0.007 0.049 5131 Dihedral : 13.735 88.138 9950 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.94 % Favored : 94.41 % Rotamer: Outliers : 0.98 % Allowed : 14.01 % Favored : 85.01 % Cbeta Deviations : 2.50 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.12), residues: 3687 helix: 0.56 (0.19), residues: 634 sheet: 0.15 (0.17), residues: 905 loop : -1.05 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP J 35 HIS 0.014 0.002 HIS C1064 PHE 0.044 0.004 PHE A1121 TYR 0.051 0.003 TYR B1067 ARG 0.006 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 290 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.7059 (m-80) cc_final: 0.6806 (m-80) REVERT: A 773 GLU cc_start: 0.7708 (tt0) cc_final: 0.7222 (tt0) REVERT: A 886 TRP cc_start: 0.6568 (p90) cc_final: 0.6219 (p90) REVERT: B 347 PHE cc_start: 0.2108 (OUTLIER) cc_final: 0.1871 (m-10) REVERT: C 156 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6185 (mm-30) REVERT: C 269 TYR cc_start: 0.7755 (m-80) cc_final: 0.7520 (m-10) REVERT: C 751 ASN cc_start: 0.8239 (m-40) cc_final: 0.7958 (m110) REVERT: C 755 GLN cc_start: 0.8440 (mt0) cc_final: 0.7962 (mm110) REVERT: C 817 PHE cc_start: 0.6784 (t80) cc_final: 0.6537 (t80) REVERT: C 869 MET cc_start: 0.8819 (mtt) cc_final: 0.8541 (mtm) REVERT: H 4 MET cc_start: 0.1101 (mtp) cc_final: -0.0427 (ttp) REVERT: I 80 MET cc_start: 0.2656 (tpt) cc_final: 0.2360 (tpp) outliers start: 29 outliers final: 9 residues processed: 316 average time/residue: 0.3621 time to fit residues: 187.7475 Evaluate side-chains 159 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 7.9990 chunk 280 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 149 optimal weight: 0.1980 chunk 290 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 336 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 370 ASN A 440 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 607 GLN A 655 HIS A 751 ASN A 755 GLN A1010 GLN B 66 HIS B 134 GLN B 239 GLN B 370 ASN B 388 ASN B 440 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 703 ASN B 751 ASN B 755 GLN B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1005 GLN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 388 ASN C 440 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 856 ASN C 935 GLN C1005 GLN C1010 GLN C1106 GLN C1108 ASN J 89 GLN H 89 GLN L 89 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 28701 Z= 0.206 Angle : 0.661 11.306 39114 Z= 0.364 Chirality : 0.047 0.207 4446 Planarity : 0.004 0.048 5131 Dihedral : 5.840 59.247 4009 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.91 % Favored : 95.88 % Rotamer: Outliers : 2.30 % Allowed : 15.70 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 3687 helix: 1.19 (0.20), residues: 651 sheet: 0.17 (0.16), residues: 1000 loop : -1.33 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.005 0.001 HIS A1088 PHE 0.016 0.002 PHE A 855 TYR 0.037 0.002 TYR A 660 ARG 0.006 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 175 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6779 (tm-30) REVERT: A 773 GLU cc_start: 0.7492 (tt0) cc_final: 0.7190 (tt0) REVERT: A 856 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7668 (p0) REVERT: A 886 TRP cc_start: 0.6525 (p90) cc_final: 0.5740 (p90) REVERT: B 347 PHE cc_start: 0.2177 (OUTLIER) cc_final: 0.1882 (m-10) REVERT: C 156 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6094 (mm-30) REVERT: C 755 GLN cc_start: 0.8229 (mt0) cc_final: 0.7941 (mm-40) REVERT: C 779 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: C 869 MET cc_start: 0.8551 (mtt) cc_final: 0.8306 (mtm) REVERT: C 949 GLN cc_start: 0.7923 (tt0) cc_final: 0.7661 (tp40) REVERT: C 1010 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7344 (mp-120) REVERT: L 4 MET cc_start: 0.0858 (mtt) cc_final: -0.2615 (tmm) outliers start: 68 outliers final: 35 residues processed: 235 average time/residue: 0.3660 time to fit residues: 145.4256 Evaluate side-chains 170 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 279 optimal weight: 0.7980 chunk 228 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 336 optimal weight: 50.0000 chunk 363 optimal weight: 6.9990 chunk 299 optimal weight: 2.9990 chunk 333 optimal weight: 40.0000 chunk 114 optimal weight: 9.9990 chunk 270 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 239 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN J 89 GLN H 