Starting phenix.real_space_refine on Wed Dec 13 01:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/12_2023/6m16_30038_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/12_2023/6m16_30038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/12_2023/6m16_30038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/12_2023/6m16_30038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/12_2023/6m16_30038_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/12_2023/6m16_30038_neut.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 14835 2.51 5 N 3888 2.21 5 O 4572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 622": "NH1" <-> "NH2" Residue "B ARG 652": "NH1" <-> "NH2" Residue "B ARG 673": "NH1" <-> "NH2" Residue "B ARG 966": "NH1" <-> "NH2" Residue "B ARG 984": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "A ARG 673": "NH1" <-> "NH2" Residue "A ARG 966": "NH1" <-> "NH2" Residue "A ARG 984": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 127": "NH1" <-> "NH2" Residue "C ARG 282": "NH1" <-> "NH2" Residue "C ARG 446": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 622": "NH1" <-> "NH2" Residue "C ARG 652": "NH1" <-> "NH2" Residue "C ARG 673": "NH1" <-> "NH2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C ARG 984": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 23433 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 7534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7534 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 924} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7534 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 924} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7534 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 924} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 12.68, per 1000 atoms: 0.54 Number of scatterers: 23433 At special positions: 0 Unit cell: (125.198, 128.381, 164.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 4572 8.00 N 3888 7.00 C 14835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 58 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 246 " distance=2.02 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 460 " distance=2.04 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 614 " distance=2.02 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS B 708 " distance=2.04 Simple disulfide: pdb=" SG CYS B 886 " - pdb=" SG CYS B 897 " distance=2.02 Simple disulfide: pdb=" SG CYS B 936 " - pdb=" SG CYS B 945 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 58 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 246 " distance=2.02 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 460 " distance=2.04 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 614 " distance=2.02 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 603 " distance=2.02 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 708 " distance=2.04 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 897 " distance=2.02 Simple disulfide: pdb=" SG CYS A 936 " - pdb=" SG CYS A 945 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 58 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 236 " - pdb=" SG CYS C 246 " distance=2.02 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.04 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 411 " - pdb=" SG CYS C 460 " distance=2.04 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 526 " - pdb=" SG CYS C 535 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 614 " distance=2.02 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 603 " distance=2.02 Simple disulfide: pdb=" SG CYS C 698 " - pdb=" SG CYS C 708 " distance=2.04 Simple disulfide: pdb=" SG CYS C 886 " - pdb=" SG CYS C 897 " distance=2.02 Simple disulfide: pdb=" SG CYS C 936 " - pdb=" SG CYS C 945 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A1205 " - " ASN A 154 " " NAG A1208 " - " ASN A 514 " " NAG A1209 " - " ASN A 520 " " NAG A1217 " - " ASN A 992 " " NAG B1205 " - " ASN B 154 " " NAG B1208 " - " ASN B 514 " " NAG B1209 " - " ASN B 520 " " NAG B1217 " - " ASN B 992 " " NAG C1205 " - " ASN C 154 " " NAG C1208 " - " ASN C 514 " " NAG C1209 " - " ASN C 520 " " NAG C1217 " - " ASN C 992 " " NAG D 1 " - " ASN B 39 " " NAG E 1 " - " ASN B 654 " " NAG F 1 " - " ASN B 973 " " NAG G 1 " - " ASN B 957 " " NAG H 1 " - " ASN A 39 " " NAG I 1 " - " ASN A 654 " " NAG J 1 " - " ASN A 973 " " NAG K 1 " - " ASN A 957 " " NAG L 1 " - " ASN C 39 " " NAG M 1 " - " ASN C 654 " " NAG N 1 " - " ASN C 973 " " NAG O 1 " - " ASN C 957 " Time building additional restraints: 8.57 Conformation dependent library (CDL) restraints added in 4.2 seconds 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5358 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 39 sheets defined 23.0% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'B' and resid 23 through 30 removed outlier: 3.738A pdb=" N LEU B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 27 " --> pdb=" O PHE B 24 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 316 through 321 removed outlier: 4.260A pdb=" N HIS B 319 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 removed outlier: 3.918A pdb=" N ASP B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 492 through 496' Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 606 through 610 Processing helix chain 'B' and resid 612 through 640 removed outlier: 3.538A pdb=" N LYS B 616 " --> pdb=" O GLY B 612 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 618 " --> pdb=" O CYS B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 659 removed outlier: 3.580A pdb=" N PHE B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 683 removed outlier: 3.504A pdb=" N PHE B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 