Starting phenix.real_space_refine on Fri Apr 12 03:23:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si7_40501/04_2024/8si7_40501_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si7_40501/04_2024/8si7_40501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si7_40501/04_2024/8si7_40501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si7_40501/04_2024/8si7_40501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si7_40501/04_2024/8si7_40501_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si7_40501/04_2024/8si7_40501_neut_trim_updated.pdb" } resolution = 2.59 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= 0.008 sd= 0.051 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: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 P 48 5.49 5 S 240 5.16 5 Cl 8 4.86 5 C 25548 2.51 5 N 6032 2.21 5 O 6884 1.98 5 H 36136 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 74897 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 17962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17962 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "B" Number of atoms: 17962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17962 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "C" Number of atoms: 17962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17962 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "D" Number of atoms: 17962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17962 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "A" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 776 Unusual residues: {' CA': 1, '3FD': 1, 'CLR': 1, 'DU0': 1, 'POV': 14} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 723 Unusual residues: {'3FD': 1, 'CLR': 1, 'DU0': 1, 'POV': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 760 Unusual residues: {'3FD': 1, 'CLR': 1, 'DU0': 2, 'POV': 13} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 634 Unusual residues: {'3FD': 1, 'CLR': 1, 'POV': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Time building chain proxies: 23.82, per 1000 atoms: 0.32 Number of scatterers: 74897 At special positions: 0 Unit cell: (146.91, 146.91, 156.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 1 19.99 Cl 8 17.00 S 240 16.00 P 48 15.00 O 6884 8.00 N 6032 7.00 C 25548 6.00 H 36136 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.06 Simple disulfide: pdb=" SG CYS A1056 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 44 " distance=2.06 Simple disulfide: pdb=" SG CYS B1056 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 44 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 44 " distance=2.06 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 44 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 44 " distance=2.06 Simple disulfide: pdb=" SG CYS D1056 " - pdb=" SG CYS D1066 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 47.48 Conformation dependent library (CDL) restraints added in 5.2 seconds 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 208 helices and 8 sheets defined 55.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.00 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.622A pdb=" N GLN A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 117 through 124 removed outlier: 3.690A pdb=" N LEU A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.585A pdb=" N GLN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 190 removed outlier: 3.797A pdb=" N VAL A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 392 through 400 removed outlier: 4.082A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 removed outlier: 3.659A pdb=" N LEU A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 471 through 478 removed outlier: 3.714A pdb=" N TYR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.838A pdb=" N HIS A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.617A pdb=" N ASN A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 631 removed outlier: 3.589A pdb=" N LEU A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 648 through 668 Processing helix chain 'A' and resid 676 through 700 removed outlier: 3.597A pdb=" N GLN A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 691 " --> pdb=" O GLY A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 721 through 727 Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.529A pdb=" N ASP A 745 " --> pdb=" O MET A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 766 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 789 through 795 removed outlier: 3.795A pdb=" N THR A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 849 removed outlier: 3.613A pdb=" N TYR A 846 " --> pdb=" O THR A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 875 removed outlier: 3.781A pdb=" N ALA A 862 " --> pdb=" O PHE A 858 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 869 " --> pdb=" O GLY A 865 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 874 " --> pdb=" O TYR A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 905 removed outlier: 3.542A pdb=" N VAL A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 956 through 982 removed outlier: 4.934A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU A 976 " --> pdb=" O TRP A 972 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 977 " --> pdb=" O TYR A 973 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 982 " --> pdb=" O ASP A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 997 Proline residue: A 988 - end of helix removed outlier: 4.159A pdb=" N GLY A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 995 " --> pdb=" O MET A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1022 Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1031 through 1035 Processing helix chain 'A' and resid 1038 through 1045 removed outlier: 3.944A pdb=" N ILE A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1070 through 1085 removed outlier: 3.582A pdb=" N THR A1073 " --> pdb=" O THR A1070 " (cutoff:3.500A) Proline residue: A1074 - end of helix removed outlier: 3.572A pdb=" N GLN A1077 " --> pdb=" O PRO A1074 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A1081 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A1082 " --> pdb=" O VAL A1079 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR A1085 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1097 removed outlier: 3.522A pdb=" N LEU A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1120 removed outlier: 3.949A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1145 Processing helix chain 'A' and resid 1164 through 1190 removed outlier: 3.509A pdb=" N LYS A1168 " --> pdb=" O GLU A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1229 removed outlier: 3.504A pdb=" N ARG A1198 " --> pdb=" O GLU A1194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A1206 " --> pdb=" O GLU A1202 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A1223 " --> pdb=" O ASN A1219 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.621A pdb=" N GLN B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 117 through 124 removed outlier: 3.689A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.585A pdb=" N GLN B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE B 161 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 190 removed outlier: 3.796A pdb=" N VAL B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 294 through 305 Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 392 through 400 removed outlier: 4.082A pdb=" N LEU B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 416 removed outlier: 3.660A pdb=" N LEU