Starting phenix.real_space_refine on Wed Feb 21 17:40:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h07_34410/02_2024/8h07_34410_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h07_34410/02_2024/8h07_34410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h07_34410/02_2024/8h07_34410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h07_34410/02_2024/8h07_34410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h07_34410/02_2024/8h07_34410_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h07_34410/02_2024/8h07_34410_neut.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.065 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 131 5.16 5 C 19807 2.51 5 N 5330 2.21 5 O 6052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "O TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 105": not complete - not flipped Residue "G ARG 19": "NH1" <-> "NH2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 36": "NH1" <-> "NH2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 105": not complete - not flipped Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 31": "NH1" <-> "NH2" Residue "M ARG 36": "NH1" <-> "NH2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M ARG 69": "NH1" <-> "NH2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "Q ARG 67": "NH1" <-> "NH2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 105": not complete - not flipped Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31320 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 939, 7115 Classifications: {'peptide': 939} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 51, 'TRANS': 887} Chain breaks: 12 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7139 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 51, 'TRANS': 896} Chain breaks: 10 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 7, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 161 Chain: "C" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7188 Classifications: {'peptide': 947} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 52, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "E" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 837 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 739 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "O" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 772 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 847 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 741 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "I" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "K" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 772 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "M" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 838 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 743 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "Q" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 772 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 16.33, per 1000 atoms: 0.52 Number of scatterers: 31320 At special positions: 0 Unit cell: (161.02, 172.66, 218.25, 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 131 16.00 O 6052 8.00 N 5330 7.00 C 19807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.11 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=1.65 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.12 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=1.65 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.27 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.65 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.06 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.06 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 93 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.06 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 NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG B1301 " - " ASN B 343 " " NAG C1301 " - " ASN C 343 " Time building additional restraints: 13.34 Conformation dependent library (CDL) restraints added in 5.5 seconds 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7722 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 76 sheets defined 17.3% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.574A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.824A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.996A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.599A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 removed outlier: 4.150A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.529A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.940A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.666A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.613A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.557A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 988 through 1033 removed outlier: 3.723A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.575A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.824A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.996A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.535A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 4.347A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.581A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.550A pdb=" N THR