89 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28701 Z= 0.171 Angle : 0.570 10.062 39114 Z= 0.307 Chirality : 0.045 0.158 4446 Planarity : 0.004 0.043 5131 Dihedral : 5.323 54.695 4005 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.71 % Rotamer: Outliers : 2.34 % Allowed : 16.31 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 3687 helix: 1.31 (0.21), residues: 635 sheet: 0.18 (0.15), residues: 983 loop : -1.34 (0.12), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.017 0.001 PHE B 106 TYR 0.019 0.001 TYR A 660 ARG 0.006 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 158 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6898 (tm-30) REVERT: A 856 ASN cc_start: 0.8194 (t0) cc_final: 0.7791 (p0) REVERT: B 347 PHE cc_start: 0.2125 (OUTLIER) cc_final: 0.1873 (m-10) REVERT: C 156 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5862 (mm-30) REVERT: C 269 TYR cc_start: 0.7312 (m-80) cc_final: 0.7083 (m-80) REVERT: C 592 PHE cc_start: 0.7880 (p90) cc_final: 0.7671 (p90) REVERT: C 755 GLN cc_start: 0.8160 (mt0) cc_final: 0.7883 (mm-40) REVERT: C 949 GLN cc_start: 0.7832 (tt0) cc_final: 0.7526 (tp-100) REVERT: L 4 MET cc_start: 0.0880 (mtt) cc_final: -0.2518 (tmm) outliers start: 69 outliers final: 36 residues processed: 218 average time/residue: 0.3469 time to fit residues: 128.6145 Evaluate side-chains 175 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 89 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 37 optimal weight: 30.0000 chunk 160 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 337 optimal weight: 10.0000 chunk 357 optimal weight: 50.0000 chunk 176 optimal weight: 0.9980 chunk 320 optimal weight: 50.0000 chunk 96 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 901 GLN A1005 GLN A1054 GLN B 239 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 755 GLN B1010 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1010 GLN J 89 GLN H 89 GLN I 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 28701 Z= 0.558 Angle : 0.723 12.840 39114 Z= 0.389 Chirality : 0.052 0.245 4446 Planarity : 0.005 0.072 5131 Dihedral : 5.622 50.198 4004 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.40 % Favored : 94.52 % Rotamer: Outliers : 2.84 % Allowed : 16.79 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3687 helix: 0.31 (0.20), residues: 627 sheet: -0.17 (0.15), residues: 996 loop : -1.64 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 886 HIS 0.008 0.002 HIS C1064 PHE 0.031 0.003 PHE B 86 TYR 0.027 0.002 TYR C 904 ARG 0.006 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 151 time to evaluate : 3.359 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: A 102 ARG cc_start: 0.7544 (mmp-170) cc_final: 0.7181 (mmp80) REVERT: A 129 LYS cc_start: 0.7403 (mptt) cc_final: 0.7119 (ttmt) REVERT: A 324 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6775 (tm-30) REVERT: A 619 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: A 856 ASN cc_start: 0.8295 (t0) cc_final: 0.7735 (p0) REVERT: A 886 TRP cc_start: 0.7404 (p90) cc_final: 0.6873 (p90) REVERT: B 347 PHE cc_start: 0.2368 (OUTLIER) cc_final: 0.2003 (m-10) REVERT: C 156 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5906 (mm-30) REVERT: C 592 PHE cc_start: 0.7800 (p90) cc_final: 0.7521 (p90) REVERT: C 675 GLN cc_start: 0.6782 (tt0) cc_final: 0.6570 (tm-30) REVERT: C 755 GLN cc_start: 0.8285 (mt0) cc_final: 0.7936 (mm-40) REVERT: C 784 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: C 817 PHE cc_start: 0.6651 (t80) cc_final: 0.6304 (t80) REVERT: C 869 MET cc_start: 0.8539 (mtt) cc_final: 0.8282 (mtm) REVERT: C 895 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: C 921 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7738 (mmtt) REVERT: C 949 GLN cc_start: 0.8247 (tt0) cc_final: 0.8026 (tp40) REVERT: C 988 GLU cc_start: 0.7772 (mp0) cc_final: 0.7536 (pm20) REVERT: L 4 MET cc_start: 0.0963 (mtt) cc_final: -0.2370 (tmm) REVERT: L 94 PHE cc_start: 0.3370 (OUTLIER) cc_final: 0.3141 (t80) outliers start: 84 outliers final: 56 residues processed: 222 average time/residue: 0.3621 time to fit residues: 136.1195 Evaluate side-chains 202 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 140 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 0.5980 chunk 203 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 305 optimal weight: 0.5980 chunk 247 