B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 452 through 460 Processing helix chain 'B' and resid 471 through 478 removed outlier: 3.714A pdb=" N TYR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.839A pdb=" N HIS B 491 " --> pdb=" O PRO B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 531 through 539 removed outlier: 3.617A pdb=" N ASN B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 631 removed outlier: 3.588A pdb=" N LEU B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 627 " --> pdb=" O ASN B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 648 through 668 Processing helix chain 'B' and resid 676 through 700 removed outlier: 3.597A pdb=" N GLN B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 691 " --> pdb=" O GLY B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 708 Processing helix chain 'B' and resid 721 through 727 Processing helix chain 'B' and resid 731 through 734 No H-bonds generated for 'chain 'B' and resid 731 through 734' Processing helix chain 'B' and resid 739 through 748 removed outlier: 3.530A pdb=" N ASP B 745 " --> pdb=" O MET B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 768 through 773 Processing helix chain 'B' and resid 789 through 795 removed outlier: 3.795A pdb=" N THR B 795 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 849 removed outlier: 3.613A pdb=" N TYR B 846 " --> pdb=" O THR B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 875 removed outlier: 3.782A pdb=" N ALA B 862 " --> pdb=" O PHE B 858 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 869 " --> pdb=" O GLY B 865 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 874 " --> pdb=" O TYR B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 905 removed outlier: 3.541A pdb=" N VAL B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 Processing helix chain 'B' and resid 923 through 943 Processing helix chain 'B' and resid 956 through 982 removed outlier: 4.934A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 976 " --> pdb=" O TRP B 972 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU B 977 " --> pdb=" O TYR B 973 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 982 " --> pdb=" O ASP B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 997 Proline residue: B 988 - end of helix removed outlier: 4.160A pdb=" N GLY B 994 " --> pdb=" O VAL B 990 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 995 " --> pdb=" O MET B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1022 Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1031 through 1035 Processing helix chain 'B' and resid 1038 through 1045 removed outlier: 3.944A pdb=" N ILE B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE B1045 " --> pdb=" O TYR B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1065 No H-bonds generated for 'chain 'B' and resid 1063 through 1065' Processing helix chain 'B' and resid 1070 through 1085 removed outlier: 3.583A pdb=" N THR B1073 " --> pdb=" O THR B1070 " (cutoff:3.500A) Proline residue: B1074 - end of helix removed outlier: 3.573A pdb=" N GLN B1077 " --> pdb=" O PRO B1074 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B1081 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B1082 " --> pdb=" O VAL B1079 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B1085 " --> pdb=" O PHE B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1097 removed outlier: 3.521A pdb=" N LEU B1092 " --> pdb=" O MET B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1120 removed outlier: 3.950A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1145 Processing helix chain 'B' and resid 1164 through 1190 removed outlier: 3.508A pdb=" N LYS B1168 " --> pdb=" O GLU B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1193 through 1229 removed outlier: 3.505A pdb=" N ARG B1198 " --> pdb=" O GLU B1194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B1206 " --> pdb=" O GLU B1202 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B1219 " --> pdb=" O GLY B1215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B1223 " --> pdb=" O ASN B1219 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER B1224 " --> pdb=" O TYR B1220 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.622A pdb=" N GLN C 37 " --> pdb=" O CYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 51 No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 117 through 124 removed outlier: 3.689A pdb=" N LEU C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.585A pdb=" N GLN C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 190 removed outlier: 3.796A pdb=" N VAL C 184 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' Processing helix chain 'C' and resid 260 through 271 Processing helix chain 'C' and resid 294 through 305 Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'C' and resid 360 through 373 Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 392 through 400 removed outlier: 4.082A pdb=" N LEU C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 416 removed outlier: 3.659A pdb=" N LEU C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 452 through 460 Processing helix chain 'C' and resid 471 through 478 removed outlier: 3.714A pdb=" N TYR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.839A pdb=" N HIS C 491 " --> pdb=" O PRO C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 531 through 539 removed outlier: 3.617A pdb=" N ASN C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 631 removed outlier: 3.588A pdb=" N LEU C 626 " --> pdb=" O LEU C 622 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE C 627 " --> pdb=" O ASN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 648 through 668 Processing helix chain 'C' and resid 676 through 700 removed outlier: 3.597A pdb=" N GLN C 681 " --> pdb=" O GLU C 677 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 691 " --> pdb=" O GLY C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 708 Processing helix chain 'C' and resid 721 through 727 Processing helix chain 'C' and resid 731 through 734 No H-bonds generated for 'chain 'C' and resid 731 through 734' Processing helix chain 'C' and resid 739 through 748 removed outlier: 3.530A pdb=" N ASP C 745 " --> pdb=" O MET C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 766 Processing helix chain 'C' and resid 768 through 773 Processing helix chain 'C' and resid 789 through 795 removed outlier: 3.794A pdb=" N THR C 795 " --> pdb=" O ALA C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 849 removed outlier: 3.614A pdb=" N TYR C 846 " --> pdb=" O THR C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 875 removed outlier: 3.781A pdb=" N ALA C 862 " --> pdb=" O PHE C 858 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 869 " --> pdb=" O GLY C 865 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 874 " --> pdb=" O TYR C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 905 removed outlier: 3.542A pdb=" N VAL C 889 " --> pdb=" O GLN C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 Processing helix chain 'C' and resid 923 through 943 Processing helix chain 'C' and resid 956 through 982 removed outlier: 4.933A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 976 " --> pdb=" O TRP C 972 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C 977 " --> pdb=" O TYR C 973 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL C 982 " --> pdb=" O ASP C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 997 Proline residue: C 988 - end of helix removed outlier: 4.159A pdb=" N GLY C 994 " --> pdb=" O VAL C 990 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 