Starting phenix.real_space_refine on Mon Feb 19 01:43:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/02_2024/6m16_30038_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/02_2024/6m16_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_30038/02_2024/6m16_30038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/02_2024/6m16_30038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/02_2024/6m16_30038_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m16_30038/02_2024/6m16_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9 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: 9 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: 9 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: 13.13, per 1000 atoms: 0.56 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: 8.43 Conformation dependent library (CDL) restraints added in 3.5 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: 2.84 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: 9.98 Time building geometry restraints manager: 8.86 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 - 20.23: 14322 20.23 - 40.46: 408 40.46 - 60.69: 93 60.69 - 80.92: 72 80.92 - 101.15: 24 Dihedral angle restraints: 14919 sinusoidal: 6540 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 14916 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: 1.130 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: 4.720 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 62.010 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.240 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.030 ------------------------------------------------------------------------------- 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 : 12.541 101.147 9426 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 : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.6706 (t70) cc_final: 0.6370 (p0) REVERT: B 523 MET cc_start: 0.8538 (mtp) cc_final: 0.8321 (mtp) REVERT: A 173 ASN cc_start: 0.8166 (m110) cc_final: 0.7938 (m-40) REVERT: A 200 ASN cc_start: 0.7750 (t0) cc_final: 0.7522 (t0) REVERT: A 386 TRP cc_start: 0.6548 (p-90) cc_final: 0.6296 (p-90) REVERT: A 390 ASP cc_start: 0.6516 (t70) cc_final: 0.6241 (p0) REVERT: A 660 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9280 (mt) REVERT: A 712 HIS cc_start: 0.8070 (m90) cc_final: 0.7741 (m-70) REVERT: A 749 MET cc_start: 0.8973 (mtm) cc_final: 0.8664 (mtp) REVERT: C 173 ASN cc_start: 0.8324 (m110) cc_final: 0.8112 (m-40) REVERT: C 390 ASP cc_start: 0.6773 (t70) cc_final: 0.6424 (p0) REVERT: C 767 GLN cc_start: 0.7948 (tp40) cc_final: 0.7687 (tt0) outliers start: 9 outliers final: 2 residues processed: 332 average time/residue: 1.2910 time to fit residues: 493.2048 Evaluate side-chains 198 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain A residue 660 LEU 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 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 899 GLN 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 C 328 ASN C 334 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN C 437 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23967 Z= 0.192 Angle : 0.646 10.042 32625 Z= 0.338 Chirality : 0.046 0.311 3807 Planarity : 0.005 0.055 4122 Dihedral : 9.659 63.585 4404 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.72 % Allowed : 6.65 % Favored : 91.63 % 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: -2.63 (0.14), residues: 2871 helix: -1.47 (0.18), residues: 591 sheet: -1.46 (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 0.016 0.002 PHE C 976 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 292 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 249 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 ARG cc_start: 0.7357 (ttp80) cc_final: 0.6935 (ttt180) REVERT: B 390 ASP cc_start: 0.6842 (t70) cc_final: 0.6506 (p0) REVERT: B 523 MET cc_start: 0.8449 (mtp) cc_final: 0.8157 (mtp) REVERT: A 276 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6888 (mtm) REVERT: A 301 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7655 (m110) REVERT: A 337 ASN cc_start: 0.5997 (m-40) cc_final: 0.5610 (p0) REVERT: A 386 TRP cc_start: 0.6564 (p-90) cc_final: 0.6265 (p-90) REVERT: A 660 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9202 (mt) REVERT: A 749 MET cc_start: 0.8910 (mtm) cc_final: 0.8664 (mtp) REVERT: A 838 LEU cc_start: 0.8743 (mt) cc_final: 0.8284 (mp) REVERT: A 950 ASP cc_start: 0.7387 (t70) cc_final: 0.7150 (t70) REVERT: C 124 ARG cc_start: 0.6536 (ptp-110) cc_final: 0.6036 (ttm-80) REVERT: C 173 ASN cc_start: 0.8345 (m110) cc_final: 0.8127 (m-40) REVERT: C 337 ASN cc_start: 0.5830 (m-40) cc_final: 0.5621 (p0) REVERT: C 390 ASP cc_start: 0.6888 (t70) cc_final: 0.6359 (p0) REVERT: C 426 TYR cc_start: 0.7828 (m-80) cc_final: 0.7525 (m-10) REVERT: C 838 LEU cc_start: 0.8731 (mt) cc_final: 0.8243 (mt) outliers start: 43 outliers final: 18 residues processed: 285 average time/residue: 1.1523 time to fit residues: 387.0466 Evaluate side-chains 219 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 814 GLU Chi-restraints excluded: chain C residue 939 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 217 optimal weight: 0.0070 chunk 178 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 283 optimal weight: 0.6980 chunk 233 optimal weight: 6.9990 chunk 259 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- 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 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 807 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN C 318 GLN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23967 Z= 0.225 Angle : 0.611 9.898 32625 Z= 0.317 Chirality : 0.045 0.297 3807 Planarity : 0.004 0.049 4122 Dihedral : 7.807 59.798 4402 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.16 % Allowed : 8.77 % Favored : 89.06 % 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: -1.74 (0.15), residues: 2871 helix: 0.14 (0.21), residues: 591 sheet: -1.17 (0.21), residues: 582 loop : -1.67 (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 A 34 PHE 0.021 0.002 PHE A 347 TYR 0.019 0.002 TYR A 636 ARG 0.005 0.000 ARG B 127 *********************** 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 285 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 231 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 ARG cc_start: 0.6855 (ptp90) cc_final: 0.6454 (ptp90) REVERT: B 252 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6728 (p0) REVERT: B 338 ARG cc_start: 0.7379 (ttp80) cc_final: 0.7143 (ttt180) REVERT: B 390 ASP cc_start: 0.6908 (t70) cc_final: 0.6538 (p0) REVERT: B 523 MET cc_start: 0.8481 (mtp) cc_final: 0.8129 (mtp) REVERT: B 712 HIS cc_start: 0.8013 (m90) cc_final: 0.7689 (m90) REVERT: A 20 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7449 (mp0) REVERT: A 185 LEU cc_start: 0.8506 (tp) cc_final: 0.7856 (mp) REVERT: A 338 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7015 (ttt90) REVERT: A 386 TRP cc_start: 0.6529 (p-90) cc_final: 0.6214 (p-90) REVERT: A 749 MET cc_start: 0.8886 (mtm) cc_final: 0.8605 (mtp) REVERT: A 767 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7692 (tp40) REVERT: A 915 MET cc_start: 0.8707 (ttm) cc_final: 0.8279 (tpp) REVERT: A 950 ASP cc_start: 0.7392 (t70) cc_final: 0.7088 (t70) REVERT: C 20 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7627 (mp0) REVERT: C 124 ARG cc_start: 0.6645 (ptp-110) cc_final: 0.6199 (ttm-80) REVERT: C 173 ASN cc_start: 0.8324 (m110) cc_final: 0.8119 (m-40) REVERT: C 426 TYR cc_start: 0.7799 (m-80) cc_final: 0.7480 (m-10) REVERT: C 838 LEU cc_start: 0.8868 (mt) cc_final: 0.8416 (mt) outliers start: 54 outliers final: 28 residues processed: 268 average time/residue: 1.1024 time to fit residues: 349.2198 Evaluate side-chains 229 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 848 ASP Chi-restraints excluded: chain C residue 939 ASP Chi-restraints excluded: chain C residue 975 THR 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: 9.9990 chunk 135 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 137 optimal weight: 0.4980 chunk 249 optimal weight: 6.9990 chunk 75 optimal weight: 0.2980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN A 337 ASN A 894 