B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.345A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.510A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.525A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.710A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.873A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.575A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.824A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.996A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 758 through 779 removed outlier: 3.588A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.617A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.737A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.789A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.705A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.701A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1022 removed outlier: 3.531A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.636A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.784A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 96 removed outlier: 3.919A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.810A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.213A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.657A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.666A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.527A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.984A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.512A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.890A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1098 removed outlier: 4.273A pdb=" N HIS A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.898A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.943A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 117 through 118 removed outlier: 3.798A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.982A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 326 through 327 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.658A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.666A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 566 through 567 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.567A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.774A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.550A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD3, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 removed outlier: 4.147A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.013A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.972A pdb=" N PHE C 106 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.961A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.658A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.665A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.826A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.347A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.547A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AE6, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL E 94 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N MET E 32 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL E 48 " --> pdb=" O MET E 32 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AF2, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AF3, first strand: chain 'J' and resid 45 through 48 removed outlier: 5.800A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain 'N' and resid 19 through 22 Processing sheet with id=AF6, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.144A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN N 39 " --> pdb=" O LEU N 93 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.571A pdb=" N PHE O 71 " --> pdb=" O CYS O 23 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER O 67 " --> pdb=" O ASP O 70 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG O 63 " --> pdb=" O THR O 74 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'O' and resid 53 through 54 removed outlier: 6.238A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL G 94 " --> pdb=" O SER G 33 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N MET G 32 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL G 48 " --> pdb=" O MET G 32 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP G 34 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AG4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AG5, first strand: chain 'H' and resid 45 through 48 removed outlier: 5.800A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AG8, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.144A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN I 39 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.571A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG K 63 " --> pdb=" O THR K 74 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AH2, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.238A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL M 94 " --> pdb=" O SER M 33 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N MET M 32 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL M 48 " --> pdb=" O MET M 32 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP M 34 " --> pdb=" O VAL M 46 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AH6, first strand: chain 'P' and resid 10 through 12 Processing sheet with id=AH7, first strand: chain 'P' and resid 45 through 48 removed outlier: 5.800A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 11 through 12 Processing sheet with id=AH9, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=AI1, first strand: chain 'Q' and resid 58 through 60 removed outlier: 5.144A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN Q 39 " --> pdb=" O LEU Q 93 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 4 through 6 removed outlier: 3.572A pdb=" N PHE R 71 " --> pdb=" O CYS R 23 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER R 67 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG R 63 " --> pdb=" O THR R 74 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AI4, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.239A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) 1061 hydrogen bonds defined for protein. 