Starting phenix.real_space_refine on Tue Feb 20 21:48:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fem_31557/02_2024/7fem_31557.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fem_31557/02_2024/7fem_31557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fem_31557/02_2024/7fem_31557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fem_31557/02_2024/7fem_31557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fem_31557/02_2024/7fem_31557.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fem_31557/02_2024/7fem_31557.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.053 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 133 5.16 5 C 18471 2.51 5 N 4731 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28977 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7782 Classifications: {'peptide': 997} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7814 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 50, 'TRANS': 950} Chain breaks: 7 Chain: "C" Number of atoms: 7831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7831 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 50, 'TRANS': 952} Chain breaks: 7 Chain: "D" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4724 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 23, 'TRANS': 554} Chain breaks: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.05, per 1000 atoms: 0.52 Number of scatterers: 28977 At special positions: 0 Unit cell: (148.24, 130.56, 238, 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 133 16.00 O 5642 8.00 N 4731 7.00 C 18471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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 B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 122 " " NAG B1311 " - " ASN B1098 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C1134 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 709 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 709 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG V 1 " - " ASN A 709 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.60 Conformation dependent library (CDL) restraints added in 5.2 seconds 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6712 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 43 sheets defined 30.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.111A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 762 through 783 removed outlier: 3.666A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.769A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.896A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 932 removed outlier: 6.574A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 removed outlier: 4.229A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.620A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.545A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1035 removed outlier: 5.081A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.924A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.741A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.905A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 738 through 744 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.569A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.579A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 898 through 907 Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.006A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.892A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.167A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 1033 removed outlier: 5.169A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.299A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.588A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.506A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.878A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.677A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.072A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.745A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.730A pdb=" N ALA C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.951A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C1015 " --> pdb=" O GLN C1011 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.027A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 92 through 101 removed outlier: 5.154A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 129 removed outlier: 3.914A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 4.296A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 173 removed outlier: 3.590A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 4.844A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 removed outlier: 3.699A pdb=" N GLY D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 226 through 248 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.857A pdb=" N LEU D 281 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 282 " --> pdb=" O TYR D 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 282' Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 307 through 319 Processing