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 182 optimal weight: 0.9980 chunk 321 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 448 ASN B1010 GLN C 218 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 957 GLN C1010 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28701 Z= 0.164 Angle : 0.546 10.930 39114 Z= 0.287 Chirality : 0.044 0.286 4446 Planarity : 0.004 0.067 5131 Dihedral : 5.109 51.675 4004 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 1.96 % Allowed : 18.41 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3687 helix: 0.98 (0.21), residues: 618 sheet: -0.03 (0.15), residues: 996 loop : -1.50 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.014 0.001 PHE A 92 TYR 0.016 0.001 TYR A 369 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 160 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6890 (tm-30) REVERT: A 619 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7115 (mt-10) REVERT: A 856 ASN cc_start: 0.8275 (t0) cc_final: 0.7997 (p0) REVERT: A 886 TRP cc_start: 0.7383 (p90) cc_final: 0.6805 (p90) REVERT: B 1072 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: C 156 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5745 (mm-30) REVERT: C 592 PHE cc_start: 0.7783 (p90) cc_final: 0.7575 (p90) REVERT: C 675 GLN cc_start: 0.6953 (tt0) cc_final: 0.6673 (tm-30) REVERT: C 755 GLN cc_start: 0.8193 (mt0) cc_final: 0.7866 (mm110) REVERT: C 779 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: C 784 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: C 949 GLN cc_start: 0.8009 (tt0) cc_final: 0.7767 (tp40) REVERT: C 979 ASP cc_start: 0.7738 (m-30) cc_final: 0.7537 (t0) REVERT: H 29 ILE cc_start: -0.2214 (OUTLIER) cc_final: -0.2644 (tt) REVERT: L 4 MET cc_start: 0.1156 (mtt) cc_final: -0.2162 (tmm) outliers start: 58 outliers final: 33 residues processed: 211 average time/residue: 0.3626 time to fit residues: 129.2324 Evaluate side-chains 185 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 94 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 357 optimal weight: 9.9990 chunk 297 optimal weight: 1.9990 chunk 165 optimal weight: 0.0060 chunk 29 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 187 optimal weight: 0.1980 overall best weight: 2.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN C 218 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28701 Z= 0.324 Angle : 0.589 11.403 39114 Z= 0.310 Chirality : 0.046 0.216 4446 Planarity : 0.004 0.070 5131 Dihedral : 5.005 52.154 4002 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 2.44 % Allowed : 18.31 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3687 helix: 0.77 (0.21), residues: 625 sheet: -0.08 (0.15), residues: 1001 loop : -1.55 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.005 0.001 HIS C1064 PHE 0.020 0.002 PHE B 86 TYR 0.020 0.002 TYR C 707 ARG 0.002 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 148 time to evaluate : 3.074 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: A 102 ARG cc_start: 0.7493 (mmp80) cc_final: 0.7264 (mmp-170) REVERT: A 324 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6914 (tm-30) REVERT: A 619 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: A 856 ASN cc_start: 0.8225 (t0) cc_final: 0.7921 (p0) REVERT: B 347 PHE cc_start: 0.2368 (OUTLIER) cc_final: 0.1985 (m-10) REVERT: B 950 ASP cc_start: 0.7795 (m-30) cc_final: 0.7577 (m-30) REVERT: B 1072 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: C 156 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5901 (mm-30) REVERT: C 755 GLN cc_start: 0.8247 (mt0) cc_final: 0.7905 (mm-40) REVERT: C 784 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: C 949 GLN cc_start: 0.8044 (tt0) cc_final: 0.7775 (tp40) REVERT: H 29 ILE cc_start: -0.2006 (OUTLIER) cc_final: -0.2493 (tt) REVERT: L 4 MET cc_start: 0.1204 (mtt) cc_final: -0.2131 (tmm) outliers start: 72 outliers final: 48 residues processed: 209 average time/residue: 0.3570 time to fit residues: 126.6714 Evaluate side-chains 196 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 142 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 50.0000 chunk 40 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 301 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 356 optimal weight: 8.9990 chunk 223 optimal weight: 0.6980 chunk 217 optimal weight: 0.0870 chunk 164 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 