2865 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: 13.37 Time building geometry restraints manager: 14.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5182 1.31 - 1.44: 8969 1.44 - 1.57: 17716 1.57 - 1.70: 0 1.70 - 1.83: 162 Bond restraints: 32029 Sorted by residual: bond pdb=" CA SER B 438 " pdb=" CB SER B 438 " ideal model delta sigma weight residual 1.527 1.462 0.065 7.60e-03 1.73e+04 7.32e+01 bond pdb=" CA SER C 438 " pdb=" CB SER C 438 " ideal model delta sigma weight residual 1.527 1.462 0.065 7.60e-03 1.73e+04 7.32e+01 bond pdb=" CA SER A 438 " pdb=" CB SER A 438 " ideal model delta sigma weight residual 1.527 1.462 0.065 7.60e-03 1.73e+04 7.30e+01 bond pdb=" C VAL A 62 " pdb=" N THR A 63 " ideal model delta sigma weight residual 1.331 1.428 -0.098 1.31e-02 5.83e+03 5.57e+01 bond pdb=" CA SER B 673 " pdb=" CB SER B 673 " ideal model delta sigma weight residual 1.538 1.456 0.082 1.22e-02 6.72e+03 4.55e+01 ... (remaining 32024 not shown) Histogram of bond angle deviations from ideal: 81.00 - 91.69: 1 91.69 - 102.39: 263 102.39 - 113.08: 16133 113.08 - 123.77: 23531 123.77 - 134.46: 3697 Bond angle restraints: 43625 Sorted by residual: angle pdb=" C THR C1077 " pdb=" CA THR C1077 " pdb=" CB THR C1077 " ideal model delta sigma weight residual 109.56 81.00 28.56 2.22e+00 2.03e-01 1.65e+02 angle pdb=" C CYS B1082 " pdb=" CA CYS B1082 " pdb=" CB CYS B1082 " ideal model delta sigma weight residual 109.90 95.05 14.85 1.56e+00 4.11e-01 9.06e+01 angle pdb=" N LYS A 814 " pdb=" CA LYS A 814 " pdb=" C LYS A 814 " ideal model delta sigma weight residual 113.02 102.57 10.45 1.20e+00 6.94e-01 7.59e+01 angle pdb=" N PRO B 812 " pdb=" CA PRO B 812 " pdb=" C PRO B 812 " ideal model delta sigma weight residual 113.47 101.04 12.43 1.43e+00 4.89e-01 7.55e+01 angle pdb=" C LYS A 440 " pdb=" CA LYS A 440 " pdb=" CB LYS A 440 " ideal model delta sigma weight residual 110.79 96.81 13.98 1.68e+00 3.54e-01 6.92e+01 ... (remaining 43620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 18077 24.33 - 48.67: 785 48.67 - 73.00: 120 73.00 - 97.34: 7 97.34 - 121.67: 3 Dihedral angle restraints: 18992 sinusoidal: 6940 harmonic: 12052 Sorted by residual: dihedral pdb=" C TYR K 94 " pdb=" N TYR K 94 " pdb=" CA TYR K 94 " pdb=" CB TYR K 94 " ideal model delta harmonic sigma weight residual -122.60 -157.52 34.92 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" C TYR O 94 " pdb=" N TYR O 94 " pdb=" CA TYR O 94 " pdb=" CB TYR O 94 " ideal model delta harmonic sigma weight residual -122.60 -157.51 34.91 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" C TYR R 94 " pdb=" N TYR R 94 " pdb=" CA TYR R 94 " pdb=" CB TYR R 94 " ideal model delta harmonic sigma weight residual -122.60 -157.46 34.86 0 2.50e+00 1.60e-01 1.94e+02 ... (remaining 18989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 4770 0.289 - 0.577: 147 0.577 - 0.866: 1 0.866 - 1.154: 0 1.154 - 1.443: 3 Chirality restraints: 4921 Sorted by residual: chirality pdb=" CA TYR K 94 " pdb=" N TYR K 94 " pdb=" C TYR K 94 " pdb=" CB TYR K 94 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.20e+01 chirality pdb=" CA TYR O 94 " pdb=" N TYR O 94 " pdb=" C TYR O 94 " pdb=" CB TYR O 94 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.20e+01 chirality pdb=" CA TYR R 94 " pdb=" N TYR R 94 " pdb=" C TYR R 94 " pdb=" CB TYR R 94 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.18e+01 ... (remaining 4918 not shown) Planarity restraints: 5690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 478 " 0.072 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO C 479 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " -0.072 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO B 479 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 478 " 0.072 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO A 479 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.064 5.00e-02 4.00e+02 ... (remaining 5687 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4333 2.76 - 3.29: 29175 3.29 - 3.83: 46429 3.83 - 4.36: 62481 4.36 - 4.90: 101340 Nonbonded interactions: 243758 Sorted by model distance: nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASN B 122 " pdb=" O ASN B 125 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASN B 122 " pdb=" N ASN B 125 " model vdw 2.312 2.520 nonbonded pdb=" O THR B1077 " pdb=" OG1 THR B1077 " model vdw 2.339 2.440 nonbonded pdb=" N MET A 902 " pdb=" O MET A 902 " model vdw 2.348 2.496 ... (remaining 243753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 41 or (resid 42 through 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 