helix chain 'D' and resid 325 through 329 Processing helix chain 'D' and resid 365 through 386 removed outlier: 3.691A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.593A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 433 through 442 removed outlier: 3.690A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 removed outlier: 4.334A pdb=" N THR D 453 " --> pdb=" O THR D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 485 removed outlier: 3.812A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.175A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 4.244A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.769A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 587 removed outlier: 4.018A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 597 removed outlier: 3.671A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.559A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 94 removed outlier: 4.033A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.922A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.795A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.235A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.235A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (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 539 through 540 Processing sheet with id=AB1, first strand: chain 'A' and resid 673 through 675 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.640A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.539A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.562A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.895A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AC1, first strand: chain 'B' and resid 169 through 171 removed outlier: 3.926A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 318 removed outlier: 7.237A pdb=" N VAL B 597 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN B 317 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 595 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.948A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 355 through 357 removed outlier: 4.456A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 554 removed outlier: 6.481A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.643A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.208A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD2, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.590A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.841A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.293A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.188A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.661A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE1, first strand: chain 'C' and resid 664 through 667 removed outlier: 5.798A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.765A pdb=" N GLN C1071 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.765A pdb=" N GLN C1071 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.819A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AE7, first strand: chain 'D' and resid 349 through 352 removed outlier: 5.654A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.95 Time building geometry restraints manager: 13.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.54: 29146 1.54 - 1.87: 486 1.87 - 2.20: 2 2.20 - 2.53: 0 2.53 - 2.86: 1 Bond restraints: 29635 Sorted by residual: bond pdb=" CB ASN D 437 " pdb=" CG ASN D 437 " ideal model delta sigma weight residual 1.516 2.858 -1.342 2.50e-02 1.60e+03 2.88e+03 bond pdb=" CD1 TYR D 279 " pdb=" CE1 TYR D 279 " ideal model delta sigma weight residual 1.382 2.131 -0.749 3.00e-02 1.11e+03 6.23e+02 bond pdb=" CD2 TYR D 279 " pdb=" CE2 TYR D 279 " ideal model delta sigma weight residual 1.382 2.084 -0.702 3.00e-02 1.11e+03 5.48e+02 bond pdb=" CE2 TYR D 279 " pdb=" CZ TYR D 279 " ideal model delta sigma weight residual 1.378 1.805 -0.427 2.40e-02 1.74e+03 3.16e+02 bond pdb=" CE1 TYR D 279 " pdb=" CZ TYR D 279 " ideal model delta sigma weight residual 1.378 1.781 -0.403 2.40e-02 1.74e+03 2.83e+02 ... (remaining 29630 not shown) Histogram of bond angle deviations from ideal: 96.77 - 104.26: 457 104.26 - 111.75: 13738 111.75 - 119.25: 10522 119.25 - 126.74: 15269 126.74 - 134.23: 319 Bond angle restraints: 40305 Sorted by residual: angle pdb=" CA ASN D 437 " pdb=" CB ASN D 437 " pdb=" CG ASN D 437 " ideal model delta sigma weight residual 112.60 123.38 -10.78 1.00e+00 1.00e+00 1.16e+02 angle pdb=" OD1 ASN D 437 " pdb=" CG ASN D 437 " pdb=" ND2 ASN D 437 " ideal model delta sigma weight residual 122.60 115.03 7.57 1.00e+00 1.00e+00 5.73e+01 angle pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 120.49 110.48 10.01 1.38e+00 5.25e-01 5.26e+01 angle pdb=" N ILE A 896 " pdb=" CA ILE A 896 " pdb=" C ILE A 896 " ideal model delta sigma weight residual 109.19 103.80 5.39 8.20e-01 1.49e+00 4.33e+01 angle pdb=" C TRP D 477 " pdb=" N TRP D 478 " pdb=" CA TRP D 478 " ideal model delta sigma weight residual 121.90 114.21 7.69 1.26e+00 6.30e-01 3.72e+01 ... (remaining 40300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.28: 