995 " --> pdb=" O MET C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1022 Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1031 through 1035 Processing helix chain 'C' and resid 1038 through 1045 removed outlier: 3.944A pdb=" N ILE C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE C1045 " --> pdb=" O TYR C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1063 through 1065 No H-bonds generated for 'chain 'C' and resid 1063 through 1065' Processing helix chain 'C' and resid 1070 through 1085 removed outlier: 3.583A pdb=" N THR C1073 " --> pdb=" O THR C1070 " (cutoff:3.500A) Proline residue: C1074 - end of helix removed outlier: 3.572A pdb=" N GLN C1077 " --> pdb=" O PRO C1074 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C1081 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C1082 " --> pdb=" O VAL C1079 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR C1085 " --> pdb=" O PHE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1097 removed outlier: 3.521A pdb=" N LEU C1092 " --> pdb=" O MET C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1120 removed outlier: 3.949A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1145 Processing helix chain 'C' and resid 1164 through 1190 removed outlier: 3.509A pdb=" N LYS C1168 " --> pdb=" O GLU C1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 1193 through 1229 removed outlier: 3.505A pdb=" N ARG C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN C1206 " --> pdb=" O GLU C1202 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN C1219 " --> pdb=" O GLY C1215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C1223 " --> pdb=" O ASN C1219 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER C1224 " --> pdb=" O TYR C1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.622A pdb=" N GLN D 37 " --> pdb=" O CYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 51 No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 54 through 60 Processing helix chain 'D' and resid 117 through 124 removed outlier: 3.690A pdb=" N LEU D 121 " --> pdb=" O PRO D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.585A pdb=" N GLN D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 190 removed outlier: 3.797A pdb=" N VAL D 184 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'D' and resid 260 through 271 Processing helix chain 'D' and resid 294 through 305 Processing helix chain 'D' and resid 320 through 330 Processing helix chain 'D' and resid 343 through 353 Processing helix chain 'D' and resid 360 through 373 Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 392 through 400 removed outlier: 4.082A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.660A pdb=" N LEU D 413 " --> pdb=" O ASP D 409 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 Processing helix chain 'D' and resid 438 through 449 Processing helix chain 'D' and resid 452 through 460 Processing helix chain 'D' and resid 471 through 478 removed outlier: 3.714A pdb=" N TYR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 496 removed outlier: 3.840A pdb=" N HIS D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 520 Processing helix chain 'D' and resid 531 through 539 removed outlier: 3.617A pdb=" N ASN D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 631 removed outlier: 3.588A pdb=" N LEU D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE D 627 " --> pdb=" O ASN D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 648 through 668 Processing helix chain 'D' and resid 676 through 700 removed outlier: 3.597A pdb=" N GLN D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 691 " --> pdb=" O GLY D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 708 Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 731 through 734 No H-bonds generated for 'chain 'D' and resid 731 through 734' Processing helix chain 'D' and resid 739 through 748 removed outlier: 3.529A pdb=" N ASP D 745 " --> pdb=" O MET D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 768 through 773 Processing helix chain 'D' and resid 789 through 795 removed outlier: 3.795A pdb=" N THR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 849 removed outlier: 3.613A pdb=" N TYR D 846 " --> pdb=" O THR D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 875 removed outlier: 3.781A pdb=" N ALA D 862 " --> pdb=" O PHE D 858 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 869 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 874 " --> pdb=" O TYR D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 905 removed outlier: 3.542A pdb=" N VAL D 889 " --> pdb=" O GLN D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 919 Processing helix chain 'D' and resid 923 through 943 Processing helix chain 'D' and resid 956 through 982 removed outlier: 4.934A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D 976 " --> pdb=" O TRP D 972 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU D 977 " --> pdb=" O TYR D 973 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP D 978 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL D 982 " --> pdb=" O ASP D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 997 Proline residue: D 988 - end of helix removed outlier: 4.160A pdb=" N GLY D 994 " --> pdb=" O VAL D 990 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS D 995 " --> pdb=" O MET D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1022 Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1031 through 1035 Processing helix chain 'D' and resid 1038 through 1045 removed outlier: 3.944A pdb=" N ILE D1044 " --> pdb=" O PRO D1040 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE D1045 " --> pdb=" O TYR D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1065 No H-bonds generated for 'chain 'D' and resid 1063 through 1065' Processing helix chain 'D' and resid 1070 through 1085 removed outlier: 3.583A pdb=" N THR D1073 " --> pdb=" O THR D1070 " (cutoff:3.500A) Proline residue: D1074 - end of helix removed outlier: 3.572A pdb=" N GLN D1077 " --> pdb=" O PRO D1074 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D1081 " --> pdb=" O ALA D1078 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D1082 " --> pdb=" O VAL D1079 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR D1085 " --> pdb=" O PHE D1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1097 removed outlier: 3.521A pdb=" N LEU D1092 " --> pdb=" O MET D1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1120 removed outlier: 3.950A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 Processing helix chain 'D' and resid 1164 through 1190 removed outlier: 3.509A pdb=" N LYS D1168 " --> pdb=" O GLU D1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 1193 through 1229 removed outlier: 3.505A pdb=" N ARG D1198 " --> pdb=" O GLU D1194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN D1206 " --> pdb=" O GLU D1202 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN D1219 " --> pdb=" O GLY D1215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D1223 " --> pdb=" O ASN D1219 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER D1224 " --> pdb=" O TYR D1220 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 92 through 96 removed outlier: 3.632A pdb=" N GLY A 93 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 110 through 112 removed outlier: 7.979A pdb=" N LEU A 111 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A 247 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 171 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ILE A 289 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL A 313 