Starting phenix.real_space_refine on Tue Feb 20 20:24:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvk_34130/02_2024/7yvk_34130.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvk_34130/02_2024/7yvk_34130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvk_34130/02_2024/7yvk_34130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvk_34130/02_2024/7yvk_34130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvk_34130/02_2024/7yvk_34130.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvk_34130/02_2024/7yvk_34130.pdb" } resolution = 3.2 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= 0.036 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 123 5.16 5 C 18441 2.51 5 N 4710 2.21 5 O 5535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I ARG 63": "NH1" <-> "NH2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 68": "NH1" <-> "NH2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 68": "NH1" <-> "NH2" Residue "O GLU 52": "OE1" <-> "OE2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28809 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "C" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.32, per 1000 atoms: 0.57 Number of scatterers: 28809 At special positions: 0 Unit cell: (192.7, 168.1, 182.86, 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 123 16.00 O 5535 8.00 N 4710 7.00 C 18441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.07 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.07 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 97 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.44 Conformation dependent library (CDL) restraints added in 5.6 seconds 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6996 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 58 sheets defined 20.5% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.896A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.695A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.539A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.506A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.826A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.989A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.681A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.034A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.981A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.006A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.633A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.823A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.554A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.510A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.962A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.648A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.229A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.005A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.829A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.601A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.785A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.622A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.634A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.529A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.760A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.010A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.597A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.075A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.876A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.811A pdb=" N THR H 92 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.549A pdb=" N ASP I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 92 removed outlier: 3.720A pdb=" N THR K 92 " --> pdb=" O PRO K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'N' and resid 88 through 92 removed outlier: 3.627A pdb=" N THR N 92 " --> pdb=" O PRO N 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 85 removed outlier: 3.666A pdb=" N ASP O 85 " --> pdb=" O ALA O 