51 or (res \ id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or r \ esid 65 or resid 89 through 95 or (resid 101 and (name N or name CA or name C or \ name O or name CB )) or resid 102 through 104 or (resid 105 and (name N or name \ CA or name C or name O or name CB )) or resid 106 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 130 o \ r resid 189 through 194 or (resid 195 and (name N or name CA or name C or name O \ or name CB )) or resid 196 through 207 or resid 216 through 226 or (resid 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 through 232 \ or (resid 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 through 238 and (name N or name CA or name C or n \ ame O or name CB )) or resid 239 through 241 or resid 264 through 303 or (resid \ 304 and (name N or name CA or name C or name O or name CB )) or resid 305 throug \ h 308 or (resid 309 through 310 and (name N or name CA or name C or name O or na \ me CB )) or resid 311 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 528 or (resid 529 through 530 and \ (name N or name CA or name C or name O or name CB )) or resid 531 through 538 or \ (resid 539 and (name N or name CA or name C or name O or name CB )) or resid 54 \ 0 through 548 or (resid 549 and (name N or name CA or name C or name O or name C \ B )) or resid 550 through 564 or (resid 565 and (name N or name CA or name C or \ name O or name CB )) or resid 566 through 573 or (resid 574 through 575 and (nam \ e N or name CA or name C or name O or name CB )) or resid 576 through 577 or (re \ sid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 or \ (resid 580 through 581 and (name N or name CA or name C or name O or name CB )) \ or resid 582 through 591 or (resid 592 and (name N or name CA or name C or name \ O or name CB )) or resid 593 through 607 or (resid 608 through 609 and (name N \ or name CA or name C or name O or name CB )) or resid 610 through 615 or (resid \ 616 and (name N or name CA or name C or name O or name CB )) or resid 617 throug \ h 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) or \ resid 620 through 643 or (resid 644 through 647 and (name N or name CA or name C \ or name O or name CB )) or resid 648 through 659 or (resid 660 and (name N or n \ ame CA or name C or name O or name CB )) or resid 661 through 662 or (resid 663 \ and (name N or name CA or name C or name O or name CB )) or resid 664 through 66 \ 5 or (resid 666 and (name N or name CA or name C or name O or name CB )) or (res \ id 667 through 670 and (name N or name CA or name C or name O or name CB )) or r \ esid 671 through 675 or resid 691 through 704 or (resid 705 through 707 and (nam \ e N or name CA or name C or name O or name CB )) or resid 708 through 710 or (re \ sid 711 through 714 and (name N or name CA or name C or name O or name CB )) or \ resid 715 through 721 or (resid 722 and (name N or name CA or name C or name O o \ r name CB )) or resid 723 through 750 or (resid 751 and (name N or name CA or na \ me C or name O or name CB )) or resid 752 through 779 or (resid 780 and (name N \ or name CA or name C or name O or name CB )) or resid 781 through 785 or (resid \ 786 and (name N or name CA or name C or name O or name CB )) or resid 787 throug \ h 789 or (resid 790 and (name N or name CA or name C or name O or name CB )) or \ resid 791 through 804 or (resid 805 and (name N or name CA or name C or name O o \ r name CB )) or resid 806 through 807 or (resid 808 and (name N or name CA or na \ me C or name O or name CB )) or resid 809 through 810 or (resid 811 and (name N \ or name CA or name C or name O or name CB )) or resid 812 through 825 or (resid \ 826 through 855 and (name N or name CA or name C or name O or name CB )) or resi \ d 856 through 857 or (resid 858 and (name N or name CA or name C or name O or na \ me CB )) or resid 859 through 882 or (resid 883 and (name N or name CA or name C \ or name O or name CB )) or resid 884 through 903 or (resid 904 and (name N or n \ ame CA or name C or name O or name CB )) or resid 905 through 914 or (resid 915 \ through 917 and (name N or name CA or name C or name O or name CB )) or resid 91 \ 8 through 933 or (resid 934 through 935 and (name N or name CA or name C or name \ O or name CB )) or resid 936 through 937 or (resid 938 and (name N or name CA o \ r name C or name O or name CB )) or resid 939 through 968 or (resid 969 and (nam \ e N or name CA or name C or name O or name CB )) or resid 970 through 972 or (re \ sid 973 and (name N or name CA or name C or name O or name CB )) or resid 974 th \ rough 983 or (resid 984 and (name N or name CA or name C or name O or name CB )) \ or resid 985 through 995 or (resid 996 through 997 and (name N or name CA or na \ me C or name O or name CB )) or resid 998 through 1003 or (resid 1004 and (name \ N or name CA or name C or name O or name CB )) or resid 1005 through 1064 or (re \ sid 1065 and (name N or name CA or name C or name O or name CB )) or resid 1066 \ through 1071 or (resid 1072 and (name N or name CA or name C or name O or name C \ B )) or resid 1073 through 1074 or (resid 1075 and (name N or name CA or name C \ or name O or name CB )) or resid 1076 through 1103 or (resid 1104 and (name N or \ name CA or name C or name O or name CB )) or resid 1105 or (resid 1106 through \ 1107 and (name N or name CA or name C or name O or name CB )) or resid 