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 92 through 96 removed outlier: 3.632A pdb=" N GLY B 93 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 110 through 112 removed outlier: 7.979A pdb=" N LEU B 111 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B 247 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 171 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ILE B 289 " --> pdb=" O PRO B 311 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL B 313 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 92 through 96 removed outlier: 3.632A pdb=" N GLY C 93 " --> pdb=" O TYR C 108 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 110 through 112 removed outlier: 7.980A pdb=" N LEU C 111 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU C 247 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 171 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ILE C 289 " --> pdb=" O PRO C 311 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C 313 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 92 through 96 removed outlier: 3.632A pdb=" N GLY D 93 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 110 through 112 removed outlier: 7.980A pdb=" N LEU D 111 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU D 247 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 171 " --> pdb=" O CYS D 200 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ILE D 289 " --> pdb=" O PRO D 311 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL D 313 " --> pdb=" O ILE D 289 " (cutoff:3.500A) 1480 hydrogen bonds defined for protein. 4260 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: 26.63 Time building geometry restraints manager: 50.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.02: 36068 1.02 - 1.23: 316 1.23 - 1.44: 15894 1.44 - 1.65: 22918 1.65 - 1.86: 404 Bond restraints: 75600 Sorted by residual: bond pdb=" C24 3FD D1306 " pdb=" C25 3FD D1306 " ideal model delta sigma weight residual 1.530 1.262 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C24 3FD A1304 " pdb=" C25 3FD A1304 " ideal model delta sigma weight residual 1.530 1.263 0.267 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C24 3FD C1305 " pdb=" C25 3FD C1305 " ideal model delta sigma weight residual 1.530 1.263 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C24 3FD B1305 " pdb=" C25 3FD B1305 " ideal model delta sigma weight residual 1.530 1.263 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C29 POV D1302 " pdb="C210 POV D1302 " ideal model delta sigma weight residual 1.333 1.519 -0.186 2.00e-02 2.50e+03 8.69e+01 ... (remaining 75595 not shown) Histogram of bond angle deviations from ideal: 95.18 - 111.84: 82662 111.84 - 128.50: 52054 128.50 - 145.16: 460 145.16 - 161.82: 0 161.82 - 178.48: 4 Bond angle restraints: 135180 Sorted by residual: angle pdb=" N LEU B 338 " pdb=" CA LEU B 338 " pdb=" C LEU B 338 " ideal model delta sigma weight residual 110.10 102.31 7.79 1.53e+00 4.27e-01 2.59e+01 angle pdb=" N LEU C 338 " pdb=" CA LEU C 338 " pdb=" C LEU C 338 " ideal model delta sigma weight residual 110.10 102.35 7.75 1.53e+00 4.27e-01 2.57e+01 angle pdb=" N LEU D 338 " pdb=" CA LEU D 338 " pdb=" C LEU D 338 " ideal model delta sigma weight residual 110.10 102.36 7.74 1.53e+00 4.27e-01 2.56e+01 angle pdb=" N LEU A 338 " pdb=" CA LEU A 338 " pdb=" C LEU A 338 " ideal model delta sigma weight residual 110.10 102.37 7.73 1.53e+00 4.27e-01 2.55e+01 angle pdb=" C28 POV A1315 " pdb=" C29 POV A1315 " pdb="C210 POV A1315 " ideal model delta sigma weight residual 127.79 113.87 13.92 3.00e+00 1.11e-01 2.15e+01 ... (remaining 135175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 35534 35.45 - 70.90: 1112 70.90 - 106.36: 130 106.36 - 141.81: 60 141.81 - 177.26: 32 Dihedral angle restraints: 36868 sinusoidal: 21160 harmonic: 15708 Sorted by residual: dihedral pdb=" CA ALA D 52 " pdb=" C ALA D 52 " pdb=" N CYS D 53 " pdb=" CA CYS D 53 " ideal model delta harmonic sigma weight residual 180.00 130.39 49.61 0 5.00e+00 4.00e-02 9.84e+01 dihedral pdb=" CA ALA B 52 " pdb=" C ALA B 52 " pdb=" N CYS B 53 " pdb=" CA CYS B 53 " ideal model delta harmonic sigma weight residual 180.00 130.39 49.61 0 5.00e+00 4.00e-02 9.84e+01 dihedral pdb=" CA ALA C 52 " pdb=" C ALA C 52 " pdb=" N CYS C 53 " pdb=" CA CYS C 53 " ideal model delta harmonic sigma weight residual 180.00 130.42 49.58 0 5.00e+00 4.00e-02 9.83e+01 ... (remaining 36865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4090 0.062 - 0.124: 1311 0.124 - 0.186: 242 0.186 - 0.247: 25 0.247 - 0.309: 16 Chirality restraints: 5684 Sorted by residual: chirality pdb=" C25 3FD C1305 " pdb=" C23 3FD C1305 " pdb=" C24 3FD C1305 " pdb=" O27 3FD C1305 " both_signs ideal model delta sigma weight residual False 2.71 2.40 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C25 3FD D1306 " pdb=" C23 3FD D1306 " pdb=" C24 3FD D1306 " pdb=" O27 3FD D1306 " both_signs ideal model delta sigma weight residual False 2.71 2.40 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C25 3FD B1305 " pdb=" C23 3FD B1305 " pdb=" C24 3FD B1305 " pdb=" O27 3FD B1305 " both_signs ideal model delta sigma weight residual False 2.71 2.40 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 5681 not shown) Planarity restraints: 10580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1097 " -0.215 2.00e-02 2.50e+03 2.49e-01 9.27e+02 pdb=" CG ASN C1097 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN C1097 " 0.207 2.00e-02 2.50e+03 pdb=" ND2 ASN C1097 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN C1097 " 0.365 2.00e-02 2.50e+03 pdb="HD22 ASN C1097 " -0.384 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D1097 " 0.215 2.00e-02 2.50e+03 2.48e-01 9.20e+02 pdb=" CG ASN D1097 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN D1097 " -0.206 2.00e-02 2.50e+03 pdb=" ND2 ASN D1097 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASN D1097 " -0.364 2.00e-02 2.50e+03 pdb="HD22 ASN D1097 " 0.382 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1097 " -0.214 2.00e-02 2.50e+03 2.47e-01 9.15e+02 pdb=" CG ASN B1097 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B1097 " 0.205 2.00e-02 2.50e+03 pdb=" ND2 ASN B1097 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN B1097 " 0.363 2.00e-02 2.50e+03 pdb="HD22 ASN B1097 " -0.381 2.00e-02 2.50e+03 ... (remaining 10577 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 4206 2.20 - 2.80: 155630 2.80 - 3.40: 199351 3.40 - 4.00: 275258 4.00 - 4.60: 430203 Nonbonded interactions: 1064648 Sorted by model distance: nonbonded pdb="HH12 ARG D 962 " pdb=" O HOH D1401 " model vdw 1.597 1.850 nonbonded pdb="HH12 ARG B 962 " pdb=" O HOH B1401 " model vdw 1.597 1.850 nonbonded pdb="HH12 ARG A 962 " pdb=" O HOH A1401 " model vdw 1.597 1.850 nonbonded pdb="HH12 ARG C 962 " pdb=" O HOH C1401 " model vdw 1.598 1.850 nonbonded pdb=" O ILE A 20 " pdb=" H PHE A 43 " model vdw 1.609 1.850 ... (remaining 1064643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 1230 or resid 1301 or (resid 1302 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name \ C29 or name C210 or name C211 or name C212 or name C213 or name C214 or name C21 \ 5 or name C216)) or resid 1303 or resid 1308 through 1311 or (resid 1312 and (na \ me N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ ame C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 o \ r name C27 or name C28 or name C29 or name O11 or name O12 or name O13 or name O \ 14 or name O21 or name O22 or name P or name C210 or name C211 or name C212 or n \ ame C213 or name C214 or name C215 or name C216 or name C217 