702 Processing helix chain 'B' and resid 723 through 727 Processing helix chain 'B' and resid 751 through 763 Processing helix chain 'B' and resid 770 through 787 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 796 through 818 removed outlier: 3.568A pdb=" N ALA B 801 " --> pdb=" O SER B 797 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 812 " --> pdb=" O GLN B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'B' and resid 830 through 836 removed outlier: 3.569A pdb=" N SER B 835 " --> pdb=" O PHE B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 886 removed outlier: 3.775A pdb=" N LEU B 850 " --> pdb=" O GLN B 846 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 857 " --> pdb=" O GLY B 853 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 877 " --> pdb=" O ARG B 873 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 881 " --> pdb=" O ARG B 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 30 removed outlier: 3.738A pdb=" N LEU A 26 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 27 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN A 28 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 316 through 321 removed outlier: 4.259A pdb=" N HIS A 319 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.918A pdb=" N ASP A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 492 through 496' Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 612 through 640 removed outlier: 3.537A pdb=" N LYS A 616 " --> pdb=" O GLY A 612 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 618 " --> pdb=" O CYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.580A pdb=" N PHE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 683 removed outlier: 3.505A pdb=" N PHE A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 702 Processing helix chain 'A' and resid 723 through 727 Processing helix chain 'A' and resid 751 through 763 Processing helix chain 'A' and resid 770 through 787 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 796 through 818 removed outlier: 3.568A pdb=" N ALA A 801 " --> pdb=" O SER A 797 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 812 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 830 through 836 removed outlier: 3.569A pdb=" N SER A 835 " --> pdb=" O PHE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 886 removed outlier: 3.775A pdb=" N LEU A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN A 874 " --> pdb=" O ALA A 870 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 30 removed outlier: 3.739A pdb=" N LEU C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 27 " --> pdb=" O PHE C 24 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN C 28 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 316 through 321 removed outlier: 4.260A pdb=" N HIS C 319 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 removed outlier: 3.918A pdb=" N ASP C 496 " --> pdb=" O ALA C 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 492 through 496' Processing helix chain 'C' and resid 591 through 597 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 606 through 610 Processing helix chain 'C' and resid 612 through 640 removed outlier: 3.537A pdb=" N LYS C 616 " --> pdb=" O GLY C 612 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 618 " --> pdb=" O CYS C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 659 removed outlier: 3.580A pdb=" N PHE C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 683 removed outlier: 3.505A pdb=" N PHE C 681 " --> pdb=" O GLU C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 702 Processing helix chain 'C' and resid 723 through 727 Processing helix chain 'C' and resid 751 through 763 Processing helix chain 'C' and resid 770 through 787 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 796 through 818 removed outlier: 3.568A pdb=" N ALA C 801 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN C 812 " --> pdb=" O GLN C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 821 No H-bonds generated for 'chain 'C' and resid 819 through 821' Processing helix chain 'C' and resid 830 through 836 removed outlier: 3.569A pdb=" N SER C 835 " --> pdb=" O PHE C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 886 removed outlier: 3.775A pdb=" N LEU C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 856 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN C 874 " --> pdb=" O ALA C 870 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 877 " --> pdb=" O ARG C 873 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 881 " --> pdb=" O ARG C 877 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.858A pdb=" N LEU C 439 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C 444 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ARG C 446 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 426 " --> pdb=" O GLU C 456 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 41 through 46 removed outlier: 3.745A pdb=" N ARG B 232 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.524A pdb=" N PHE B 211 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 73 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 165 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN B 188 " --> pdb=" O THR C 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.820A pdb=" N LEU B 125 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU B 150 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 256 through 262 removed outlier: 5.514A pdb=" N VAL B 257 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR B 469 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER B 259 " --> pdb=" O VAL B 467 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 467 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 267 through 270 