17124 22.28 - 44.56: 1015 44.56 - 66.84: 202 66.84 - 89.12: 36 89.12 - 111.40: 12 Dihedral angle restraints: 18389 sinusoidal: 7966 harmonic: 10423 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.73 83.27 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 12.25 80.75 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 172.74 -79.74 1 1.00e+01 1.00e-02 7.89e+01 ... (remaining 18386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4494 0.118 - 0.236: 194 0.236 - 0.354: 8 0.354 - 0.472: 5 0.472 - 0.590: 4 Chirality restraints: 4705 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" CB THR D 445 " pdb=" CA THR D 445 " pdb=" OG1 THR D 445 " pdb=" CG2 THR D 445 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.39e+00 ... (remaining 4702 not shown) Planarity restraints: 5175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 461 " -0.033 2.00e-02 2.50e+03 3.53e-02 3.11e+01 pdb=" CG TRP D 461 " 0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP D 461 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP D 461 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 461 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 461 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 461 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 461 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 279 " -0.039 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" CG TYR D 279 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR D 279 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 279 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR D 279 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR D 279 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR D 279 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR D 279 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 441 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C LYS D 441 " -0.069 2.00e-02 2.50e+03 pdb=" O LYS D 441 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN D 442 " 0.023 2.00e-02 2.50e+03 ... (remaining 5172 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 480 2.59 - 3.16: 26579 3.16 - 3.74: 42400 3.74 - 4.32: 59171 4.32 - 4.90: 93280 Nonbonded interactions: 221910 Sorted by model distance: nonbonded pdb=" OG SER C 813 " pdb=" OE1 GLU C 868 " model vdw 2.008 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" NZ LYS B 195 " model vdw 2.091 2.520 nonbonded pdb=" OG SER B 375 " pdb=" O ALA B 435 " model vdw 2.093 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE2 GLU C 191 " model vdw 2.093 2.440 nonbonded pdb=" ND2 ASN B 394 " pdb=" OH TYR C 200 " model vdw 2.113 2.520 ... (remaining 221905 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' selection = (chain 'B' and (resid 27 through 68 or resid 81 through 165 or (resid 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 243 or r \ esid 264 through 1147 or resid 1301 through 1307)) selection = (chain 'C' and (resid 27 through 68 or resid 81 through 165 or (resid 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 172 or r \ esid 187 through 243 or resid 264 through 621 or resid 641 through 1147 or resid \ 1301 through 1307)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 0.040 Extract box with map and model: 11.560 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 77.890 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.342 29635 Z= 0.842 Angle : 1.086 11.371 40305 Z= 0.627 Chirality : 0.061 0.590 4705 Planarity : 0.007 0.097 5132 Dihedral : 14.634 111.401 11554 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.01 % Favored : 88.84 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.12), residues: 3523 helix: -1.95 (0.14), residues: 983 sheet: -2.01 (0.20), residues: 573 loop : -3.18 (0.12), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.004 TRP D 461 HIS 0.012 0.002 HIS A1083 PHE 0.035 0.003 PHE C 888 TYR 0.046 0.002 TYR D 279 ARG 0.011 0.001 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8596 (ptt-90) cc_final: 0.8093 (ttp80) REVERT: A 776 LYS cc_start: 0.8610 (tttt) cc_final: 0.8345 (tppp) REVERT: B 118 LEU cc_start: 0.9335 (tp) cc_final: 0.8532 (pp) REVERT: B 740 MET cc_start: 0.8412 (mmt) cc_final: 0.8171 (tpp) REVERT: B 763 LEU cc_start: 0.9509 (mt) cc_final: 0.9292 (mp) REVERT: B 1030 SER cc_start: 0.9200 (p) cc_final: 0.8448 (p) REVERT: D 366 MET cc_start: 0.9224 (mpp) cc_final: 0.8843 (mmt) REVERT: D 376 MET cc_start: 0.7000 (mtm) cc_final: 0.6696 (ttm) REVERT: D 557 MET cc_start: 0.8383 (tmm) cc_final: 0.7849 (mmt) REVERT: D 611 SER cc_start: 0.8817 (p) cc_final: 0.7234 (t) REVERT: D 613 TYR cc_start: 0.2994 (p90) cc_final: 0.2726 (t80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.4166 time to fit residues: 115.2267 Evaluate side-chains 89 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 279 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 169 optimal weight: 0.0980 chunk 207 optimal weight: 5.9990 chunk 323 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 928 ASN B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C1005 