1108 thro \ ugh 1118 or (resid 1119 through 1122 and (name N or name CA or name C or name O \ or name CB )) or resid 1123 through 1131 or (resid 1132 and (name N or name CA o \ r name C or name O or name CB )) or resid 1133 through 1136 or (resid 1137 and ( \ name N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'B' and (resid 27 through 41 or (resid 42 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 51 or (resid 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 53 through 95 or (res \ id 101 and (name N or name CA or name C or name O or name CB )) or resid 102 thr \ ough 103 or (resid 104 through 105 and (name N or name CA or name C or name O or \ name CB )) or resid 106 through 107 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 or (resid 119 and (name N or name CA or \ name C or name O or name CB )) or resid 120 or resid 126 through 129 or (resid \ 130 and (name N or name CA or name C or name O or name CB )) or resid 189 throug \ h 196 or (resid 201 and (name N or name CA or name C or name O or name CB )) or \ resid 202 through 205 or (resid 206 and (name N or name CA or name C or name O o \ r name CB )) or resid 207 or resid 216 through 226 or (resid 227 and (name N or \ name CA or name C or name O or name CB )) or resid 228 or (resid 229 and (name N \ or name CA or name C or name O or name CB )) or resid 230 or (resid 231 and (na \ me N or name CA or name C or name O or name CB )) or resid 232 through 234 or (r \ esid 235 through 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 240 or (resid 241 through 264 and (name N or name CA or name \ C or name O or name CB )) or resid 265 through 266 or (resid 267 and (name N or \ name CA or name C or name O or name CB )) or resid 268 through 318 or (resid 319 \ and (name N or name CA or name C or name O or name CB )) or resid 320 through 3 \ 31 or (resid 332 and (name N or name CA or name C or name O or name CB )) or res \ id 333 through 528 or (resid 529 through 530 and (name N or name CA or name C or \ name O or name CB )) or resid 531 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 538 or (resid 539 and \ (name N or name CA or name C or name O or name CB )) or resid 540 through 543 o \ r (resid 544 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 45 through 559 or (resid 560 and (name N or name CA or name C or name O or name \ CB )) or resid 561 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 583 or (resid 584 and (name N or name \ CA or name C or name O or name CB )) or resid 585 through 586 or (resid 587 and \ (name N or name CA or name C or name O or name CB )) or resid 588 through 598 o \ r (resid 599 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 00 through 645 or (resid 646 through 647 and (name N or name CA or name C or nam \ e O or name CB )) or resid 648 through 665 or (resid 666 and (name N or name CA \ or name C or name O or name CB )) or resid 667 through 675 or resid 691 through \ 706 or (resid 707 and (name N or name CA or name C or name O or name CB )) or re \ sid 708 through 713 or (resid 714 and (name N or name CA or name C or name O or \ name CB )) or resid 715 through 721 or (resid 722 and (name N or name CA or name \ C or name O or name CB )) or resid 723 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 779 or (resid 78 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 781 through \ 785 or (resid 786 and (name N or name CA or name C or name O or name CB )) or re \ sid 787 through 803 or (resid 804 through 805 and (name N or name CA or name C o \ r name O or name CB )) or resid 806 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 812 through 813 or (resid 814 an \ d (name N or name CA or name C or name O or name CB )) or resid 815 or (resid 81 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 817 through \ 826 or (resid 855 and (name N or name CA or name C or name O or name CB )) or re \ sid 856 through 857 or (resid 858 and (name N or name CA or name C or name O or \ name CB )) or resid 859 through 894 or (resid 895 and (name N or name CA or name \ C or name O or name CB )) or resid 896 through 901 or (resid 902 through 904 an \ d (name N or name CA or name C or name O or name CB )) or resid 905 through 911 \ or (resid 912 and (name N or name CA or name C or name O or name CB )) or resid \ 913 through 914 or (resid 915 through 917 and (name N or name CA or name C or na \ me O or name CB )) or resid 918 through 933 or (resid 934 through 935 and (name \ N or name CA or name C or name O or name CB )) or resid 936 through 944 or (resi \ d 945 and (name N or name CA or name C or name O or name CB )) or resid 946 thro \ ugh 968 or (resid 969 and (name N or name CA or name C or name O or name CB )) o \ r resid 970 through 972 or (resid 973 and (name N or name CA or name C or name O \ or name CB )) or resid 974 through 983 or (resid 984 and (name N or name CA or \ name C or name O or name CB )) or resid 985 through 986 or resid 988 through 996 \ or (resid 997 and (name N or name CA or name C or name O or name CB )) or resid \ 998 through 1028 or (resid 1029 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1030 through 1033 or (resid 1034 and (name N or name CA or na \ me C or name O or name CB )) or resid 1035 through 1076 or (resid 1077 through 1 \ 078 and (name N or name CA or name C or name O or name CB )) or resid 1079 throu \ gh 1095 or (resid 1096 and (name N or name CA or name C or name O or name CB )) \ or resid 1097 through 1118 or (resid 1119 through 1122 and (name N or name CA or \ name C or name O or name CB )) or resid 1123 through 1136 or (resid 1137 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'C' and (resid 27 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 63 or (resid 64 and (name N or nam \ e CA or name C or name O or name CB )) or resid 65 or resid 89 or (resid 90 and \ (name N or name CA or name C or name O or name CB )) or resid 91 through 103 or \ (resid 104 through 105 and (name N or name CA or name C or name O or name CB )) \ or resid 106 through 107 or resid 117 through 120 or resid 126 through 127 or (r \ esid 128 and (name N or name CA or name C or name O or name CB )) or resid 129 o \ r (resid 130 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 89 through 194 or (resid 195 and (name N or name CA or name C or name O or name \ CB )) or resid 196 or (resid 201 and (name N or name CA or name C or name O or n \ ame CB )) or resid 202 through 205 or (resid 206 and (name N or name CA or name \ C or name O or name CB )) or resid 207 through 230 or (resid 231 and (name N or \ name CA or name C or name O or name CB )) or resid 232 through 236 or (resid 237 \ through 238 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 39 through 241 or resid 263 or resid 265 through 266 or (resid 267 and (name N o \ r name CA or name C or name O or name CB )) or resid 268 through 303 or (resid 3 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 305 through \ 308 or (resid 309 through 310 and (name N or name CA or name C or name O or nam \ e CB )) or resid 311 through 529 or (resid 530 and (name N or name CA or name C \ or name O or name CB )) or resid 531 through 533 or (resid 534 and (name N or na \ me CA or name C or name O or name CB )) or resid 535 through 548 or (resid 549 a \ nd (name N or name CA or name C or name O or name CB )) or resid 550 through 559 \ or (resid 560 and (name N or name CA or name C or name O or name CB )) or resid \ 561 through 564 or (resid 565 and (name N or name CA or name C or name O or nam \ e CB )) or resid 566 through 567 or (resid 568 and (name N or name CA or name C \ or name O or name CB )) or resid 569 through 573 or (resid 574 through 575 and ( \ name N or name CA or name C or name O or name CB )) or resid 576 through 577 or \ (resid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 \ or (resid 580 through 581 and (name N or name CA or name C or name O or name CB \ )) or resid 582 through 586 or (resid 587 and (name N or name CA or name C or n \ ame O or name CB )) or resid 588 through 591 or (resid 592 and (name N or name C \ A or name C or name O or name CB )) or resid 593 through 598 or (resid 599 and ( \ name N or name CA or name C or name O or name CB )) or resid 600 through 607 or \ (resid 608 through 609 and (name N or name CA or name C or name O or name CB )) \ or resid 610 through 615 or (resid 616 and (name N or name CA or name C or name \ O or name CB )) or resid 617 through 618 or (resid 619 and (name N or name CA or \ name C or name O or name CB )) or resid 620 through 643 or (resid 644 through 6 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 648 through \ 659 or (resid 660 and (name N or name CA or name C or name O or name CB )) or r \ esid 661 through 662 or (resid 663 and (name N or name CA or name C or name O or \ name CB )) or resid 664 through 669 or (resid 670 and (name N or name CA or nam \ e C or name O or name CB )) or resid 671 through 704 or (resid 705 through 707 a \ nd (name N or name CA or name C or name O or name CB )) or resid 708 through 710 \ or (resid 711 through 714 and (name N or name CA or name C or name O or name CB \ )) or resid 715 through 725 or (resid 726 and (name N or name CA or name C or n \ ame O or name CB )) or resid 727 through 750 or (resid 751 and (name N or name C \ A or name C or name O or name CB )) or resid 752 through 754 or (resid 755 and ( \ name N or name CA or name C or name O or name CB )) or resid 756 through 789 or \ (resid 790 and (name N or name CA or name C or name O or name CB )) or resid 791 \ through 803 or (resid 804 through 805 and (name N or name CA or name C or name \ O or name CB )) or resid 806 through 807 or (resid 808 and (name N or name CA or \ name C or name O or name CB )) or resid 809 through 815 or (resid 816 and (name \ N or name CA or name C or name O or name CB )) or resid 817 through 825 or (res \ id 826 through 855 and (name N or name CA or name C or name O or name CB )) or r \ esid 856 through 882 or (resid 883 and (name N or name CA or name C or name O or \ name CB )) or resid 884 through 893 or (resid 894 through 895 and (name N or na \ me CA or name C or name O or name CB )) or resid 896 through 901 or (resid 902 t \ hrough 904 and (name N or name CA or name C or name O or name CB )) or resid 905 \ through 908 or (resid 909 and (name N or name CA or name C or name O or name CB \ )) or resid 910 through 911 or (resid 912 and (name N or name CA or name C or n \ ame O or name CB )) or resid 913 through 915 or (resid 916 through 917 and (name \ N or name CA or name C or name O or name CB )) or resid 918 through 937 or (res \ id 938 and (name N or name CA or name C or name O or name CB )) or resid 939 thr \ ough 944 or (resid 945 and (name N or name CA or name C or name O or name