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.545A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.585A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.864A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.085A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.473A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.103A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.199A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.852A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.852A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.479A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.959A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.472A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.771A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.464A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.901A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.825A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.067A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.011A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.965A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.776A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.776A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.408A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 788 through 789 removed outlier: 6.041A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.621A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 29 through 31 removed outlier: 8.382A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.882A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.043A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.817A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 391 through 392 removed outlier: 4.058A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.011A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.662A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.662A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.548A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.708A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.402A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 9 through 10 removed outlier: 6.624A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 9 through 10 Processing sheet with id=AF1, first strand: chain 'I' and resid 18 through 20 Processing sheet with id=AF2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'K' and resid 59 through 61 removed outlier: 5.743A pdb=" N TRP K 49 " --> pdb=" O ARG K 40 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG K 40 " --> pdb=" O TRP K 49 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA K 51 " --> pdb=" O TRP K 38 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR K 95 " --> pdb=" O THR K 113 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR K 113 " --> pdb=" O TYR K 95 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.934A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AF7, first strand: chain 'L' and resid 18 through 20 Processing sheet with id=AF8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AG1, first strand: chain 'N' and resid 59 through 61 removed outlier: 5.342A pdb=" N TRP N 49 " --> pdb=" O ARG N 40 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG N 40 " --> pdb=" O TRP N 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA N 51 " --> pdb=" O TRP N 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 9 through 10 removed outlier: 6.919A pdb=" N TRP O 37 " --> pdb=" O MET O 49 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 9 through 10 Processing sheet with id=AG4, first strand: chain 'O' and resid 18 through 20 1150 hydrogen bonds defined for protein. 3042 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: 14.72 Time building geometry restraints manager: 12.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5697 1.32 - 1.46: 10531 1.46 - 1.59: 13109 1.59 - 1.73: 8 1.73 - 1.87: 145 Bond restraints: 29490 Sorted by residual: bond pdb=" C PRO B 863 " pdb=" O PRO B 863 " ideal model delta sigma weight residual 1.233 1.185 0.048 1.12e-02 7.97e+03 1.81e+01 bond pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 1.808 1.674 0.134 3.30e-02 9.18e+02 1.65e+01 bond pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " ideal model delta sigma weight residual 1.808 1.679 0.129 3.30e-02 9.18e+02 1.52e+01 bond pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 1.808 1.680 0.128 3.30e-02 9.18e+02 1.52e+01 bond pdb=" CB TRP B 886 " pdb=" CG TRP B 886 " ideal model delta sigma weight residual 1.498 1.384 0.114 3.10e-02 1.04e+03 1.36e+01 ... (remaining 29485 not shown) Histogram of bond angle deviations from ideal: 93.99 - 102.15: 59 102.15 - 110.30: 8514 110.30 - 118.45: 14595 118.45 - 126.60: 16735 126.60 - 134.75: 381 Bond angle restraints: 40284 Sorted by residual: angle pdb=" C VAL O 53 " pdb=" N SER O 54 " pdb=" CA SER O 54 " ideal model delta sigma