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.339 29635 Z= 0.691 Angle : 0.733 11.301 40305 Z= 0.387 Chirality : 0.049 0.448 4705 Planarity : 0.005 0.070 5132 Dihedral : 10.435 105.614 5064 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.83 % Favored : 92.05 % Rotamer: Outliers : 0.19 % Allowed : 5.69 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.99 (0.13), residues: 3523 helix: -0.92 (0.16), residues: 1001 sheet: -1.57 (0.20), residues: 580 loop : -2.81 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 461 HIS 0.006 0.001 HIS A1083 PHE 0.036 0.002 PHE D 315 TYR 0.032 0.002 TYR D 279 ARG 0.007 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8454 (ptt-90) cc_final: 0.8099 (ttp80) REVERT: A 1050 MET cc_start: 0.7618 (ptp) cc_final: 0.7385 (ptp) REVERT: B 118 LEU cc_start: 0.9432 (tp) cc_final: 0.8719 (pp) REVERT: B 731 MET cc_start: 0.8932 (ptp) cc_final: 0.8709 (ptm) REVERT: B 763 LEU cc_start: 0.9470 (mt) cc_final: 0.9231 (mp) REVERT: C 223 LEU cc_start: 0.7798 (mp) cc_final: 0.7451 (mt) REVERT: C 900 MET cc_start: 0.8322 (mmt) cc_final: 0.7962 (mmt) REVERT: C 1029 MET cc_start: 0.8701 (tpp) cc_final: 0.7990 (tpp) REVERT: D 323 MET cc_start: 0.6027 (tpt) cc_final: 0.5771 (tpp) REVERT: D 360 MET cc_start: 0.7390 (mmm) cc_final: 0.6343 (mmt) REVERT: D 366 MET cc_start: 0.9073 (mpp) cc_final: 0.8842 (mmt) REVERT: D 557 MET cc_start: 0.8411 (tmm) cc_final: 0.7868 (mmt) REVERT: D 611 SER cc_start: 0.8914 (p) cc_final: 0.7568 (t) REVERT: D 613 TYR cc_start: 0.3326 (p90) cc_final: 0.2984 (t80) outliers start: 6 outliers final: 3 residues processed: 132 average time/residue: 0.3896 time to fit residues: 87.4175 Evaluate side-chains 92 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 323 optimal weight: 7.9990 chunk 349 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 321 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 437 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 96 GLN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.334 29635 Z= 0.718 Angle : 0.725 10.379 40305 Z= 0.380 Chirality : 0.048 0.443 4705 Planarity : 0.005 0.069 5132 Dihedral : 9.525 104.982 5064 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.60 % Favored : 91.29 % Rotamer: Outliers : 0.13 % Allowed : 5.05 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.13), residues: 3523 helix: -0.65 (0.16), residues: 1011 sheet: -1.49 (0.20), residues: 601 loop : -2.63 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 461 HIS 0.008 0.001 HIS D 345 PHE 0.028 0.002 PHE B 906 TYR 0.025 0.002 TYR D 279 ARG 0.012 0.001 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.7831 (m-80) cc_final: 0.7553 (m-80) REVERT: A 1050 MET cc_start: 0.7493 (ptp) cc_final: 0.6869 (ptp) REVERT: B 731 MET cc_start: 0.9039 (ptp) cc_final: 0.8788 (ptm) REVERT: B 763 LEU cc_start: 0.9428 (mt) cc_final: 0.9185 (mp) REVERT: C 900 MET cc_start: 0.8473 (mmt) cc_final: 0.8107 (mmt) REVERT: D 323 MET cc_start: 0.6045 (tpt) cc_final: 0.5722 (tpp) REVERT: D 366 MET cc_start: 0.9063 (mpp) cc_final: 0.8834 (mmt) REVERT: D 376 MET cc_start: 0.5788 (ptp) cc_final: 0.5548 (ptp) REVERT: D 474 MET cc_start: 0.6906 (tmm) cc_final: 0.6298 (tmm) REVERT: D 478 TRP cc_start: 0.4627 (OUTLIER) cc_final: 0.3414 (m100) REVERT: D 557 MET cc_start: 0.8203 (tmm) cc_final: 0.7894 (mmt) outliers start: 4 outliers final: 2 residues processed: 113 average time/residue: 0.3935 time to fit residues: 76.6100 Evaluate side-chains 86 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 217 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 308 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 52 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 442 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.333 29635 Z= 0.700 Angle : 0.681 10.489 40305 Z= 0.358 Chirality : 0.048 0.452 4705 Planarity : 0.005 0.070 5132 Dihedral : 8.935 103.570 5064 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.66 % Favored : 92.19 % Rotamer: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.13), residues: 3523 helix: -0.37 (0.16), residues: 1007 sheet: -1.18 (0.20), residues: 596 loop : -2.47 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 478 HIS 0.010 0.001 HIS D 493 PHE 0.016 0.002 PHE A 275 TYR 0.022 0.001 TYR D 279 ARG 0.007 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 3.373 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.8730 (mmm) cc_final: 0.8494 (tpp) REVERT: A 1050 MET cc_start: 0.7723 (ptp) cc_final: 0.7438 (ptp) REVERT: B 731 MET cc_start: 0.9081 (ptp) cc_final: 0.8811 (ptm) REVERT: B 763 LEU cc_start: 0.9401 (mt) cc_final: 0.9169 (mp) REVERT: D 297 MET cc_start: 0.6207 (mtt) cc_final: 0.5999 (mtp) REVERT: D 366 MET cc_start: 0.9088 (mpp) cc_final: 0.8861 (mmt) REVERT: D 376 MET cc_start: 0.5858 (ptp) cc_final: 0.5604 (ptp) REVERT: D 557 MET cc_start: 0.8323 (tmm) cc_final: 0.7938 (mmt) outliers start: 2 outliers final: 0 residues processed: 109 average time/residue: 0.3773 time to fit residues: 71.4209 Evaluate side-chains 76 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 293 optimal weight: 0.0010 chunk 237 