removed outlier: 3.546A pdb=" N TYR B 426 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ARG B 446 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 444 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 439 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR B 440 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 277 through 278 removed outlier: 7.703A pdb=" N SER B 277 " --> pdb=" O ILE B 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 296 through 298 removed outlier: 7.071A pdb=" N ILE B 383 " --> pdb=" O ASN B 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB1, first strand: chain 'B' and resid 393 through 394 removed outlier: 4.111A pdb=" N GLN A 188 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 165 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 73 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 211 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 516 through 523 removed outlier: 6.654A pdb=" N SER B 516 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARG B 546 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ALA B 518 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN B 925 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS B 572 " --> pdb=" O PRO B 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 574 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 921 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 576 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR B 919 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU B 578 " --> pdb=" O PHE B 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE B 917 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 580 " --> pdb=" O MET B 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET B 915 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 921 " --> pdb=" O HIS B 902 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS B 902 " --> pdb=" O LEU B 921 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN B 925 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS B 572 " --> pdb=" O PRO B 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 574 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 921 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 576 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR B 919 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU B 578 " --> pdb=" O PHE B 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE B 917 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 580 " --> pdb=" O MET B 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET B 915 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 932 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU B 953 " --> pdb=" O THR B 932 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 587 through 590 removed outlier: 3.841A pdb=" N GLN B 710 " --> pdb=" O VAL B 717 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 979 through 982 removed outlier: 3.752A pdb=" N CYS B 945 " --> pdb=" O VAL B 982 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 41 through 46 removed outlier: 3.744A pdb=" N ARG A 232 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 125 through 127 removed outlier: 6.820A pdb=" N LEU A 125 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU A 150 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 256 through 262 removed outlier: 5.514A pdb=" N VAL A 257 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A 469 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER A 259 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 467 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 267 through 270 removed outlier: 3.545A pdb=" N TYR A 426 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ARG A 446 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 444 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 439 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR A 440 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 277 through 278 removed outlier: 7.702A pdb=" N SER A 277 " --> pdb=" O ILE A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 296 through 298 removed outlier: 7.071A pdb=" N ILE A 383 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AC5, first strand: chain 'A' and resid 393 through 394 removed outlier: 4.106A pdb=" N GLN C 188 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 165 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 73 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 211 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 516 through 523 removed outlier: 6.654A pdb=" N SER A 516 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N ARG A 546 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ALA A 518 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN A 925 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS A 572 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 574 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 921 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU A 576 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR A 919 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU A 578 " --> pdb=" O PHE A 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE A 917 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE A 580 " --> pdb=" O MET A 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET A 915 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 921 " --> pdb=" O HIS A 902 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS A 902 " --> pdb=" O LEU A 921 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN A 925 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS A 572 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 574 