ASN C 77 GLN C 104 ASN C 337 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 23967 Z= 0.155 Angle : 0.535 9.823 32625 Z= 0.283 Chirality : 0.043 0.292 3807 Planarity : 0.004 0.050 4122 Dihedral : 6.647 59.261 4398 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.28 % Allowed : 9.50 % Favored : 88.22 % 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: -1.25 (0.16), residues: 2871 helix: 0.93 (0.22), residues: 591 sheet: -0.92 (0.22), residues: 576 loop : -1.49 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 110 HIS 0.004 0.001 HIS A 34 PHE 0.017 0.001 PHE C 613 TYR 0.015 0.001 TYR A 636 ARG 0.007 0.000 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 275 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 218 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7702 (mp) REVERT: B 252 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6760 (p0) REVERT: B 276 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6638 (mtm) REVERT: B 390 ASP cc_start: 0.6710 (t70) cc_final: 0.6479 (p0) REVERT: B 420 THR cc_start: 0.8804 (t) cc_final: 0.8579 (t) REVERT: B 523 MET cc_start: 0.8407 (mtp) cc_final: 0.8085 (mtp) REVERT: B 712 HIS cc_start: 0.8013 (m90) cc_final: 0.7694 (m90) REVERT: A 185 LEU cc_start: 0.8468 (tp) cc_final: 0.7817 (mp) REVERT: A 281 GLU cc_start: 0.6674 (mp0) cc_final: 0.6427 (mp0) REVERT: A 386 TRP cc_start: 0.6547 (p-90) cc_final: 0.6278 (p-90) REVERT: A 420 THR cc_start: 0.8942 (t) cc_final: 0.8714 (t) REVERT: A 915 MET cc_start: 0.8669 (ttm) cc_final: 0.8307 (tpp) REVERT: C 20 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7499 (mp0) REVERT: C 124 ARG cc_start: 0.6325 (ptp-110) cc_final: 0.5921 (ttp-110) REVERT: C 426 TYR cc_start: 0.7789 (m-80) cc_final: 0.7456 (m-10) REVERT: C 436 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: C 608 PHE cc_start: 0.7999 (t80) cc_final: 0.7754 (t80) outliers start: 57 outliers final: 28 residues processed: 261 average time/residue: 1.0573 time to fit residues: 328.7525 Evaluate side-chains 226 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 848 ASP Chi-restraints excluded: chain C residue 939 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 0.2980 chunk 249 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 894 ASN B 899 GLN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN A 328 ASN A 444 GLN C 34 HIS C 104 ASN C 337 ASN C 472 ASN C 894 ASN C 899 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.144 23967 Z= 0.508 Angle : 0.743 10.993 32625 Z= 0.385 Chirality : 0.051 0.305 3807 Planarity : 0.005 0.059 4122 Dihedral : 7.162 60.768 4398 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.00 % Allowed : 10.06 % Favored : 86.94 % 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: -1.54 (0.15), residues: 2871 helix: 0.47 (0.21), residues: 615 sheet: -0.89 (0.21), residues: 561 loop : -1.69 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 386 HIS 0.007 0.002 HIS A 712 PHE 0.028 0.003 PHE C 432 TYR 0.029 0.003 TYR C 636 ARG 0.008 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 277 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 202 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 ARG cc_start: 0.7240 (ptp90) cc_final: 0.7039 (ptp90) REVERT: B 252 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6593 (p0) REVERT: B 276 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6603 (mtm) REVERT: B 374 TRP cc_start: 0.6177 (p-90) cc_final: 0.5946 (p-90) REVERT: B 523 MET cc_start: 0.8485 (mtp) cc_final: 0.8175 (mtp) REVERT: B 712 HIS cc_start: 0.8087 (m90) cc_final: 0.7772 (m90) REVERT: A 20 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7427 (mp0) REVERT: A 281 GLU cc_start: 0.6834 (mp0) cc_final: 0.6503 (mp0) REVERT: A 386 TRP cc_start: 0.6502 (p-90) cc_final: 0.6202 (p-90) REVERT: A 848 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7531 (OUTLIER) REVERT: A 950 ASP cc_start: 0.7436 (t70) cc_final: 0.7183 (t70) REVERT: C 124 ARG cc_start: 0.6911 (ptp-110) cc_final: 0.6543 (ttp-110) REVERT: C 154 ASN cc_start: 0.7060 (t0) cc_final: 0.6701 (t0) REVERT: C 426 TYR cc_start: 0.7857 (m-80) cc_final: 