weight residual 121.58 107.92 13.66 1.95e+00 2.63e-01 4.91e+01 angle pdb=" CA CYS C 738 " pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 114.40 129.22 -14.82 2.30e+00 1.89e-01 4.15e+01 angle pdb=" C VAL L 53 " pdb=" N SER L 54 " pdb=" CA SER L 54 " ideal model delta sigma weight residual 121.58 109.19 12.39 1.95e+00 2.63e-01 4.03e+01 angle pdb=" CA CYS A 590 " pdb=" CB CYS A 590 " pdb=" SG CYS A 590 " ideal model delta sigma weight residual 114.40 128.64 -14.24 2.30e+00 1.89e-01 3.83e+01 angle pdb=" C ILE C 332 " pdb=" N THR C 333 " pdb=" CA THR C 333 " ideal model delta sigma weight residual 121.80 134.75 -12.95 2.16e+00 2.14e-01 3.60e+01 ... (remaining 40279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 16330 17.53 - 35.05: 1185 35.05 - 52.58: 267 52.58 - 70.10: 79 70.10 - 87.63: 19 Dihedral angle restraints: 17880 sinusoidal: 6987 harmonic: 10893 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 174.00 -81.00 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 171.16 -78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -161.57 75.57 1 1.00e+01 1.00e-02 7.21e+01 ... (remaining 17877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3817 0.098 - 0.196: 833 0.196 - 0.294: 73 0.294 - 0.392: 9 0.392 - 0.490: 5 Chirality restraints: 4737 Sorted by residual: chirality pdb=" CA PHE C 855 " pdb=" N PHE C 855 " pdb=" C PHE C 855 " pdb=" CB PHE C 855 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.00e+00 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 2.05 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CA CYS A 760 " pdb=" N CYS A 760 " pdb=" C CYS A 760 " pdb=" CB CYS A 760 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 4734 not shown) Planarity restraints: 5127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 102 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO K 103 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO K 103 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO K 103 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE N 102 " 0.069 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO N 103 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO N 103 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO N 103 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 102 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.65e+01 pdb=" N PRO H 103 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.056 5.00e-02 4.00e+02 ... (remaining 5124 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 479 2.63 - 3.20: 26596 3.20 - 3.77: 41240 3.77 - 4.33: 55621 4.33 - 4.90: 96888 Nonbonded interactions: 220824 Sorted by model distance: nonbonded pdb=" NH2 ARG L 56 " pdb=" O SER L 61 " model vdw 2.063 2.520 nonbonded pdb=" O ILE H 105 " pdb=" OH TYR I 38 " model vdw 2.102 2.440 nonbonded pdb=" O TRP A 353 " pdb=" NH1 ARG A 466 " model vdw 2.116 2.520 nonbonded pdb=" O TRP C 353 " pdb=" NH1 ARG C 466 " model vdw 2.128 2.520 nonbonded pdb=" OG SER A 366 " pdb=" ND2 ASN A 388 " model vdw 2.136 2.520 ... (remaining 220819 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 27 through 1146 or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 1146 or resid 1301 through 1311)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 7.700 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: 29.400 Check model and map are aligned: 0.450 Set scattering table: 0.250 Process input model: 82.880 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.200 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.017 0.142 29490 Z= 1.082 Angle : 1.304 21.090 40284 Z= 0.713 Chirality : 0.079 0.490 4737 Planarity : 0.008 0.107 5127 Dihedral : 13.294 87.631 10749 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.47 % Favored : 94.20 % Rotamer: Outliers : 1.23 % Allowed : 8.86 % Favored : 89.92 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % 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: -2.67 (0.12), residues: 3690 helix: 0.05 (0.19), residues: 665 sheet: -1.85 (0.14), residues: 1035 loop : -2.43 (0.12), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP A 64 HIS 0.019 0.003 HIS B1048 PHE 0.052 0.005 PHE B 92 TYR 0.046 0.004 TYR A 170 ARG 0.016 0.002 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 GLN cc_start: 0.8078 (mt0) cc_final: 0.7245 (tm-30) REVERT: C 237 ARG cc_start: 0.7763 (mtp180) cc_final: 0.7072 (ptt-90) REVERT: C 355 ARG cc_start: 0.7497 (tpt170) cc_final: 0.7127 (tpp80) REVERT: C 488 CYS cc_start: -0.0698 (OUTLIER) cc_final: -0.1096 (m) REVERT: B 237 ARG cc_start: 0.7353 (mtp180) cc_final: 0.6923 (ptm160) REVERT: B 238 PHE cc_start: 0.6411 (p90) cc_final: 0.6087 (p90) REVERT: B 354 ASN cc_start: 0.8285 (t0) cc_final: 0.7660 (t0) REVERT: B 403 ARG cc_start: 0.6504 (ttm-80) cc_final: 0.5350 (ttm-80) REVERT: B 488 CYS cc_start: 0.3973 (OUTLIER) cc_final: 0.3608 (t) REVERT: B 983 ARG cc_start: 0.6896 (mtm110) cc_final: 0.6519 (mtm110) REVERT: H 39 ILE cc_start: 0.6962 (mt) cc_final: 0.6620 (mm) REVERT: H 40 ARG cc_start: 0.8531 (ptt180) cc_final: 0.7689 (ttp80) REVERT: H 47 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.6972 (mm) REVERT: H 74 ASP cc_start: 0.8598 (t0) cc_final: 0.8397 (t0) REVERT: I 39 GLN cc_start: 0.6889 (tm-30) cc_final: 0.6650 (tt0) REVERT: I 49 MET cc_start: 0.6828 (mmp) cc_final: 0.6623 (mmm) REVERT: N 4 LEU cc_start: 0.3207 (OUTLIER) cc_final: 0.1958 (tt) REVERT: O 49 MET cc_start: 0.2954 (tpp) cc_final: 0.2209 (ttt) outliers start: 37 outliers final: 10 residues processed: 279 average time/residue: 0.4274 time to fit residues: 186.2730 Evaluate side-chains 188 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 0.9980 chunk 279 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 289 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 175 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 335 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 709 ASN A 762 GLN A 955 ASN A1088 HIS C 218 GLN C 481 ASN C 709 ASN C 856 ASN C1088 HIS C1098 ASN C1134 ASN B 188 ASN B 417 ASN B 532 ASN B 657 ASN B 709 ASN B 762 GLN B 978 ASN B1088 HIS B1134 ASN H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN K 41 GLN K 78 ASN L 33 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29490 Z= 0.208 Angle : 0.648 10.825 40284 Z= 0.338 Chirality : 0.046 0.259 4737 Planarity : 0.005 0.077 5127 Dihedral : 6.792 59.392 4774 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 2.35 % Allowed : 11.28 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.56 (0.13), residues: 3690 helix: 1.38 (0.21), residues: 656 sheet: -0.81 (0.15), residues: 1025 loop : -2.06 (0.12), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 436 HIS 0.003 0.001 HIS C1088 PHE 0.014 0.001 PHE A 106 TYR 0.020 0.001 TYR A1138 ARG 0.006 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 215 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 GLN cc_start: 0.8050 (mt0) cc_final: 0.7340 (tm-30) REVERT: C 237 ARG cc_start: 0.7868 (mtp180) cc_final: 0.7236 (ptt-90) REVERT: C 355 ARG cc_start: 0.7535 (tpt170) cc_final: 0.7242 (tpp80) REVERT: B 237 ARG cc_start: 0.7220 (mtp180) cc_final: 0.6887 (ptm160) REVERT: B 403 ARG cc_start: 0.6591 (ttm-80) cc_final: 0.5536 (ttm-80) REVERT: B 525 CYS cc_start: 0.5674 (OUTLIER) cc_final: 0.5098 (m) REVERT: B 619 GLU cc_start: 0.8403 (pt0) cc_final: 0.8200 (pt0) REVERT: B 983 ARG cc_start: 0.6909 (mtm110) cc_final: 0.6503 (mtm110) REVERT: H 24 PHE cc_start: 0.8100 (p90) cc_final: 0.7678 (p90) REVERT: I 81 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7283 (pt0) REVERT: N 101 THR cc_start: 0.7349 (OUTLIER) cc_final: 0.7082 (m) REVERT: O 49 MET cc_start: 0.3198 (tpp) cc_final: 0.2383 (ttt) outliers start: 71 outliers final: 34 residues processed: 275 average time/residue: 0.3979 time to fit residues: 179.7301 Evaluate side-chains 207 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 171 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 95 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 228 optimal weight: 0.0050 chunk 92 optimal weight: 0.6980 chunk 335 optimal weight: 8.9990 chunk 362 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 chunk 332 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 269 optimal weight: 3.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A1005 GLN A1074 ASN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 751 ASN B 762 GLN H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29490 Z= 0.201 Angle : 0.593 11.626 40284 Z= 0.308 Chirality : 0.045 0.327 4737 Planarity : 0.004 0.058 5127 Dihedral : 6.038 58.520 4762 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.07 % Favored : 94.82 % Rotamer: Outliers : 2.65 % Allowed : 12.74 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.14 (0.13), residues: 3690 helix: 1.75 (0.21), residues: 671 sheet: -0.55 (0.15), residues: 1010 loop : -1.81 (0.12), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.002 0.000 HIS B1048 PHE 0.021 0.001 PHE B 168 TYR 