901 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28701 Z= 0.149 Angle : 0.516 10.942 39114 Z= 0.269 Chirality : 0.043 0.176 4446 Planarity : 0.004 0.069 5131 Dihedral : 4.663 54.198 4002 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 1.35 % Allowed : 19.22 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 3687 helix: 1.33 (0.21), residues: 622 sheet: 0.15 (0.16), residues: 962 loop : -1.45 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.003 0.001 HIS C1088 PHE 0.016 0.001 PHE B 342 TYR 0.020 0.001 TYR A 160 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 3.095 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: A 324 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6955 (tm-30) REVERT: A 574 ASP cc_start: 0.8049 (p0) cc_final: 0.7783 (p0) REVERT: A 619 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7088 (mt-10) REVERT: A 856 ASN cc_start: 0.8223 (t0) cc_final: 0.8007 (p0) REVERT: B 347 PHE cc_start: 0.2366 (OUTLIER) cc_final: 0.2004 (m-10) REVERT: B 981 LEU cc_start: 0.8229 (mm) cc_final: 0.8028 (mm) REVERT: B 1072 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: C 156 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5825 (mm-30) REVERT: C 231 ILE cc_start: 0.8517 (mm) cc_final: 0.8262 (mt) REVERT: C 740 MET cc_start: 0.8594 (mmm) cc_final: 0.8235 (mmt) REVERT: C 755 GLN cc_start: 0.8127 (mt0) cc_final: 0.7857 (mm-40) REVERT: C 804 GLN cc_start: 0.8366 (mt0) cc_final: 0.7858 (mm-40) REVERT: H 29 ILE cc_start: -0.2119 (OUTLIER) cc_final: -0.2564 (tt) REVERT: L 4 MET cc_start: 0.1202 (mtt) cc_final: -0.2091 (tmm) outliers start: 40 outliers final: 31 residues processed: 194 average time/residue: 0.3726 time to fit residues: 121.7552 Evaluate side-chains 184 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 242 optimal weight: 0.9990 chunk 176 optimal weight: 0.0980 chunk 33 optimal weight: 20.0000 chunk 280 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 448 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28701 Z= 0.174 Angle : 0.517 11.030 39114 Z= 0.268 Chirality : 0.043 0.151 4446 Planarity : 0.004 0.068 5131 Dihedral : 4.555 54.367 4002 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.67 % Favored : 95.25 % Rotamer: Outliers : 1.59 % Allowed : 19.26 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 3687 helix: 1.34 (0.21), residues: 627 sheet: 0.21 (0.16), residues: 967 loop : -1.41 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.004 0.001 HIS B 66 PHE 0.016 0.001 PHE B 342 TYR 0.022 0.001 TYR A 160 ARG 0.010 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6969 (tm-30) REVERT: A 869 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7938 (mtt) REVERT: B 347 PHE cc_start: 0.2556 (OUTLIER) cc_final: 0.2169 (m-10) REVERT: B 780 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 1072 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: C 231 ILE cc_start: 0.8532 (mm) cc_final: 0.8276 (mt) REVERT: C 740 MET cc_start: 0.8592 (mmm) cc_final: 0.8238 (mmt) REVERT: C 755 GLN cc_start: 0.8147 (mt0) cc_final: 0.7873 (mm-40) REVERT: C 784 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: C 804 GLN cc_start: 0.8400 (mt0) cc_final: 0.7891 (mm-40) REVERT: H 29 ILE cc_start: -0.2328 (OUTLIER) cc_final: -0.2779 (tt) REVERT: L 4 MET cc_start: 0.1124 (mtt) cc_final: -0.2144 (tmm) outliers start: 47 outliers final: 31 residues processed: 194 average time/residue: 0.3575 time to fit residues: 117.1271 Evaluate side-chains 183 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 40.0000 chunk 341 optimal weight: 50.0000 chunk 311 optimal weight: 30.0000 chunk 332 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 144 optimal weight: 40.0000 chunk 260 optimal weight: 5.9990 chunk 101 optimal weight: 0.0670 chunk 300 optimal weight: 0.5980 chunk 314 optimal weight: 7.9990 chunk 331 optimal weight: 0.0770 overall best weight: 1.