CB )) \ or resid 946 through 986 or resid 988 through 995 or (resid 996 through 997 and \ (name N or name CA or name C or name O or name CB )) or resid 998 through 1003 o \ r (resid 1004 and (name N or name CA or name C or name O or name CB )) or resid \ 1005 through 1049 or (resid 1050 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1051 through 1064 or (resid 1065 and (name N or name CA or na \ me C or name O or name CB )) or resid 1066 through 1074 or (resid 1075 and (name \ N or name CA or name C or name O or name CB )) or resid 1076 or (resid 1077 thr \ ough 1078 and (name N or name CA or name C or name O or name CB )) or resid 1079 \ through 1095 or (resid 1096 and (name N or name CA or name C or name O or name \ CB )) or resid 1097 through 1105 or (resid 1106 through 1107 and (name N or name \ CA or name C or name O or name CB )) or resid 1108 through 1119 or (resid 1120 \ through 1122 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 123 through 1137 or resid 1301)) } ncs_group { reference = (chain 'E' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 117)) selection = (chain 'G' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 45 or (resid 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 60 or (resid 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 63 or (re \ sid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thro \ ugh 117)) selection = (chain 'M' and (resid 2 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 117)) } ncs_group { reference = (chain 'H' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 107)) selection = (chain 'J' and (resid 1 through 68 or (resid 69 and (name N or name CA or name C \ or name O or name CB )) or resid 70 through 107)) selection = (chain 'P' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 68 or (resid 69 and (name \ N or name CA or name C or name O or name CB )) or resid 70 through 107)) } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'R' } 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: 2.540 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: 10.300 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 82.650 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.230 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:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 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 : 0.013 0.106 32029 Z= 0.876 Angle : 1.931 28.559 43625 Z= 1.414 Chirality : 0.141 1.443 4921 Planarity : 0.007 0.120 5687 Dihedral : 13.356 121.674 11138 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.54 % Favored : 93.80 % Rotamer: Outliers : 1.16 % Allowed : 12.35 % Favored : 86.48 % Cbeta Deviations : 2.10 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 4094 helix: 1.61 (0.19), residues: 583 sheet: 0.10 (0.15), residues: 1189 loop : -0.86 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP N 103 HIS 0.013 0.003 HIS B1064 PHE 0.037 0.003 PHE C1121 TYR 0.045 0.003 TYR C 265 ARG 0.008 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 329 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 GLN cc_start: 0.6187 (tm-30) cc_final: 0.5957 (tm-30) REVERT: B 740 MET cc_start: 0.7281 (ttt) cc_final: 0.7048 (ttt) REVERT: C 675 GLN cc_start: 0.6072 (tm130) cc_final: 0.5852 (tp40) REVERT: C 869 MET cc_start: 0.8091 (mtt) cc_final: 0.7800 (mtt) REVERT: N 105 TRP cc_start: 0.1065 (OUTLIER) cc_final: -0.0193 (t60) REVERT: H 4 MET cc_start: 0.0169 (mtp) cc_final: -0.0200 (tmt) REVERT: M 32 MET cc_start: -0.0406 (mmm) cc_final: -0.0739 (tmm) outliers start: 38 outliers final: 10 residues processed: 362 average time/residue: 1.0482 time to fit residues: 471.0490 Evaluate side-chains 216 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 205 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain N residue 105 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 40.0000 chunk 310 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 209 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 321 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 372 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 405 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 580 GLN A 613 GLN A 616 ASN A 709 ASN A 955 ASN A 965 GLN A1058 HIS A1135 ASN B 321 GLN B 405 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 544 ASN B 606 ASN B 762 GLN B1074 ASN B1113 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 613 GLN C 779 GLN C 895 GLN C1108 ASN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN J 92 HIS N 33 HIS N 35 HIS O 6 GLN G 54 ASN H 92 HIS ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 38 GLN M 54 ASN P 92 HIS Q 35 HIS R 6 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32029 Z= 0.279 Angle : 0.701 9.330 43625 Z= 0.380 Chirality : 0.048 0.253 4921 Planarity : 0.005 0.056 5687 Dihedral : 6.060 66.415 4556 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.84 % Favored : 95.11 % Rotamer: Outliers : 3.03 % Allowed : 14.53 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4094 helix: 1.18 (0.21), residues: 601 sheet: -0.18 (0.15), residues: 1217 loop : -1.07 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.009 0.002 HIS N 104 PHE 0.034 0.002 PHE B 541 TYR 0.028 0.002 TYR C 265 ARG 0.008 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 224 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 820 ASP cc_start: 0.6115 (OUTLIER) cc_final: 