0.023 0.001 TYR A1138 ARG 0.003 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 181 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 GLN cc_start: 0.8084 (mt0) cc_final: 0.7369 (tm-30) REVERT: C 237 ARG cc_start: 0.7842 (mtp180) cc_final: 0.7237 (ptt-90) REVERT: B 237 ARG cc_start: 0.7242 (mtp180) cc_final: 0.6903 (ptm160) REVERT: B 403 ARG cc_start: 0.6638 (ttm-80) cc_final: 0.5465 (ttm-80) REVERT: B 453 TYR cc_start: 0.7486 (p90) cc_final: 0.6798 (p90) REVERT: B 455 LEU cc_start: 0.8678 (tp) cc_final: 0.8139 (tt) REVERT: B 493 GLN cc_start: 0.6692 (mp10) cc_final: 0.6172 (mp10) REVERT: B 886 TRP cc_start: 0.7451 (OUTLIER) cc_final: 0.7132 (m-90) REVERT: I 81 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7306 (pt0) REVERT: N 101 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7256 (m) REVERT: O 49 MET cc_start: 0.3211 (tpp) cc_final: 0.2395 (ttt) outliers start: 80 outliers final: 50 residues processed: 249 average time/residue: 0.3759 time to fit residues: 155.2762 Evaluate side-chains 221 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 169 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 37 optimal weight: 50.0000 chunk 160 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 336 optimal weight: 30.0000 chunk 356 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 319 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN A1134 ASN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN C 856 ASN C1074 ASN C1098 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1074 ASN B1098 ASN H 78 ASN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 29490 Z= 0.387 Angle : 0.655 11.538 40284 Z= 0.343 Chirality : 0.048 0.288 4737 Planarity : 0.005 0.057 5127 Dihedral : 6.049 58.886 4758 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.69 % Favored : 94.25 % Rotamer: Outliers : 3.35 % Allowed : 14.96 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.03 (0.13), residues: 3690 helix: 1.59 (0.21), residues: 674 sheet: -0.40 (0.15), residues: 1023 loop : -1.71 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 436 HIS 0.004 0.001 HIS C1058 PHE 0.021 0.002 PHE A 92 TYR 0.028 0.002 TYR C 265 ARG 0.005 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 165 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 GLN cc_start: 0.8169 (mt0) cc_final: 0.7404 (tm-30) REVERT: C 237 ARG cc_start: 0.8022 (mtp180) cc_final: 0.7307 (ptt-90) REVERT: C 355 ARG cc_start: 0.7688 (tpp80) cc_final: 0.7151 (tpt170) REVERT: B 237 ARG cc_start: 0.7250 (mtp180) cc_final: 0.6931 (ptm160) REVERT: B 329 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8606 (m-10) REVERT: B 403 ARG cc_start: 0.6730 (ttm-80) cc_final: 0.5619 (ttm-80) REVERT: B 455 LEU cc_start: 0.8632 (tp) cc_final: 0.8183 (tt) REVERT: B 493 GLN cc_start: 0.6846 (mp10) cc_final: 0.6259 (mp10) REVERT: B 886 TRP cc_start: 0.7638 (OUTLIER) cc_final: 0.7193 (m-90) REVERT: I 56 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8318 (tmm-80) REVERT: I 81 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7303 (pt0) REVERT: O 49 MET cc_start: 0.3162 (tpp) cc_final: 0.2273 (ttt) outliers start: 101 outliers final: 67 residues processed: 254 average time/residue: 0.3914 time to fit residues: 164.7738 Evaluate side-chains 225 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 155 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 3.9990 chunk 202 optimal weight: 0.0060 chunk 5 optimal weight: 2.9990 chunk 265 optimal weight: 0.0870 chunk 147 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 182 optimal weight: 0.6980 chunk 320 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN B 965 GLN H 78 ASN H 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 29490 Z= 0.169 Angle : 0.558 12.802 40284 Z= 0.290 Chirality : 0.044 0.271 4737 Planarity : 0.004 0.051 5127 Dihedral : 5.495 56.182 4757 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 2.95 % Allowed : 16.05 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.68 (0.13), residues: 3690 helix: 2.04 (0.21), residues: 660 sheet: -0.07 (0.15), residues: 1035 loop : -1.59 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 258 HIS 0.002 0.000 HIS B1048 PHE 0.013 0.001 PHE B 168 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 182 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8127 (tpt-90) cc_final: 0.7579 (mmt180) REVERT: A 398 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6748 (m-30) REVERT: C 218 GLN cc_start: 0.8142 (mt0) cc_final: 0.7400 (tm-30) REVERT: C 237 ARG cc_start: 0.7914 (mtp180) cc_final: 0.7282 (ptt-90) REVERT: C 355 ARG cc_start: 0.7799 (tpp80) cc_final: 0.7273 (tpp80) REVERT: C 902 MET cc_start: 0.7927 (tpp) cc_final: 0.7715 (mmt) REVERT: B 403 ARG cc_start: 0.6788 (ttm-80) cc_final: 0.5625 (ttm-80) REVERT: B 455 LEU cc_start: 0.8666 (tp) cc_final: 0.8209 (tt) REVERT: B 493 GLN cc_start: 0.6827 (mp10) cc_final: 0.6252 (mp10) REVERT: B 619 GLU cc_start: 0.8253 (pt0) cc_final: 0.7938 (pt0) REVERT: B 752 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9126 (tt) REVERT: B 886 TRP cc_start: 0.7393 (m-90) cc_final: 0.7187 (m-90) REVERT: I 56 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8357 (tmm-80) REVERT: I 81 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7329 (pt0) REVERT: O 49 MET cc_start: 0.3137 (tpp) cc_final: 0.2273 (ttt) outliers start: 89 outliers final: 61 residues processed: 261 average time/residue: 0.3724 time to fit residues: 161.5014 Evaluate side-chains 228 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 164 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 357 optimal weight: 20.0000 chunk 296 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 187 optimal weight: 0.2980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C1098 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 965 GLN H 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29490 Z= 0.205 Angle : 0.559 11.845 40284 Z= 0.290 Chirality : 0.044 0.297 4737 Planarity : 0.004 0.047 5127 Dihedral : 5.312 54.423 4757 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.69 % Rotamer: Outliers : 3.28 % Allowed : 16.22 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.58 (0.13), residues: 3690 helix: 2.06 (0.21), residues: 660 sheet: 0.06 (0.16), residues: 1023 loop : -1.53 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.002 0.001 HIS C1058 PHE 0.013 0.001 PHE C 238 TYR 0.022 0.001 TYR B1067 ARG 0.003 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 169 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6864 (m-30) REVERT: C 218 GLN cc_start: 0.8165 (mt0) cc_final: 0.7428 (tm-30) REVERT: C 237 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7322 (ptt-90) REVERT: C 355 ARG cc_start: 0.7812 (tpp80) cc_final: 0.7240 (tpp80) REVERT: C 902 MET cc_start: 0.7920 (tpp) cc_final: 0.7704 (mmt) REVERT: B 403 ARG cc_start: 0.6830 (ttm-80) cc_final: 0.5676 (ttm-80) REVERT: B 455 LEU cc_start: 0.8675 (tp) cc_final: 0.8206 (tt) REVERT: B 493 GLN cc_start: 0.6845 (mp10) cc_final: 0.6226 (mp10) REVERT: B 619 GLU cc_start: 0.8287 (pt0) cc_final: 0.7953 (pt0) REVERT: B 752 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9112 (tt) REVERT: H 40 ARG cc_start: 0.8440 (ptt180) cc_final: 0.8071 (ptt-90) REVERT: I 49 MET cc_start: 0.5841 (mmp) cc_final: 0.5207 (mmp) REVERT: I 56 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8362 (tmm-80) REVERT: I 81 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7348 (pt0) REVERT: O 49 MET cc_start: 0.3110 (tpp) cc_final: 0.2299 (ttt) outliers start: 99 outliers final: 70 residues processed: 258 average time/residue: 0.3814 time to fit residues: 164.6026 Evaluate side-chains 237 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 164 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 202 optimal weight: 0.3980 chunk 300 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 355 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1098 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN H 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29490 Z= 0.253 Angle : 0.571 11.514 40284 Z= 0.298 Chirality : 0.045 0.273 4737 Planarity : 0.004 0.047 5127 Dihedral : 5.258 54.605 4757 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.63 % Rotamer: Outliers : 3.18 % Allowed : 16.72 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.49 (0.14), residues: 3690 helix: 2.08 (0.21), residues: 656 sheet: 0.12 (0.16), residues: 1038 loop : -1.46 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.003 0.001 HIS C1064 PHE 0.015 0.001 PHE C 238 TYR 0.023 0.001 TYR B1067 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 172 time to evaluate : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 GLN cc_start: 0.8171 (mt0) cc_final: 0.7430 (tm-30) REVERT: C 237 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7324 (ptt-90) REVERT: C 355 ARG cc_start: 0.7820 (tpp80) cc_final: 0.7247 (tpp80) REVERT: C 422 ASN cc_start: 0.5596 (OUTLIER) cc_final: 