0.7507 (m-10) REVERT: C 436 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.6849 (m-80) REVERT: C 609 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7418 (mtt90) outliers start: 75 outliers final: 43 residues processed: 259 average time/residue: 1.0281 time to fit residues: 317.2115 Evaluate side-chains 235 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 188 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 609 ARG Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 848 ASP Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 939 ASP Chi-restraints excluded: chain C residue 975 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 163 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN C 34 HIS C 104 ASN C 337 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 23967 Z= 0.193 Angle : 0.564 11.511 32625 Z= 0.296 Chirality : 0.044 0.301 3807 Planarity : 0.004 0.053 4122 Dihedral : 6.564 59.863 4398 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.40 % Allowed : 11.06 % Favored : 86.54 % 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: 1.24 (0.22), residues: 600 sheet: -0.67 (0.23), residues: 507 loop : -1.49 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.003 0.001 HIS A 552 PHE 0.016 0.001 PHE C 494 TYR 0.016 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 271 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 211 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 ARG cc_start: 0.6745 (ptp90) cc_final: 0.6124 (ttp-110) REVERT: B 185 LEU cc_start: 0.8278 (tm) cc_final: 0.7824 (mp) REVERT: B 252 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6601 (p0) REVERT: B 420 THR cc_start: 0.8833 (t) cc_final: 0.8572 (t) REVERT: B 712 HIS cc_start: 0.8028 (m90) cc_final: 0.7676 (m90) REVERT: A 20 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7325 (mp0) REVERT: A 185 LEU cc_start: 0.8492 (tp) cc_final: 0.7906 (mp) REVERT: A 281 GLU cc_start: 0.6752 (mp0) cc_final: 0.6457 (mp0) REVERT: A 386 TRP cc_start: 0.6555 (p-90) cc_final: 0.6270 (p-90) REVERT: A 420 THR cc_start: 0.8853 (t) cc_final: 0.8597 (t) REVERT: A 848 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7449 (OUTLIER) REVERT: A 915 MET cc_start: 0.8686 (ttm) cc_final: 0.8414 (tpp) REVERT: C 20 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7575 (mp0) REVERT: C 301 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7771 (m-40) REVERT: C 303 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7711 (mt) REVERT: C 426 TYR cc_start: 0.7851 (m-80) cc_final: 0.7494 (m-10) REVERT: C 436 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: C 609 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7731 (mtp85) outliers start: 60 outliers final: 41 residues processed: 255 average time/residue: 1.1016 time to fit residues: 333.5165 Evaluate side-chains 234 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 188 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 609 ARG Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 848 ASP Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 939 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 277 optimal weight: 0.0970 chunk 173 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 B 615 GLN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN A 328 ASN C 34 HIS C 104 ASN C 337 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 23967 Z= 0.322 Angle : 0.628 9.903 32625 Z= 0.326 Chirality : 0.046 0.298 3807 Planarity : 0.004 0.056 4122 Dihedral : 6.533 59.932 4398 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.56 % Allowed : 11.46 % Favored : 85.98 % 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: -1.12 (0.16), residues: 2871 helix: 1.15 (0.22), residues: 603 sheet: -0.73 (0.22), residues: 561 loop : -1.51 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 129 HIS 0.005 0.001 HIS A 34 PHE 0.020 0.002 PHE B 432 TYR 0.021 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 263 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 199 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 ARG cc_start: 0.6977 (ptp90) cc_final: 0.6482 (ttp-110) REVERT: B 420 