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 901 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28701 Z= 0.263 Angle : 0.547 11.153 39114 Z= 0.284 Chirality : 0.044 0.155 4446 Planarity : 0.004 0.045 5131 Dihedral : 4.573 55.546 3999 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 1.62 % Allowed : 19.56 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 3687 helix: 1.16 (0.21), residues: 621 sheet: 0.15 (0.16), residues: 950 loop : -1.43 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.004 0.001 HIS H 92 PHE 0.018 0.001 PHE B1121 TYR 0.022 0.001 TYR A 160 ARG 0.012 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 157 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7494 (mmp80) cc_final: 0.7054 (mmp-170) REVERT: A 324 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6904 (tm-30) REVERT: A 886 TRP cc_start: 0.7987 (p90) cc_final: 0.7747 (p90) REVERT: B 347 PHE cc_start: 0.2430 (OUTLIER) cc_final: 0.2003 (m-10) REVERT: B 1072 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: C 170 TYR cc_start: 0.7526 (t80) cc_final: 0.7270 (t80) REVERT: C 231 ILE cc_start: 0.8541 (mm) cc_final: 0.8274 (mt) REVERT: C 755 GLN cc_start: 0.8159 (mt0) cc_final: 0.7849 (mm110) REVERT: C 784 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: J 4 MET cc_start: 0.0724 (ptp) cc_final: 0.0358 (ptp) REVERT: H 29 ILE cc_start: -0.1934 (OUTLIER) cc_final: -0.2309 (tt) REVERT: L 4 MET cc_start: 0.1245 (mtt) cc_final: -0.2070 (tmm) outliers start: 48 outliers final: 39 residues processed: 196 average time/residue: 0.3576 time to fit residues: 119.8899 Evaluate side-chains 198 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 155 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 0.4980 chunk 351 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 244 optimal weight: 50.0000 chunk 368 optimal weight: 8.9990 chunk 339 optimal weight: 30.0000 chunk 293 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.184 28701 Z= 0.349 Angle : 0.681 59.134 39114 Z= 0.378 Chirality : 0.046 0.532 4446 Planarity : 0.004 0.091 5131 Dihedral : 4.593 55.534 3999 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 1.69 % Allowed : 19.97 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 3687 helix: 1.11 (0.21), residues: 621 sheet: 0.15 (0.16), residues: 950 loop : -1.44 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 PHE 0.019 0.002 PHE B1121 TYR 0.022 0.001 TYR E 91 ARG 0.026 0.001 ARG E 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7374 Ramachandran restraints generated. 3687 Oldfield, 0 Emsley, 3687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 156 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7485 (mmp80) cc_final: 0.7055 (mmp-170) REVERT: A 324 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6904 (tm-30) REVERT: A 856 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7310 (t0) REVERT: A 886 TRP cc_start: 0.7991 (p90) cc_final: 0.7752 (p90) REVERT: B 347 PHE cc_start: 0.2433 (OUTLIER) cc_final: 0.2005 (m-10) REVERT: B 1072 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: C 170 TYR cc_start: 0.7528 (t80) cc_final: 0.7267 (t80) REVERT: C 231 ILE cc_start: 0.8542 (mm) cc_final: 0.8276 (mt) REVERT: C 755 GLN cc_start: 0.8163 (mt0) cc_final: 0.7852 (mm110) REVERT: C 784 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: J 4 MET cc_start: 0.0729 (ptp) cc_final: 0.0369 (ptp) REVERT: H 29 ILE cc_start: -0.1911 (OUTLIER) cc_final: -0.2311 (tt) REVERT: L 4 MET cc_start: 0.1246 (mtt) cc_final: -0.2069 (tmm) outliers start: 50 outliers final: 41 residues processed: 194 average time/residue: 0.3633 time to fit residues: 120.2785 Evaluate side-chains 200 residues out of total 3242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 154 time to evaluate : 4.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 3.9990 chunk 312 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 43 optimal weight: 40.0000 chunk 81 optimal weight: 0.9990 chunk 293 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.204532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.163637 restraints weight = 38778.297| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.39 r_work: 0.3706 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.434 28701 Z= 0.444 Angle : 0.633 39.022 39114 Z= 0.374 Chirality : 0.046 0.265 4446 Planarity : 0.005 0.206 5131 Dihedral : 4.593 55.534 3999 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 1.59 % Allowed : 19.97 % Favored : 78.44 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 3687 helix: 1.11 (0.21), residues: 621 sheet: 0.15 (0.16), residues: 950 loop : -1.44 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 PHE 0.019 0.002 PHE B1121 TYR 0.022 0.001 TYR E 91 ARG 0.026 0.001 ARG E 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5354.24 seconds wall clock time: 98 minutes 40.31 seconds (5920.31 seconds total)