0.4379 (p0) REVERT: C 902 MET cc_start: 0.7894 (tpp) cc_final: 0.7669 (mmt) REVERT: B 403 ARG cc_start: 0.6837 (ttm-80) cc_final: 0.5695 (ttm-80) REVERT: B 406 GLU cc_start: 0.7652 (tp30) cc_final: 0.7425 (tp30) REVERT: B 455 LEU cc_start: 0.8726 (tp) cc_final: 0.8295 (tt) REVERT: B 493 GLN cc_start: 0.6812 (mp10) cc_final: 0.6216 (mp10) REVERT: B 619 GLU cc_start: 0.8324 (pt0) cc_final: 0.7953 (pt0) REVERT: B 752 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9111 (tt) REVERT: H 40 ARG cc_start: 0.8447 (ptt180) cc_final: 0.8111 (ptt-90) REVERT: H 49 TRP cc_start: 0.5610 (t60) cc_final: 0.5357 (t60) REVERT: I 56 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8410 (tmm-80) REVERT: I 84 ASP cc_start: 0.6947 (m-30) cc_final: 0.6372 (m-30) REVERT: O 49 MET cc_start: 0.3112 (tpp) cc_final: 0.2378 (ttt) outliers start: 96 outliers final: 74 residues processed: 257 average time/residue: 0.3935 time to fit residues: 170.0987 Evaluate side-chains 240 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 163 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 175 optimal weight: 0.1980 chunk 33 optimal weight: 8.9990 chunk 279 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 913 GLN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29490 Z= 0.198 Angle : 0.549 11.909 40284 Z= 0.285 Chirality : 0.044 0.251 4737 Planarity : 0.004 0.047 5127 Dihedral : 5.057 54.089 4757 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 2.92 % Allowed : 17.21 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.42 (0.14), residues: 3690 helix: 2.13 (0.21), residues: 658 sheet: 0.19 (0.16), residues: 1045 loop : -1.44 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 64 HIS 0.013 0.001 HIS C 519 PHE 0.015 0.001 PHE B 106 TYR 0.035 0.001 TYR B 266 ARG 0.005 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 174 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 GLN cc_start: 0.8170 (mt0) cc_final: 0.7459 (tm-30) REVERT: C 237 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7298 (ptt-90) REVERT: C 355 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7266 (tpp80) REVERT: C 422 ASN cc_start: 0.5522 (OUTLIER) cc_final: 0.4320 (p0) REVERT: C 1002 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7412 (tm-30) REVERT: B 403 ARG cc_start: 0.6815 (ttm-80) cc_final: 0.5673 (ttm-80) REVERT: B 406 GLU cc_start: 0.7589 (tp30) cc_final: 0.7374 (tp30) REVERT: B 455 LEU cc_start: 0.8728 (tp) cc_final: 0.8297 (tt) REVERT: B 493 GLN cc_start: 0.6821 (mp10) cc_final: 0.6223 (mp10) REVERT: B 619 GLU cc_start: 0.8299 (pt0) cc_final: 0.7947 (pt0) REVERT: B 752 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9101 (tt) REVERT: H 40 ARG cc_start: 0.8449 (ptt180) cc_final: 0.8079 (ptt-90) REVERT: I 56 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8436 (tmm-80) REVERT: I 81 GLN cc_start: 0.7937 (pt0) cc_final: 0.7698 (pm20) REVERT: I 84 ASP cc_start: 0.6843 (m-30) cc_final: 0.6167 (m-30) REVERT: O 49 MET cc_start: 0.3057 (tpp) cc_final: 0.2268 (ttt) outliers start: 88 outliers final: 76 residues processed: 251 average time/residue: 0.3755 time to fit residues: 157.7809 Evaluate side-chains 243 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 164 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 9.9990 chunk 340 optimal weight: 0.2980 chunk 310 optimal weight: 5.9990 chunk 331 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 260 optimal weight: 4.9990 chunk 101 optimal weight: 0.0270 chunk 299 optimal weight: 4.9990 chunk 313 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 overall best weight: 2.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 29490 Z= 0.362 Angle : 0.617 12.553 40284 Z= 0.323 Chirality : 0.047 0.267 4737 Planarity : 0.004 0.048 5127 Dihedral : 5.378 55.562 4756 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 3.15 % Allowed : 17.25 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.53 (0.14), residues: 3690 helix: 1.93 (0.21), residues: 655 sheet: 0.11 (0.15), residues: 1057 loop : -1.46 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 64 HIS 0.013 0.001 HIS C 519 PHE 0.018 0.002 PHE C 86 TYR 0.033 0.002 TYR B 266 ARG 0.004 0.000 ARG A1091 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 167 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 GLN cc_start: 0.8175 (mt0) cc_final: 0.7385 (tm-30) REVERT: C 237 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7325 (ptt-90) REVERT: C 355 ARG cc_start: 0.7912 (tpp80) cc_final: 