or name C218)))) selection = (chain 'B' and (resid 3 through 1230 or resid 1301 or (resid 1302 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name \ C29 or name C210 or name C211 or name C212 or name C213 or name C214 or name C21 \ 5 or name C216)) or resid 1303 or resid 1308 through 1310 or (resid 1311 through \ 1312 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27 or name C28 or name C29 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name P or name C210 or name C211 or n \ ame C212 or name C213 or name C214 or name C215 or name C216 or name C217 or nam \ e C218)))) selection = (chain 'C' and (resid 3 through 1230 or resid 1301 or (resid 1302 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name \ C29 or name C210 or name C211 or name C212 or name C213 or name C214 or name C21 \ 5 or name C216)) or resid 1303 or resid 1308 through 1310 or (resid 1311 through \ 1312 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27 or name C28 or name C29 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name P or name C210 or name C211 or n \ ame C212 or name C213 or name C214 or name C215 or name C216 or name C217 or nam \ e C218)))) selection = (chain 'D' and (resid 3 through 1230 or resid 1301 through 1303 or resid 1308 th \ rough 1310 or (resid 1311 through 1312 and (name N or name C1 or name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ P or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 \ or name C216 or name C217 or name C218)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.860 Extract box with map and model: 8.460 Check model and map are aligned: 0.820 Set scattering table: 0.530 Process input model: 182.580 Find NCS groups from input model: 3.510 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 208.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.015 0.268 39464 Z= 0.911 Angle : 1.224 13.919 53044 Z= 0.603 Chirality : 0.062 0.309 5684 Planarity : 0.010 0.235 6352 Dihedral : 19.214 177.261 16228 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.09 % Favored : 90.18 % Rotamer: Outliers : 0.20 % Allowed : 3.98 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.38 % 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: -4.99 (0.10), residues: 4388 helix: -3.21 (0.07), residues: 2632 sheet: -4.02 (0.25), residues: 188 loop : -3.06 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP A1042 HIS 0.017 0.002 HIS D 329 PHE 0.074 0.004 PHE C 858 TYR 0.068 0.004 TYR A 870 ARG 0.033 0.002 ARG B1115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 751 time to evaluate : 4.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.5104 (tt0) cc_final: 0.4477 (pm20) REVERT: A 369 MET cc_start: 0.3710 (mmp) cc_final: 0.3319 (mpm) REVERT: A 481 LYS cc_start: 0.6711 (mptt) cc_final: 0.6334 (mppt) REVERT: A 488 MET cc_start: 0.7697 (tpt) cc_final: 0.7295 (tpt) REVERT: A 956 HIS cc_start: 0.7017 (m-70) cc_final: 0.6631 (m-70) REVERT: A 1161 PHE cc_start: 0.7438 (t80) cc_final: 0.6807 (m-80) REVERT: B 488 MET cc_start: 0.7380 (tpt) cc_final: 0.6978 (tpt) REVERT: B 956 HIS cc_start: 0.7086 (m-70) cc_final: 0.6813 (m-70) REVERT: B 1161 PHE cc_start: 0.7538 (t80) cc_final: 0.7304 (m-80) REVERT: C 488 MET cc_start: 0.7561 (tpt) cc_final: 0.7186 (tpt) REVERT: C 956 HIS cc_start: 0.7120 (m-70) cc_final: 0.6842 (m-70) REVERT: C 1161 PHE cc_start: 0.7552 (t80) cc_final: 0.7295 (m-80) REVERT: D 211 GLU cc_start: 0.5119 (tt0) cc_final: 0.4864 (tp30) REVERT: D 369 MET cc_start: 0.3663 (mmp) cc_final: 0.3355 (mpm) REVERT: D 459 ILE cc_start: 0.7077 (mt) cc_final: 0.6654 (pp) REVERT: D 481 LYS cc_start: 0.6689 (mptt) cc_final: 0.6349 (mppt) REVERT: D 488 MET cc_start: 0.7736 (tpt) cc_final: 0.7308 (tpt) REVERT: D 1161 PHE cc_start: 0.7466 (t80) cc_final: 0.6862 (m-80) outliers start: 8 outliers final: 1 residues processed: 759 average time/residue: 2.6012 time to fit residues: 2405.4325 Evaluate side-chains 394 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 4.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 4.9990 chunk 333 optimal weight: 4.9990 chunk 185 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 224 optimal weight: 30.0000 chunk 178 optimal weight: 0.8980 chunk 344 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 209 optimal weight: 0.6980 chunk 256 optimal weight: 9.9990 chunk 399 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 177 ASN A 240 ASN A 295 ASN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 432 GLN A 968 ASN B 27 HIS B 177 ASN B 240 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN B 432 GLN B 955 ASN B 968 ASN C 27 HIS C 177 ASN C 240 ASN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN C 432 GLN C 951 ASN C 955 ASN C 968 ASN ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS D 177 ASN D 240 ASN D 295 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN D 432 GLN D 968 ASN ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39464 Z= 0.221 Angle : 0.682 7.952 53044 Z= 0.356 Chirality : 0.041 0.148 5684 Planarity : 0.006 0.073 6352 Dihedral : 22.709 174.499 7554 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.00 % Favored : 90.63 % Rotamer: Outliers : 2.20 % Allowed : 10.01 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -3.23 (0.11), residues: 4388 helix: -1.57 (0.09), residues: 2692 sheet: -3.51 (0.26), residues: 208 loop : -2.78 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1042 HIS 0.006 0.001 HIS B 70 PHE 0.020 0.002 PHE C1038 TYR 0.018 0.002 TYR B 870 ARG 0.005 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 383 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.5053 (tt0) cc_final: 0.4421 (pm20) REVERT: A 481 LYS cc_start: 0.6652 (mptt) cc_final: 0.6239 (mppt) REVERT: A 680 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7535 (mmtm) REVERT: A 704 MET cc_start: 0.8516 (mmt) cc_final: 0.8112 (mmt) REVERT: A 714 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6882 (pttm) REVERT: A 956 HIS cc_start: 0.6721 (m-70) cc_final: 0.6337 (m-70) REVERT: A 1161 PHE cc_start: 0.7362 (t80) cc_final: 0.6803 (m-80) REVERT: A 1202 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 704 MET cc_start: 0.8630 (mmt) cc_final: 0.7917 (mmt) REVERT: B 714 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6867 (pttm) REVERT: B 956 HIS cc_start: 0.6870 (m-70) cc_final: 0.6561 (m-70) REVERT: C 714 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6892 (pttm) REVERT: C 956 HIS cc_start: 0.6851 (m-70) cc_final: 0.6533 (m-70) REVERT: C 1161 PHE cc_start: 0.7482 (t80) cc_final: 0.7269 (m-80) REVERT: D 211 GLU cc_start: 0.5101 (tt0) cc_final: 0.4569 (pm20) REVERT: D 481 LYS cc_start: 0.6625 (mptt) cc_final: 0.6252 (mppt) REVERT: D 680 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7528 (mmtm) REVERT: D 704 MET cc_start: 0.8714 (mmm) cc_final: 0.8493 (mmt) REVERT: D 714 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6901 (pttm) REVERT: D 956 HIS cc_start: 0.6765 (m-70) cc_final: 0.6327 (m-70) REVERT: D 1161 PHE cc_start: 0.7391 (t80) cc_final: 0.6865 (m-80) outliers start: 86 outliers final: 30 residues processed: 444 average time/residue: 2.2664 time to fit residues: 1264.3301 Evaluate side-chains 373 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 337 time to evaluate : 4.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 680 LYS Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 790 ASP Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 899 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 0.0770 chunk 124 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 400 optimal weight: 3.9990 chunk 432 optimal weight: 7.9990 chunk 356 optimal weight: 10.0000 chunk 396 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 321 optimal weight: 0.3980 overall best weight: 2.