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 921 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU A 576 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR A 919 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU A 578 " --> pdb=" O PHE A 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE A 917 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE A 580 " --> pdb=" O MET A 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET A 915 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 932 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU A 953 " --> pdb=" O THR A 932 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 587 through 590 removed outlier: 3.841A pdb=" N GLN A 710 " --> pdb=" O VAL A 717 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 979 through 982 removed outlier: 3.752A pdb=" N CYS A 945 " --> pdb=" O VAL A 982 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.745A pdb=" N ARG C 232 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.821A pdb=" N LEU C 125 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU C 150 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 256 through 262 removed outlier: 5.514A pdb=" N VAL C 257 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR C 469 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER C 259 " --> pdb=" O VAL C 467 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 467 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 277 through 278 removed outlier: 7.703A pdb=" N SER C 277 " --> pdb=" O ILE C 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 296 through 298 removed outlier: 7.071A pdb=" N ILE C 383 " --> pdb=" O ASN C 377 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 343 through 344 Processing sheet with id=AD8, first strand: chain 'C' and resid 516 through 523 removed outlier: 6.654A pdb=" N SER C 516 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARG C 546 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N ALA C 518 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN C 925 " --> pdb=" O LEU C 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS C 572 " --> pdb=" O PRO C 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 574 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 921 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU C 576 " --> pdb=" O TYR C 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C 919 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU C 578 " --> pdb=" O PHE C 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE C 917 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE C 580 " --> pdb=" O MET C 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET C 915 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU C 921 " --> pdb=" O HIS C 902 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS C 902 " --> pdb=" O LEU C 921 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN C 925 " --> pdb=" O LEU C 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS C 572 " --> pdb=" O PRO C 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 574 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 921 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU C 576 " --> pdb=" O TYR C 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C 919 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU C 578 " --> pdb=" O PHE C 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE C 917 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE C 580 " --> pdb=" O MET C 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET C 915 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 932 " --> pdb=" O LEU C 953 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU C 953 " --> pdb=" O THR C 932 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 587 through 590 removed outlier: 3.841A pdb=" N GLN C 710 " --> pdb=" O VAL C 717 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 979 through 982 removed outlier: 3.751A pdb=" N CYS C 945 " --> pdb=" O VAL C 982 " (cutoff:3.500A) 763 hydrogen bonds defined for protein. 2055 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: 9.65 Time building geometry restraints manager: 9.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6529 1.33 - 1.45: 5755 1.45 - 1.58: 11497 1.58 - 1.70: 0 1.70 - 1.83: 186 Bond restraints: 23967 Sorted by residual: bond pdb=" C LEU B 499 " pdb=" N PRO B 500 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.11e-02 8.12e+03 8.45e+00 bond pdb=" C LEU C 499 " pdb=" N PRO C 500 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.11e-02 8.12e+03 8.40e+00 bond pdb=" C LEU A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.11e-02 8.12e+03 8.35e+00 bond pdb=" CG1 ILE A 742 " pdb=" CD1 ILE A 742 " ideal model delta sigma weight residual 1.513 1.404 0.109 3.90e-02 6.57e+02 7.88e+00 bond pdb=" CG1 ILE B 742 " pdb=" CD1 ILE B 742 " ideal model delta sigma weight residual 1.513 1.404 0.109 3.90e-02 6.57e+02 7.86e+00 ... (remaining 23962 not shown) Histogram of bond angle deviations from ideal: 97.34 - 104.70: 359 104.70 - 112.05: 11509 112.05 - 119.41: 8229 119.41 - 126.76: 12212 126.76 - 134.12: 316 Bond angle restraints: 32625 Sorted by residual: angle pdb=" N VAL A 120 " pdb=" CA VAL A 120 " pdb=" C VAL A 120 " ideal model delta sigma weight residual 108.12 114.19 -6.07 1.34e+00 5.57e-01 2.05e+01 angle pdb=" N VAL B 120 " pdb=" CA VAL B 120 " pdb=" C VAL B 120 " ideal model delta sigma weight residual 108.12 114.19 -6.07 1.34e+00 5.57e-01 2.05e+01 angle pdb=" N VAL C 120 " pdb=" CA VAL C 120 " pdb=" C VAL C 120 " ideal model delta sigma weight residual 108.12 114.19 -6.07 1.34e+00 5.57e-01 2.05e+01 angle pdb=" N ASP B 598 " pdb=" CA ASP B 598 " pdb=" C ASP B 598 " ideal model delta sigma weight residual 111.02 