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 308 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 388 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.319 29635 Z= 0.738 Angle : 0.719 10.115 40305 Z= 0.377 Chirality : 0.048 0.454 4705 Planarity : 0.005 0.068 5132 Dihedral : 8.592 102.727 5064 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.57 % Favored : 91.31 % Rotamer: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % 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: -2.31 (0.14), residues: 3523 helix: -0.31 (0.16), residues: 1004 sheet: -1.18 (0.20), residues: 604 loop : -2.42 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 275 HIS 0.005 0.001 HIS A1083 PHE 0.029 0.002 PHE A 823 TYR 0.034 0.002 TYR D 279 ARG 0.007 0.001 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 731 MET cc_start: 0.9166 (ptp) cc_final: 0.8924 (ptm) REVERT: B 740 MET cc_start: 0.7551 (tpp) cc_final: 0.7344 (tpp) REVERT: B 763 LEU cc_start: 0.9418 (mt) cc_final: 0.9185 (mp) REVERT: C 900 MET cc_start: 0.8695 (mmp) cc_final: 0.8294 (mmm) REVERT: D 495 GLU cc_start: 0.9014 (pt0) cc_final: 0.8746 (pm20) REVERT: D 557 MET cc_start: 0.8275 (tmm) cc_final: 0.7910 (mmt) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.4171 time to fit residues: 74.7354 Evaluate side-chains 76 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 344 optimal weight: 10.0000 chunk 285 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1101 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 658 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.331 29635 Z= 0.694 Angle : 0.660 10.722 40305 Z= 0.345 Chirality : 0.047 0.462 4705 Planarity : 0.005 0.074 5132 Dihedral : 8.174 101.168 5064 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.95 % Favored : 92.96 % Rotamer: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % 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: -2.07 (0.14), residues: 3523 helix: -0.06 (0.17), residues: 999 sheet: -1.01 (0.21), residues: 601 loop : -2.30 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 275 HIS 0.005 0.001 HIS A1083 PHE 0.018 0.001 PHE A 823 TYR 0.030 0.001 TYR D 279 ARG 0.006 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 3.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 731 MET cc_start: 0.9079 (ptp) cc_final: 0.8850 (ptm) REVERT: B 763 LEU cc_start: 0.9410 (mt) cc_final: 0.9151 (mp) REVERT: C 515 PHE cc_start: 0.7533 (m-10) cc_final: 0.7291 (m-10) REVERT: C 900 MET cc_start: 0.8715 (mmp) cc_final: 0.8342 (mmt) REVERT: D 62 MET cc_start: 0.8818 (ptp) cc_final: 0.8596 (ptp) REVERT: D 360 MET cc_start: 0.6815 (mmm) cc_final: 0.6605 (mmm) REVERT: D 376 MET cc_start: 0.5085 (ptp) cc_final: 0.4835 (ptp) REVERT: D 495 GLU cc_start: 0.8838 (pt0) cc_final: 0.8580 (pm20) REVERT: D 557 MET cc_start: 0.8307 (tmm) cc_final: 0.7997 (mmt) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.3927 time to fit residues: 75.1546 Evaluate side-chains 77 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 289 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 343 optimal weight: 0.6980 chunk 214 optimal weight: 0.7980 chunk 209 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN B 658 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.334 29635 Z= 0.677 Angle : 0.631 10.581 40305 Z= 0.330 Chirality : 0.047 0.455 4705 Planarity : 0.004 0.074 5132 Dihedral : 7.763 100.019 5064 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.78 % Favored : 93.13 % Rotamer: Outliers : 0.03 % Allowed : 1.34 % Favored : 98.63 % Cbeta Deviations : 0.00 % 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: -1.84 (0.14), residues: 3523 helix: 0.17 (0.17), residues: 997 sheet: -0.92 (0.20), residues: 623 loop : -2.17 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 478 HIS 0.005 0.001 HIS A1083 PHE 0.017 0.001 PHE C 490 TYR 0.031 0.001 TYR D 279 ARG 0.005 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 3.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 658 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7799 (p0) REVERT: C 900 MET cc_start: 0.8735 (mmp) cc_final: 0.8246 (mmt) REVERT: D 249 MET cc_start: 0.7941 (mmp) cc_final: 0.7728 (mmm) REVERT: D 323 MET cc_start: 0.6513 (tpt) cc_final: 0.6153 (tpp) REVERT: D 376 MET cc_start: 0.5029 (ptp) cc_final: 0.4736 (ptp) REVERT: D 495 GLU cc_start: 0.8395 (pt0) cc_final: 0.8187 (pm20) REVERT: D 557 MET cc_start: 0.8290 (tmm) cc_final: 0.8071 (mmt) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.4118 time to fit residues: 76.7112 Evaluate side-chains 74 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 218 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 169 optimal weight: 0.0970 chunk 31 optimal weight: 10.0000 chunk 269 optimal weight: 2.