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 39464 Z= 0.249 Angle : 0.629 6.522 53044 Z= 0.323 Chirality : 0.041 0.153 5684 Planarity : 0.005 0.087 6352 Dihedral : 20.843 178.994 7552 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.91 % Favored : 90.63 % Rotamer: Outliers : 1.53 % Allowed : 10.90 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -2.23 (0.12), residues: 4388 helix: -0.67 (0.09), residues: 2668 sheet: -3.06 (0.28), residues: 208 loop : -2.58 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1042 HIS 0.006 0.001 HIS B 149 PHE 0.016 0.002 PHE D 365 TYR 0.021 0.002 TYR A 870 ARG 0.006 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 385 time to evaluate : 4.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6169 (mtm) cc_final: 0.5961 (mtp) REVERT: A 211 GLU cc_start: 0.5107 (tt0) cc_final: 0.4499 (pm20) REVERT: A 369 MET cc_start: 0.2951 (mpm) cc_final: 0.2738 (mpm) REVERT: A 481 LYS cc_start: 0.6634 (mptt) cc_final: 0.6217 (mppt) REVERT: A 680 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7560 (tptp) REVERT: A 714 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6862 (pttm) REVERT: A 956 HIS cc_start: 0.6801 (m-70) cc_final: 0.6414 (m-70) REVERT: A 1161 PHE cc_start: 0.7353 (t80) cc_final: 0.6813 (m-80) REVERT: B 680 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7773 (tptp) REVERT: B 704 MET cc_start: 0.8734 (mmt) cc_final: 0.8224 (mmt) REVERT: B 714 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6869 (pttm) REVERT: B 956 HIS cc_start: 0.6965 (m-70) cc_final: 0.6670 (m-70) REVERT: C 160 LEU cc_start: 0.8377 (tp) cc_final: 0.8156 (tt) REVERT: C 714 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6897 (pttm) REVERT: C 1161 PHE cc_start: 0.7466 (t80) cc_final: 0.7241 (m-80) REVERT: D 130 MET cc_start: 0.6304 (mtm) cc_final: 0.6092 (mtp) REVERT: D 481 LYS cc_start: 0.6621 (mptt) cc_final: 0.6239 (mppt) REVERT: D 680 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7558 (tptp) REVERT: D 714 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6877 (pttm) REVERT: D 956 HIS cc_start: 0.6880 (m-70) cc_final: 0.6458 (m-70) REVERT: D 1161 PHE cc_start: 0.7382 (t80) cc_final: 0.6876 (m-80) outliers start: 60 outliers final: 29 residues processed: 417 average time/residue: 2.2893 time to fit residues: 1195.5997 Evaluate side-chains 362 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 326 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 680 LYS Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 680 LYS Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 1031 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 3.9990 chunk 300 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 191 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 401 optimal weight: 0.5980 chunk 425 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 HIS D 955 ASN ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39464 Z= 0.207 Angle : 0.589 6.295 53044 Z= 0.303 Chirality : 0.040 0.151 5684 Planarity : 0.005 0.058 6352 Dihedral : 19.993 179.603 7552 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.71 % Favored : 90.84 % Rotamer: Outliers : 1.76 % Allowed : 11.21 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -1.65 (0.12), residues: 4388 helix: -0.16 (0.10), residues: 2660 sheet: -2.82 (0.29), residues: 208 loop : -2.43 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1042 HIS 0.017 0.001 HIS B 426 PHE 0.014 0.002 PHE B 935 TYR 0.016 0.002 TYR D 870 ARG 0.005 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 346 time to evaluate : 4.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6196 (mtm) cc_final: 0.5980 (mtp) REVERT: A 211 GLU cc_start: 0.5071 (tt0) cc_final: 0.4520 (pm20) REVERT: A 680 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7623 (tptp) REVERT: A 714 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6826 (pttm) REVERT: A 794 MET cc_start: 0.5477 (OUTLIER) cc_final: 0.5199 (mtt) REVERT: A 878 MET cc_start: 0.8078 (mtm) cc_final: 0.7709 (mtm) REVERT: A 1161 PHE cc_start: 0.7346 (t80) cc_final: 0.6801 (m-80) REVERT: B 714 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6801 (pttm) REVERT: C 714 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6915 (pttm) REVERT: C 878 MET cc_start: 0.7985 (mtm) cc_final: 0.7636 (mtm) REVERT: C 1161 PHE cc_start: 0.7455 (t80) cc_final: 0.7235 (m-80) REVERT: D 211 GLU cc_start: 0.5085 (tt0) cc_final: 0.4654 (pm20) REVERT: D 532 ARG cc_start: 0.7040 (ttm170) cc_final: 0.6812 (ttm-80) REVERT: D 680 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7633 (tptp) REVERT: D 714 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6850 (pttm) REVERT: D 794 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.5294 (mtt) REVERT: D 1161 PHE cc_start: 0.7363 (t80) cc_final: 0.6847 (m-80) outliers start: 69 outliers final: 32 residues processed: 377 average time/residue: 2.4453 time to fit residues: 1144.4235 Evaluate side-chains 354 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 314 time to evaluate : 4.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 1085 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 1085 TYR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 1085 TYR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 680 LYS Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 1085 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 217 optimal weight: 10.0000 chunk 381 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39464 Z= 0.274 Angle : 0.611 5.999 53044 Z= 0.313 Chirality : 0.041 0.152 5684 Planarity : 0.005 0.053 6352 Dihedral : 19.460 171.704 7552 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.30 % Favored : 90.25 % Rotamer: Outliers : 1.79 % Allowed : 11.70 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -1.34 (0.12), residues: 4388 helix: 0.07 (0.10), residues: 2684 sheet: -2.51 (0.32), residues: 208 loop : -2.35 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 857 HIS 0.007 0.002 HIS A1137 PHE 0.016 0.002 PHE B 533 TYR 0.030 0.002 TYR B 505 ARG 0.005 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 324 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6826 (pttm) REVERT: A 794 MET cc_start: 0.5431 (OUTLIER) cc_final: 0.5194 (mtt) REVERT: A 878 MET cc_start: 0.8446 (mtm) cc_final: 0.8192 (mtm) REVERT: A 1161 PHE cc_start: 0.7363 (t80) cc_final: 0.6839 (m-80) REVERT: B 714 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6818 (pttm) REVERT: C 714 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6837 (pttm) REVERT: C 1161 PHE cc_start: 0.7476 (t80) cc_final: 0.7245 (m-80) REVERT: D 200 CYS cc_start: 0.6630 (m) cc_final: 0.6333 (t) REVERT: D 665 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: D 714 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6839 (pttm) REVERT: D 794 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.5312 (mtt) REVERT: D 1161 PHE cc_start: 0.7388 (t80) cc_final: 0.6890 (m-80) outliers start: 70 outliers final: 28 residues processed: 367 average time/residue: 2.4748 time to fit residues: 1135.2501 Evaluate side-chains 337 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 984 GLN Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 984 GLN Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 984 GLN Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 984 GLN Chi-restraints excluded: chain D residue 1031 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 0.3980 chunk 383 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 425 optimal weight: 1.9990 chunk 353 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 35 optimal weight: 30.0000 chunk 140 optimal weight: 10.0000 chunk 223 optimal weight: 0.7980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 39464 Z= 0.197 Angle : 0.563 8.674 53044 Z= 0.289 Chirality : 0.039 0.154 5684 Planarity : 0.004 0.047 6352 Dihedral : 18.526 160.255 7552 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.32 % Favored : 91.23 % Rotamer: Outliers : 1.69 % Allowed : 12.16 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4388 helix: 0.42 (0.10), residues: 2680 sheet: -2.51 (0.30), residues: 236 loop : -2.24 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 857 HIS 0.009 0.001 HIS B 426 PHE 0.015 0.002 PHE C1038 TYR 0.024 0.002 TYR A 505 ARG 0.004 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 319 time to evaluate : 4.