115.88 -4.86 1.22e+00 6.72e-01 1.59e+01 angle pdb=" N ASP C 598 " pdb=" CA ASP C 598 " pdb=" C ASP C 598 " ideal model delta sigma weight residual 111.02 115.87 -4.85 1.22e+00 6.72e-01 1.58e+01 ... (remaining 32620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.42: 14279 19.42 - 38.84: 418 38.84 - 58.26: 87 58.26 - 77.68: 66 77.68 - 97.10: 12 Dihedral angle restraints: 14862 sinusoidal: 6483 harmonic: 8379 Sorted by residual: dihedral pdb=" CB CYS A 19 " pdb=" SG CYS A 19 " pdb=" SG CYS A 58 " pdb=" CB CYS A 58 " ideal model delta sinusoidal sigma weight residual -86.00 -15.49 -70.51 1 1.00e+01 1.00e-02 6.40e+01 dihedral pdb=" CB CYS B 19 " pdb=" SG CYS B 19 " pdb=" SG CYS B 58 " pdb=" CB CYS B 58 " ideal model delta sinusoidal sigma weight residual -86.00 -15.54 -70.46 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS C 19 " pdb=" SG CYS C 19 " pdb=" SG CYS C 58 " pdb=" CB CYS C 58 " ideal model delta sinusoidal sigma weight residual -86.00 -15.56 -70.44 1 1.00e+01 1.00e-02 6.39e+01 ... (remaining 14859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3296 0.095 - 0.191: 472 0.191 - 0.286: 30 0.286 - 0.381: 3 0.381 - 0.476: 6 Chirality restraints: 3807 Sorted by residual: chirality pdb=" C1 NAG B1208 " pdb=" ND2 ASN B 514 " pdb=" C2 NAG B1208 " pdb=" O5 NAG B1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" C1 NAG A1208 " pdb=" ND2 ASN A 514 " pdb=" C2 NAG A1208 " pdb=" O5 NAG A1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" C1 NAG C1208 " pdb=" ND2 ASN C 514 " pdb=" C2 NAG C1208 " pdb=" O5 NAG C1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 3804 not shown) Planarity restraints: 4146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 681 " 0.018 2.00e-02 2.50e+03 2.55e-02 1.14e+01 pdb=" CG PHE A 681 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 681 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 681 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 681 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 681 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 681 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 681 " -0.017 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE B 681 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 681 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE B 681 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 681 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE B 681 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 681 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 681 " -0.017 2.00e-02 2.50e+03 2.53e-02 1.12e+01 pdb=" CG PHE C 681 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE C 681 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE C 681 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 681 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE C 681 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 681 " -0.003 2.00e-02 2.50e+03 ... (remaining 4143 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 30 1.90 - 2.65: 356 2.65 - 3.40: 28894 3.40 - 4.15: 55185 4.15 - 4.90: 99016 Nonbonded interactions: 183481 Sorted by model distance: nonbonded pdb=" ND2 ASN A 337 " pdb=" N LEU C 838 " model vdw 1.146 3.200 nonbonded pdb=" ND2 ASN B 337 " pdb=" N LEU A 838 " model vdw 1.147 3.200 nonbonded pdb=" N LEU B 838 " pdb=" ND2 ASN C 337 " model vdw 1.153 3.200 nonbonded pdb=" OD1 ASN A 337 " pdb=" C LEU C 838 " model vdw 1.156 3.270 nonbonded pdb=" OE2 GLU A 822 " pdb=" CA GLY C 611 " model vdw 1.157 3.440 ... (remaining 183476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.820 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 63.450 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.220 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: 0.000 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.011 0.109 23967 Z= 0.691 Angle : 1.065 11.577 32625 Z= 0.590 Chirality : 0.069 0.476 3807 Planarity : 0.008 0.070 4122 Dihedral : 11.544 97.097 9369 Min Nonbonded Distance : 1.146 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.52 % Favored : 92.37 % Rotamer: Outliers : 0.36 % Allowed : 2.16 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -4.10 (0.12), residues: 2871 helix: -4.24 (0.09), residues: 591 sheet: -2.02 (0.18), residues: 627 loop : -2.45 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP B 752 HIS 0.018 0.004 HIS A 902 PHE 0.055 0.005 PHE A 681 TYR 0.037 0.004 TYR A 479 ARG 0.012 0.002 ARG B 877 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 323 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 332 average time/residue: 1.3082 time to fit residues: 500.8103 Evaluate side-chains 191 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 3.4622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 188 GLN B 318 GLN B 334 ASN ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 767 GLN ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 ASN B 925 ASN B 987 ASN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN A 200 ASN A 318 GLN A 328 ASN A 334 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 525 ASN A 783 GLN ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A 925 ASN A 987 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 188 GLN C 200 ASN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 ASN C 334 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN C 525 ASN ** C 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 ASN C 925 ASN C 987 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23967 Z= 0.203 Angle : 0.649 10.035 32625 Z= 0.340 Chirality : 0.045 0.311 3807 Planarity : 0.005 0.056 4122 Dihedral : 8.713 63.840 4341 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.72 % Allowed : 6.85 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.14), residues: 