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 606 ASN B 658 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.333 29635 Z= 0.694 Angle : 0.649 10.566 40305 Z= 0.337 Chirality : 0.046 0.461 4705 Planarity : 0.004 0.072 5132 Dihedral : 7.637 99.636 5064 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.82 % Rotamer: Outliers : 0.03 % Allowed : 1.05 % Favored : 98.91 % 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: -1.77 (0.14), residues: 3523 helix: 0.22 (0.17), residues: 995 sheet: -0.80 (0.21), residues: 607 loop : -2.14 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 478 HIS 0.009 0.001 HIS C 655 PHE 0.023 0.001 PHE C 490 TYR 0.029 0.001 TYR D 279 ARG 0.006 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.7437 (t80) cc_final: 0.6730 (t80) REVERT: C 900 MET cc_start: 0.8624 (mmp) cc_final: 0.8139 (mmt) REVERT: D 376 MET cc_start: 0.5038 (ptp) cc_final: 0.4748 (ptp) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.3637 time to fit residues: 63.0770 Evaluate side-chains 72 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 9.9990 chunk 328 optimal weight: 20.0000 chunk 299 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 288 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 chunk 318 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 710 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.334 29635 Z= 0.734 Angle : 0.712 10.589 40305 Z= 0.369 Chirality : 0.048 0.473 4705 Planarity : 0.005 0.071 5132 Dihedral : 7.737 99.885 5064 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.43 % Favored : 91.46 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.52 % Cbeta Deviations : 0.00 % 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: -1.91 (0.14), residues: 3523 helix: 0.12 (0.17), residues: 984 sheet: -0.97 (0.20), residues: 636 loop : -2.21 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 478 HIS 0.011 0.001 HIS D 493 PHE 0.028 0.002 PHE B 906 TYR 0.028 0.002 TYR D 279 ARG 0.006 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 392 PHE cc_start: 0.8241 (m-80) cc_final: 0.7824 (m-10) REVERT: C 168 PHE cc_start: 0.7501 (t80) cc_final: 0.6705 (t80) REVERT: C 900 MET cc_start: 0.8570 (mmp) cc_final: 0.8026 (mmt) REVERT: C 1029 MET cc_start: 0.8671 (tpp) cc_final: 0.8171 (tpp) REVERT: D 323 MET cc_start: 0.6399 (tpt) cc_final: 0.6191 (tpp) REVERT: D 360 MET cc_start: 0.6907 (mmm) cc_final: 0.6495 (mmm) outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.3941 time to fit residues: 67.7847 Evaluate side-chains 75 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 3.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.3980 chunk 338 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 354 optimal weight: 8.9990 chunk 326 optimal weight: 8.9990 chunk 282 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.333 29635 Z= 0.777 Angle : 0.791 10.573 40305 Z= 0.408 Chirality : 0.049 0.498 4705 Planarity : 0.005 0.071 5132 Dihedral : 8.080 99.339 5064 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.14 % Favored : 90.75 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % 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: -2.20 (0.14), residues: 3523 helix: -0.21 (0.16), residues: 993 sheet: -1.18 (0.20), residues: 634 loop : -2.33 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 473 HIS 0.008 0.002 HIS D 374 PHE 0.036 0.002 PHE B 906 TYR 0.033 0.002 TYR A 873 ARG 0.008 0.001 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 392 PHE cc_start: 0.8411 (m-80) cc_final: 0.7931 (m-10) REVERT: B 607 GLN cc_start: 0.8069 (mt0) cc_final: 0.7764 (mt0) REVERT: C 168 PHE cc_start: 0.7523 (t80) cc_final: 0.7156 (t80) REVERT: C 900 MET cc_start: 0.8509 (mmp) cc_final: 0.8277 (mmt) REVERT: D 62 MET cc_start: 0.8942 (ptp) cc_final: 0.8725 (ptp) REVERT: D 323 MET cc_start: 0.6631 (tpt) cc_final: 0.6056 (tpp) REVERT: D 360 MET cc_start: 0.6744 (mmm) cc_final: 0.6527 (mmm) REVERT: D 582 ARG cc_start: 0.9200 (tpm170) cc_final: 0.8560 (ptt90) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.3903 time to fit residues: 61.2316 Evaluate side-chains 72 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 7.9990 chunk 300 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 260 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 0.3980 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 913 GLN B 658 ASN B 965 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.081968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054579 restraints weight = 158834.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055693 restraints weight = 88740.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.056476 restraints weight = 60894.701| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.333 29635 Z= 0.680 Angle : 0.647 10.555 40305 Z= 0.337 Chirality : 0.047 0.485 4705 Planarity : 0.004 0.073 5132 Dihedral : 7.578 98.327 5064 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 0.03 % Allowed : 0.42 % Favored : 99.55 % 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: -1.80 (0.14), residues: 3523 helix: 0.32 (0.17), residues: 981 sheet: -1.00 (0.20), residues: 625 loop : -2.16 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 478 HIS 0.007 0.001 HIS D 378 PHE 0.021 0.001 PHE A 906 TYR 0.028 0.001 TYR D 279 ARG 0.012 0.001 ARG D 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4215.40 seconds wall clock time: 80 minutes 6.39 seconds (4806.39 seconds total)