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 CYS cc_start: 0.6543 (m) cc_final: 0.6134 (t) REVERT: A 270 ILE cc_start: 0.7173 (mm) cc_final: 0.6884 (mt) REVERT: A 369 MET cc_start: 0.2855 (mpm) cc_final: 0.2624 (mpm) REVERT: A 665 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: A 714 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6818 (pttm) REVERT: A 1161 PHE cc_start: 0.7318 (t80) cc_final: 0.6815 (m-80) REVERT: A 1175 GLU cc_start: 0.7290 (pt0) cc_final: 0.6945 (mt-10) REVERT: B 270 ILE cc_start: 0.8070 (mm) cc_final: 0.7627 (mt) REVERT: B 714 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6812 (pttm) REVERT: B 879 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: B 1175 GLU cc_start: 0.7411 (pt0) cc_final: 0.7192 (mt-10) REVERT: C 270 ILE cc_start: 0.8048 (mm) cc_final: 0.7634 (mt) REVERT: C 714 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6856 (pttm) REVERT: C 1161 PHE cc_start: 0.7435 (t80) cc_final: 0.7223 (m-80) REVERT: D 270 ILE cc_start: 0.7307 (mm) cc_final: 0.6983 (mt) REVERT: D 665 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: D 714 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6846 (pttm) REVERT: D 1161 PHE cc_start: 0.7336 (t80) cc_final: 0.6860 (m-80) outliers start: 66 outliers final: 27 residues processed: 360 average time/residue: 2.3467 time to fit residues: 1053.5557 Evaluate side-chains 338 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 304 time to evaluate : 4.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 1031 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 4.9990 chunk 47 optimal weight: 0.0570 chunk 242 optimal weight: 7.9990 chunk 310 optimal weight: 0.8980 chunk 240 optimal weight: 8.9990 chunk 358 optimal weight: 9.9990 chunk 237 optimal weight: 10.0000 chunk 424 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 258 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 39464 Z= 0.166 Angle : 0.537 5.586 53044 Z= 0.276 Chirality : 0.038 0.139 5684 Planarity : 0.004 0.084 6352 Dihedral : 17.792 149.696 7552 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.68 % Favored : 90.86 % Rotamer: Outliers : 1.53 % Allowed : 12.49 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4388 helix: 0.74 (0.10), residues: 2676 sheet: -2.38 (0.31), residues: 236 loop : -2.21 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 857 HIS 0.006 0.001 HIS B 426 PHE 0.012 0.001 PHE B 533 TYR 0.016 0.001 TYR A 505 ARG 0.012 0.000 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 307 time to evaluate : 4.162 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 200 CYS cc_start: 0.6460 (m) cc_final: 0.6046 (t) REVERT: A 665 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: A 714 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6748 (pttm) REVERT: A 754 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7077 (ttm-80) REVERT: A 1161 PHE cc_start: 0.7312 (t80) cc_final: 0.6807 (m-80) REVERT: A 1175 GLU cc_start: 0.7260 (pt0) cc_final: 0.6914 (mt-10) REVERT: B 714 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6739 (pttm) REVERT: B 1175 GLU cc_start: 0.7417 (pt0) cc_final: 0.7191 (mt-10) REVERT: C 714 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6757 (pttm) REVERT: C 1161 PHE cc_start: 0.7407 (t80) cc_final: 0.7198 (m-80) REVERT: D 665 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: D 714 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6766 (pttm) REVERT: D 754 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7060 (ttm-80) REVERT: D 879 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: D 1161 PHE cc_start: 0.7331 (t80) cc_final: 0.6851 (m-80) outliers start: 60 outliers final: 29 residues processed: 348 average time/residue: 2.3963 time to fit residues: 1039.6943 Evaluate side-chains 342 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 304 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 984 GLN Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 984 GLN Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 951 ASN Chi-restraints excluded: chain C residue 984 GLN Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 754 ARG Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 984 GLN Chi-restraints excluded: chain D residue 1031 SER Chi-restraints excluded: chain D residue 1180 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 269 optimal weight: 8.9990 chunk 288 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN B 305 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 984 GLN ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 ASN D 984 GLN ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 39464 Z= 0.392 Angle : 0.669 7.363 53044 Z= 0.337 Chirality : 0.044 0.174 5684 Planarity : 0.006 0.082 6352 Dihedral : 19.108 159.044 7552 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.02 % Favored : 90.59 % Rotamer: Outliers : 1.66 % Allowed : 12.77 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 4388 helix: 0.35 (0.10), residues: 2664 sheet: -2.48 (0.30), residues: 236 loop : -2.23 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 128 HIS 0.010 0.002 HIS B 644 PHE 0.019 0.002 PHE B 936 TYR 0.024 0.002 TYR A 953 ARG 0.014 0.001 ARG C 530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 317 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6315 (mtm) cc_final: 0.6105 (mtp) REVERT: A 494 ARG cc_start: 0.7361 (ttp-110) cc_final: 0.6467 (ttm110) REVERT: A 665 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: A 714 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6904 (pttm) REVERT: A 746 MET cc_start: 0.8875 (mtp) cc_final: 0.8674 (mtm) REVERT: A 1161 PHE cc_start: 0.7388 (t80) cc_final: 0.6869 (m-80) REVERT: A 1175 GLU cc_start: 0.7282 (pt0) cc_final: 0.6741 (mt-10) REVERT: B 494 ARG cc_start: 0.7489 (ttp-110) cc_final: 0.6909 (ttm110) REVERT: B 714 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6899 (pttm) REVERT: B 879 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: B 1135 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8017 (mp) REVERT: C 494 ARG cc_start: 0.7512 (ttp-110) cc_final: 0.6822 (ttm110) REVERT: C 714 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6953 (pttm) REVERT: C 879 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: C 1161 PHE cc_start: 0.7508 (t80) cc_final: 0.7253 (m-80) REVERT: D 494 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.6534 (ttm110) REVERT: D 665 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: D 714 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6905 (pttm) REVERT: D 879 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: D 1135 