THR cc_start: 0.8872 (t) cc_final: 0.8620 (t) REVERT: B 712 HIS cc_start: 0.8057 (m90) cc_final: 0.7710 (m90) REVERT: A 185 LEU cc_start: 0.8541 (tp) cc_final: 0.7921 (mp) REVERT: A 281 GLU cc_start: 0.6830 (mp0) cc_final: 0.6520 (mp0) REVERT: A 420 THR cc_start: 0.8887 (t) cc_final: 0.8610 (t) REVERT: A 915 MET cc_start: 0.8721 (ttm) cc_final: 0.8376 (tpp) REVERT: C 20 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7572 (mp0) REVERT: C 124 ARG cc_start: 0.6995 (ptp-110) cc_final: 0.6485 (ttm-80) REVERT: C 426 TYR cc_start: 0.7853 (m-80) cc_final: 0.7494 (m-10) REVERT: C 436 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: C 609 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7781 (mtp180) outliers start: 64 outliers final: 45 residues processed: 250 average time/residue: 1.0877 time to fit residues: 322.3035 Evaluate side-chains 236 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 189 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 609 ARG Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 848 ASP Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 939 ASP 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: 0.0370 chunk 83 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 218 optimal weight: 10.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 B 104 ASN B 337 ASN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS C 328 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 23967 Z= 0.154 Angle : 0.532 9.817 32625 Z= 0.279 Chirality : 0.043 0.293 3807 Planarity : 0.004 0.050 4122 Dihedral : 5.978 58.777 4398 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.08 % Allowed : 11.98 % 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: -0.75 (0.16), residues: 2871 helix: 1.78 (0.22), residues: 594 sheet: -0.56 (0.23), residues: 513 loop : -1.34 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 129 HIS 0.003 0.001 HIS A 34 PHE 0.019 0.001 PHE C 494 TYR 0.016 0.001 TYR B 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 257 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 205 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 ARG cc_start: 0.6698 (ptp90) cc_final: 0.6158 (ttp-110) REVERT: B 185 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7816 (mp) REVERT: B 420 THR cc_start: 0.8826 (t) cc_final: 0.8619 (t) REVERT: B 712 HIS cc_start: 0.8029 (m90) cc_final: 0.7669 (m90) REVERT: A 20 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7380 (mp0) REVERT: A 185 LEU cc_start: 0.8510 (tp) cc_final: 0.7871 (mp) REVERT: A 420 THR cc_start: 0.8829 (t) cc_final: 0.8582 (t) REVERT: A 915 MET cc_start: 0.8627 (ttm) cc_final: 0.8356 (tpp) REVERT: C 20 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7525 (mp0) REVERT: C 124 ARG cc_start: 0.6797 (ptp-110) cc_final: 0.6377 (ttp-110) REVERT: C 436 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.6804 (m-80) outliers start: 52 outliers final: 35 residues processed: 244 average time/residue: 1.0618 time to fit residues: 310.4496 Evaluate side-chains 235 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 939 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.7980 chunk 265 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 203 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 104 ASN B 337 ASN B 615 GLN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN C 34 HIS ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 23967 Z= 0.219 Angle : 0.563 9.789 32625 Z= 0.294 Chirality : 0.044 0.290 3807 Planarity : 0.004 0.050 4122 Dihedral : 5.871 57.722 4398 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.12 % Allowed : 12.14 % Favored : 85.74 % 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: -0.73 (0.16), residues: 2871 helix: 1.73 (0.22), residues: 594 sheet: -0.58 (0.22), residues: 561 loop : -1.31 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 129 HIS 0.003 0.001 HIS C 34 PHE 0.017 0.001 PHE B 211 TYR 0.017 0.001 TYR B 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 257 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 204 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 ARG cc_start: 