2871 helix: -1.42 (0.18), residues: 591 sheet: -1.49 (0.20), residues: 582 loop : -1.99 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 110 HIS 0.006 0.001 HIS C 112 PHE 0.018 0.002 PHE A 494 TYR 0.016 0.001 TYR B 865 ARG 0.006 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 251 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 18 residues processed: 285 average time/residue: 1.1754 time to fit residues: 394.1892 Evaluate side-chains 213 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 2.472 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 0.2219 time to fit residues: 3.8921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 217 optimal weight: 0.3980 chunk 178 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 283 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 259 optimal weight: 0.0670 chunk 89 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN B 807 ASN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN A 318 GLN A 328 ASN A 807 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN C 318 GLN C 437 ASN C 807 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23967 Z= 0.201 Angle : 0.590 9.877 32625 Z= 0.308 Chirality : 0.044 0.298 3807 Planarity : 0.004 0.049 4122 Dihedral : 7.239 59.923 4341 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.08 % Allowed : 8.97 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.15), residues: 2871 helix: 0.15 (0.21), residues: 591 sheet: -1.19 (0.21), residues: 582 loop : -1.68 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 110 HIS 0.004 0.001 HIS C 918 PHE 0.019 0.002 PHE B 347 TYR 0.018 0.001 TYR A 636 ARG 0.004 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 230 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 24 residues processed: 266 average time/residue: 1.0882 time to fit residues: 343.7345 Evaluate side-chains 220 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 2.758 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.2708 time to fit residues: 5.7485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 135 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 328 ASN B 337 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN B 899 GLN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN A 328 ASN A 437 ASN A 894 ASN A 899 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN C 318 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN C 894 ASN C 899 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 23967 Z= 0.372 Angle : 0.670 10.014 32625 Z= 0.348 Chirality : 0.048 0.302 3807 Planarity : 0.005 0.053 4122 Dihedral : 7.085 59.843 4341 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.68 % Allowed : 9.54 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.58 (0.15), residues: 2871 helix: 0.41 (0.21), residues: 600 sheet: -1.14 (0.21), residues: 588 loop : -1.60 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 110 HIS 0.005 0.001 HIS A 918 PHE 0.024 0.002 PHE C 432 TYR 0.025 0.002 TYR C 636 ARG 0.007 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 201 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 44 residues processed: 253 average time/residue: 1.0894 time to fit residues: 328.2811 Evaluate side-chains 231 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 2.748 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 39 residues processed: 5 average time/residue: 0.4139 time to fit residues: 6.3781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 3.9990 chunk 158 optimal weight: 0.1980 chunk 4 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 249 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN A 444 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 23967 Z= 0.327 Angle : 0.630 9.955 32625 Z= 0.329 Chirality : 0.047 0.304 3807 Planarity : 0.005 0.055 4122 Dihedral : 6.905 59.856 4341 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.80 % Allowed : 10.34 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.37 (0.15), residues: 2871 helix: 0.73 (0.21), residues: 600 sheet: -0.86 (0.21), residues: 561 loop : -1.59 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.005 0.001 HIS A 34 PHE 0.020 0.002 PHE A 432 TYR 0.022 0.002 TYR C 636 ARG 0.009 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 202 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 45 residues processed: 257 average time/residue: 1.1450 time to fit residues: 348.3694 Evaluate side-chains 224 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 179 time to evaluate : 2.688 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 41 residues processed: 4 average time/residue: 0.2455 time to fit residues: 5.3702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 2.9990 chunk 250 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 163 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 278 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 23967 Z= 0.199 Angle : 0.559 9.842 32625 Z= 0.294 Chirality : 0.043 0.298 3807 Planarity : 0.004 0.052 4122 Dihedral : 6.457 59.735 4341 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.64 % Allowed : 10.78 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.16), residues: 2871 helix: 1.22 (0.22), residues: 600 sheet: -0.66 (0.22), residues: 549 loop : -1.50 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 376 HIS 0.003 0.001 HIS A 552 PHE 0.015 0.001 PHE C 494 TYR 0.018 0.001 TYR C 636 ARG 0.007 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 197 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 48 residues processed: 251 average time/residue: 1.0924 time to fit residues: 327.4671 Evaluate side-chains 229 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 181 time to evaluate : 2.603 