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7695 (mp) REVERT: D 1161 PHE cc_start: 0.7390 (t80) cc_final: 0.6873 (m-80) outliers start: 65 outliers final: 35 residues processed: 356 average time/residue: 2.5467 time to fit residues: 1118.1948 Evaluate side-chains 351 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 305 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 984 GLN Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 984 GLN Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 649 MET Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 879 GLU Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 984 GLN Chi-restraints excluded: chain D residue 1031 SER Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1180 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 4.9990 chunk 406 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 chunk 395 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 310 optimal weight: 0.5980 chunk 121 optimal weight: 0.3980 chunk 357 optimal weight: 6.9990 chunk 373 optimal weight: 4.9990 chunk 393 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39464 Z= 0.210 Angle : 0.576 6.286 53044 Z= 0.296 Chirality : 0.039 0.150 5684 Planarity : 0.005 0.073 6352 Dihedral : 18.396 151.721 7552 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.75 % Favored : 90.82 % Rotamer: Outliers : 1.40 % Allowed : 13.13 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4388 helix: 0.58 (0.10), residues: 2676 sheet: -2.51 (0.29), residues: 236 loop : -2.18 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 857 HIS 0.006 0.001 HIS C 491 PHE 0.015 0.002 PHE B 935 TYR 0.017 0.001 TYR A 505 ARG 0.009 0.000 ARG C 530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 308 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6271 (mtm) cc_final: 0.6056 (mtp) REVERT: A 530 ARG cc_start: 0.7286 (mmt-90) cc_final: 0.7024 (mmt90) REVERT: A 665 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: A 714 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6772 (pttm) REVERT: A 1161 PHE cc_start: 0.7358 (t80) cc_final: 0.6830 (m-80) REVERT: B 494 ARG cc_start: 0.7474 (ttp-110) cc_final: 0.6893 (ttm110) REVERT: B 714 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6760 (pttm) REVERT: C 494 ARG cc_start: 0.7466 (ttp-110) cc_final: 0.6898 (ttm110) REVERT: C 532 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7052 (ttt-90) REVERT: C 714 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6794 (pttm) REVERT: C 879 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: C 1161 PHE cc_start: 0.7467 (t80) cc_final: 0.7255 (m-80) REVERT: D 530 ARG cc_start: 0.7329 (mmt-90) cc_final: 0.7083 (mmt90) REVERT: D 532 ARG cc_start: 0.7083 (ttm170) cc_final: 0.6837 (ttm-80) REVERT: D 665 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: D 714 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6784 (pttm) REVERT: D 754 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7065 (ttm-80) REVERT: D 879 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: D 1161 PHE cc_start: 0.7374 (t80) cc_final: 0.6875 (m-80) outliers start: 55 outliers final: 27 residues processed: 340 average time/residue: 2.4436 time to fit residues: 1032.1038 Evaluate side-chains 340 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 303 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1180 MET Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1180 MET Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 879 GLU Chi-restraints excluded: chain C residue 951 ASN Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 754 ARG Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 1031 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 9.9990 chunk 417 optimal weight: 3.9990 chunk 255 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 438 optimal weight: 2.9990 chunk 403 optimal weight: 3.9990 chunk 349 optimal weight: 0.4980 chunk 36 optimal weight: 10.0000 chunk 269 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 39464 Z= 0.216 Angle : 0.566 7.026 53044 Z= 0.288 Chirality : 0.039 0.158 5684 Planarity : 0.004 0.048 6352 Dihedral : 17.719 141.779 7552 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.05 % Favored : 90.59 % Rotamer: Outliers : 1.10 % Allowed : 13.38 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4388 helix: 0.75 (0.10), residues: 2676 sheet: -2.43 (0.29), residues: 236 loop : -2.11 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 417 HIS 0.006 0.001 HIS B 426 PHE 0.017 0.002 PHE C 533 TYR 0.016 0.001 TYR A 505 ARG 0.003 0.000 ARG A 530 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 302 time to evaluate : 4.201 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 130 MET cc_start: 0.6225 (mtm) cc_final: 0.6013 (mtp) REVERT: A 530 ARG cc_start: 0.7255 (mmt-90) cc_final: 0.6994 (mmt90) REVERT: A 665 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: A 754 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7096 (ttm-80) REVERT: A 1161 PHE cc_start: 0.7352 (t80) cc_final: 0.6823 (m-80) REVERT: B 494 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.6939 (ttm110) REVERT: C 494 ARG cc_start: 0.7475 (ttp-110) cc_final: 0.6919 (ttm110) REVERT: C 879 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: C 1161 PHE cc_start: 0.7456 (t80) cc_final: 0.7242 (m-80) REVERT: D 494 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.6601 (ttm110) REVERT: D 530 ARG cc_start: 0.7329 (mmt-90) cc_final: 0.7089 (mmt90) REVERT: D 532 ARG cc_start: 0.7009 (ttm170) cc_final: 0.6783 (ttm-80) REVERT: D 665 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: D 754 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7070 (ttm-80) REVERT: D 879 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: D 1161 PHE cc_start: 0.7371 (t80) cc_final: 0.6871 (m-80) outliers start: 43 outliers final: 24 residues processed: 325 average time/residue: 2.5567 time to fit residues: 1035.6119 Evaluate side-chains 330 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 300 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1180 MET Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 879 GLU Chi-restraints excluded: chain C residue 951 ASN Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 754 ARG Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 879 GLU Chi-restraints excluded: chain D residue 951 ASN Chi-restraints excluded: chain D residue 1031 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 1.9990 chunk 371 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 321 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 349 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 chunk 359 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.208004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.130961 restraints weight = 110440.204| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.21 r_work: 0.3289 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39464 Z= 0.204 Angle : 0.556 5.871 53044 Z= 0.283 Chirality : 0.039 0.156 5684 Planarity : 0.004 0.047 6352 Dihedral : 17.293 135.165 7552 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.25 % Rotamer: Outliers : 0.79 % Allowed : 13.82 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 4388 helix: 0.85 (0.10), residues: 2680 sheet: -2.35 (0.29), residues: 236 loop : -2.11 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 857 HIS 0.006 0.001 HIS B 426 PHE 0.014 0.001 PHE B 533 TYR 0.015 0.001 TYR A 505 ARG 0.004 0.000 ARG C 525 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20711.86 seconds wall clock time: 356 minutes 20.96 seconds (21380.96 seconds total)