0.7372 (tpp80) REVERT: C 422 ASN cc_start: 0.5342 (OUTLIER) cc_final: 0.4508 (p0) REVERT: C 1002 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 403 ARG cc_start: 0.6929 (ttm-80) cc_final: 0.5759 (ttm-80) REVERT: B 453 TYR cc_start: 0.7752 (p90) cc_final: 0.7174 (p90) REVERT: B 455 LEU cc_start: 0.8738 (tp) cc_final: 0.8251 (tt) REVERT: B 493 GLN cc_start: 0.6849 (mp10) cc_final: 0.6215 (mp10) REVERT: B 619 GLU cc_start: 0.8381 (pt0) cc_final: 0.8028 (pt0) REVERT: B 752 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9128 (tt) REVERT: H 40 ARG cc_start: 0.8453 (ptt180) cc_final: 0.8091 (ptt-90) REVERT: I 56 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8437 (tmm-80) REVERT: I 81 GLN cc_start: 0.7926 (pt0) cc_final: 0.7689 (pm20) REVERT: I 84 ASP cc_start: 0.6826 (m-30) cc_final: 0.6188 (m-30) REVERT: O 49 MET cc_start: 0.2971 (tpp) cc_final: 0.2145 (ttt) outliers start: 95 outliers final: 81 residues processed: 253 average time/residue: 0.3864 time to fit residues: 162.8899 Evaluate side-chains 244 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 160 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 243 optimal weight: 6.9990 chunk 367 optimal weight: 20.0000 chunk 338 optimal weight: 9.9990 chunk 292 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 226 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 913 GLN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1098 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 29490 Z= 0.420 Angle : 0.651 13.422 40284 Z= 0.341 Chirality : 0.048 0.276 4737 Planarity : 0.005 0.051 5127 Dihedral : 5.661 55.413 4756 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 3.05 % Allowed : 17.45 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.68 (0.13), residues: 3690 helix: 1.72 (0.21), residues: 654 sheet: -0.02 (0.15), residues: 1072 loop : -1.51 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 64 HIS 0.013 0.001 HIS C 519 PHE 0.019 0.002 PHE C 86 TYR 0.035 0.002 TYR B 266 ARG 0.004 0.001 ARG A1091 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 163 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 GLN cc_start: 0.8192 (mt0) cc_final: 0.7189 (tm-30) REVERT: C 355 ARG cc_start: 0.7892 (tpp80) cc_final: 0.7351 (tpp80) REVERT: C 422 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4285 (p0) REVERT: C 1002 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 403 ARG cc_start: 0.6978 (ttm-80) cc_final: 0.5803 (ttm-80) REVERT: B 455 LEU cc_start: 0.8740 (tp) cc_final: 0.8264 (tt) REVERT: B 493 GLN cc_start: 0.6881 (mp10) cc_final: 0.6255 (mp10) REVERT: B 619 GLU cc_start: 0.8410 (pt0) cc_final: 0.8067 (pt0) REVERT: B 752 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9130 (tt) REVERT: B 983 ARG cc_start: 0.6873 (mtm110) cc_final: 0.6494 (mtm110) REVERT: H 40 ARG cc_start: 0.8450 (ptt180) cc_final: 0.8122 (ptt-90) REVERT: I 56 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8354 (tmm-80) REVERT: I 81 GLN cc_start: 0.7903 (pt0) cc_final: 0.7667 (pm20) REVERT: I 84 ASP cc_start: 0.6852 (m-30) cc_final: 0.6217 (m-30) REVERT: O 49 MET cc_start: 0.2904 (tpp) cc_final: 0.2067 (ttt) outliers start: 92 outliers final: 87 residues processed: 245 average time/residue: 0.3904 time to fit residues: 159.9840 Evaluate side-chains 247 residues out of total 3267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 157 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 293 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 301 optimal weight: 0.3980 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.161826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098738 restraints weight = 52652.397| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.13 r_work: 0.3314 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29490 Z= 0.185 Angle : 0.568 12.611 40284 Z= 0.296 Chirality : 0.044 0.247 4737 Planarity : 0.004 0.048 5127 Dihedral : 5.343 54.250 4756 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.58 % Rotamer: Outliers : 2.79 % Allowed : 17.74 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.50 (0.14), residues: 3690 helix: 2.06 (0.21), residues: 646 sheet: 0.07 (0.15), residues: 1061 loop : -1.43 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 64 HIS 0.012 0.001 HIS C 519 PHE 0.030 0.001 PHE A 906 TYR 0.023 0.001 TYR B1067 ARG 0.003 0.000 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7451.59 seconds wall clock time: 135 minutes 57.48 seconds (8157.48 seconds total)