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 43 residues processed: 5 average time/residue: 0.2442 time to fit residues: 5.9572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 203 optimal weight: 20.0000 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 277 optimal weight: 0.3980 chunk 173 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 23967 Z= 0.295 Angle : 0.606 9.922 32625 Z= 0.316 Chirality : 0.045 0.297 3807 Planarity : 0.004 0.054 4122 Dihedral : 6.417 58.775 4341 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.64 % Allowed : 11.42 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.09 (0.16), residues: 2871 helix: 1.22 (0.22), residues: 600 sheet: -0.69 (0.22), residues: 513 loop : -1.50 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 129 HIS 0.004 0.001 HIS A 34 PHE 0.019 0.002 PHE C 432 TYR 0.020 0.002 TYR C 636 ARG 0.006 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 192 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 54 residues processed: 245 average time/residue: 1.0960 time to fit residues: 319.5112 Evaluate side-chains 231 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 177 time to evaluate : 2.382 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 48 residues processed: 6 average time/residue: 0.2314 time to fit residues: 5.7533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 218 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 ASN C 864 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 23967 Z= 0.230 Angle : 0.572 9.852 32625 Z= 0.298 Chirality : 0.044 0.297 3807 Planarity : 0.004 0.053 4122 Dihedral : 6.164 58.326 4341 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.52 % Allowed : 11.66 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.98 (0.16), residues: 2871 helix: 1.42 (0.22), residues: 600 sheet: -0.67 (0.22), residues: 555 loop : -1.47 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 129 HIS 0.004 0.001 HIS A 34 PHE 0.017 0.001 PHE C 494 TYR 0.018 0.001 TYR C 636 ARG 0.006 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 195 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 50 residues processed: 247 average time/residue: 1.0796 time to fit residues: 319.7720 Evaluate side-chains 238 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 188 time to evaluate : 2.496 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 48 residues processed: 2 average time/residue: 0.2488 time to fit residues: 4.4498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN B 615 GLN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 ASN C 34 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 23967 Z= 0.246 Angle : 0.581 9.848 32625 Z= 0.303 Chirality : 0.044 0.296 3807 Planarity : 0.004 0.052 4122 Dihedral : 6.023 57.828 4341 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.44 % Allowed : 11.98 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.92 (0.16), residues: 2871 helix: 1.55 (0.22), residues: 591 sheet: -0.65 (0.22), residues: 555 loop : -1.43 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 129 HIS 0.004 0.001 HIS C 712 PHE 0.017 0.001 PHE C 494 TYR 0.019 0.002 TYR C 636 ARG 0.006 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 195 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 52 residues processed: 246 average time/residue: 1.1225 time to fit residues: 329.0069 Evaluate side-chains 236 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 184 time to evaluate : 2.786 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 49 residues processed: 3 average time/residue: 0.2094 time to fit residues: 4.7395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 5.9990 chunk 273 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 337 ASN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 23967 Z= 0.260 Angle : 0.588 9.865 32625 Z= 0.306 Chirality : 0.045 0.297 3807 Planarity : 0.004 0.052 4122 Dihedral : 5.953 58.452 4341 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.32 % Allowed : 12.10 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.94 (0.16), residues: 2871 helix: 1.53 (0.22), residues: 591 sheet: -0.69 (0.21), residues: 594 loop : -1.44 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 129 HIS 0.004 0.001 HIS A 34 PHE 0.018 0.002 PHE C 494 TYR 0.019 0.002 TYR B 636 ARG 0.006 0.000 ARG B 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 50 residues processed: 240 average time/residue: 1.1433 time to fit residues: 328.0598 Evaluate side-chains 241 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 191 time to evaluate : 2.578 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 47 residues processed: 3 average time/residue: 1.0182 time to fit residues: 7.1104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.0270 chunk 243 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.8244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN C 34 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.104678 restraints weight = 28308.677| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.17 r_work: 0.2933 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 23967 Z= 0.356 Angle : 0.651 9.973 32625 Z= 0.337 Chirality : 0.047 0.302 3807 Planarity : 0.005 0.056 4122 Dihedral : 6.197 59.690 4341 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.16 % Allowed : 12.34 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.16), residues: 2871 helix: 1.31 (0.21), residues: 591 sheet: -0.72 (0.21), residues: 591 loop : -1.50 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 129 HIS 0.004 0.001 HIS A 34 PHE 0.022 0.002 PHE C 432 TYR 0.022 0.002 TYR C 636 ARG 0.008 0.001 ARG B 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6834.21 seconds wall clock time: 123 minutes 25.04 seconds (7405.04 seconds total)