0.6724 (ptp90) cc_final: 0.6166 (ttp-110) REVERT: B 185 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7808 (mp) REVERT: B 296 ARG cc_start: 0.6256 (mtt90) cc_final: 0.5739 (mtm-85) REVERT: A 20 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7308 (mp0) REVERT: A 185 LEU cc_start: 0.8497 (tp) cc_final: 0.7875 (mp) REVERT: A 420 THR cc_start: 0.8856 (t) cc_final: 0.8613 (t) REVERT: A 915 MET cc_start: 0.8686 (ttm) cc_final: 0.8396 (tpp) REVERT: C 20 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7521 (mp0) REVERT: C 124 ARG cc_start: 0.6956 (ptp-110) cc_final: 0.6643 (ttm-80) REVERT: C 436 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.6838 (m-80) outliers start: 53 outliers final: 40 residues processed: 242 average time/residue: 1.0411 time to fit residues: 299.5782 Evaluate side-chains 239 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 848 ASP Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 939 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.7980 chunk 273 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 286 optimal weight: 0.3980 chunk 264 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 337 ASN B 615 GLN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN C 34 HIS C 864 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 23967 Z= 0.199 Angle : 0.547 9.791 32625 Z= 0.286 Chirality : 0.043 0.291 3807 Planarity : 0.004 0.050 4122 Dihedral : 5.698 57.484 4398 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.96 % Allowed : 12.54 % 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: -0.66 (0.16), residues: 2871 helix: 1.82 (0.22), residues: 594 sheet: -0.58 (0.22), residues: 522 loop : -1.25 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 129 HIS 0.003 0.001 HIS C 712 PHE 0.017 0.001 PHE C 494 TYR 0.017 0.001 TYR B 636 ARG 0.005 0.000 ARG A 249 ********************** 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 259 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 210 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 ARG cc_start: 0.6680 (ptp90) cc_final: 0.6143 (ttp-110) REVERT: B 185 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7808 (mp) REVERT: B 296 ARG cc_start: 0.6212 (mtt90) cc_final: 0.5745 (mtm-85) REVERT: B 712 HIS cc_start: 0.8043 (m90) cc_final: 0.7694 (m90) REVERT: A 20 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7291 (mp0) REVERT: A 185 LEU cc_start: 0.8502 (tp) cc_final: 0.7878 (mp) REVERT: A 276 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6932 (mtm) REVERT: A 420 THR cc_start: 0.8847 (t) cc_final: 0.8606 (t) REVERT: A 915 MET cc_start: 0.8690 (ttm) cc_final: 0.8341 (tpp) REVERT: C 436 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.6804 (m-80) outliers start: 49 outliers final: 39 residues processed: 245 average time/residue: 1.0830 time to fit residues: 315.6180 Evaluate side-chains 248 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 206 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 939 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 228 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 337 ASN B 472 ASN B 615 GLN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN A 864 ASN C 34 HIS C 925 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.104835 restraints weight = 28437.487| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.23 r_work: 0.2921 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 23967 Z= 0.535 Angle : 0.749 10.099 32625 Z= 0.387 Chirality : 0.052 0.305 3807 Planarity : 0.005 0.062 4122 Dihedral : 6.529 59.109 4398 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.36 % Allowed : 12.42 % Favored : 85.22 % 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: -1.28 (0.15), residues: 2871 helix: 0.84 (0.21), residues: 621 sheet: -0.75 (0.21), residues: 600 loop : -1.60 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 129 HIS 0.006 0.002 HIS A 918 PHE 0.028 0.003 PHE C 432 TYR 0.025 0.003 TYR C 636 ARG 0.008 0.001 ARG B 673 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6761.20 seconds wall clock time: 121 minutes 53.22 seconds (7313.22 seconds total)