0.5860 (p0) REVERT: B 1038 LYS cc_start: 0.7228 (mmtt) cc_final: 0.6899 (mmtt) REVERT: C 909 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6289 (pp) REVERT: N 105 TRP cc_start: 0.1632 (OUTLIER) cc_final: -0.0050 (t60) REVERT: H 4 MET cc_start: -0.0404 (mtp) cc_final: -0.0617 (tmt) REVERT: M 32 MET cc_start: -0.0096 (mmm) cc_final: -0.0601 (tmm) outliers start: 99 outliers final: 38 residues processed: 303 average time/residue: 0.9924 time to fit residues: 380.7626 Evaluate side-chains 224 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain N residue 105 TRP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain M residue 102 ASP Chi-restraints excluded: chain R residue 28 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 206 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 309 optimal weight: 50.0000 chunk 253 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 372 optimal weight: 40.0000 chunk 402 optimal weight: 10.0000 chunk 332 optimal weight: 5.9990 chunk 369 optimal weight: 6.9990 chunk 127 optimal weight: 0.0770 chunk 299 optimal weight: 10.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 388 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 901 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 613 GLN B 762 GLN B 978 ASN B1088 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN R 53 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32029 Z= 0.357 Angle : 0.694 10.792 43625 Z= 0.371 Chirality : 0.049 0.221 4921 Planarity : 0.005 0.059 5687 Dihedral : 5.757 55.997 4548 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 4.08 % Allowed : 16.43 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 4094 helix: 0.46 (0.20), residues: 616 sheet: -0.37 (0.15), residues: 1219 loop : -1.16 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.008 0.002 HIS A1048 PHE 0.027 0.002 PHE C 541 TYR 0.028 0.002 TYR C 265 ARG 0.006 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 181 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1038 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6736 (mttm) REVERT: B 1010 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: B 1111 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.6869 (tp30) REVERT: C 909 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6260 (pp) REVERT: G 32 MET cc_start: 0.1410 (mmt) cc_final: 0.0348 (ptm) REVERT: M 32 MET cc_start: -0.0652 (mmm) cc_final: -0.1085 (tmm) outliers start: 133 outliers final: 66 residues processed: 294 average time/residue: 0.9247 time to fit residues: 351.6331 Evaluate side-chains 238 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 168 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1057 PRO Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain N residue 105 TRP Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain K residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 368 optimal weight: 9.9990 chunk 280 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 374 optimal weight: 50.0000 chunk 396 optimal weight: 0.0370 chunk 195 optimal weight: 5.9990 chunk 354 optimal weight: 40.0000 chunk 106 optimal weight: 8.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 978 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 762 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32029 Z= 0.238 Angle : 0.619 11.021 43625 Z= 0.324 Chirality : 0.045 0.181 4921 Planarity : 0.005 0.058 5687 Dihedral : 5.399 56.006 4548 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.13 % Favored : 94.85 % Rotamer: Outliers : 3.46 % Allowed : 17.84 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4094 helix: 0.74 (0.21), residues: 623 sheet: -0.42 (0.15), residues: 1224 loop : -1.18 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.005 0.001 HIS C1048 PHE 0.020 0.002 PHE B 541 TYR 0.021 0.001 TYR C 265 ARG 0.005 0.000 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 176 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1038 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6302 (mttm) REVERT: B 745 ASP cc_start: 0.3975 (OUTLIER) cc_final: 0.3560 (m-30) REVERT: C 567 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7085 (mpp80) REVERT: C 675 GLN cc_start: 0.5924 (OUTLIER) cc_final: 0.4698 (tm130) REVERT: C 740 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.6115 (ttt) REVERT: C 909 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6267 (pp) REVERT: G 32 MET cc_start: 0.1511 (mmt) cc_final: 0.0592 (ptm) REVERT: H 4 MET cc_start: 0.2937 (tmt) cc_final: 0.1050 (pp-130) REVERT: M 32 MET cc_start: -0.0834 (mmm) cc_final: -0.1165 (tmm) REVERT: P 4 MET cc_start: 0.2431 (tpt) cc_final: 0.1260 (ttt) outliers start: 113 outliers final: 63 residues processed: 266 average time/residue: 0.9129 time to fit residues: 314.9955 Evaluate side-chains 230 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 161 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 330 optimal weight: 50.0000 chunk 224 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 295 optimal weight: 8.9990 chunk 163 optimal weight: 0.4980 chunk 338 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 0.6980 chunk 355 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 978 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 32029 Z= 0.418 Angle : 0.699 10.819 43625 Z= 0.370 Chirality : 0.049 0.224 4921 Planarity : 0.005 0.073 5687 Dihedral : 5.618 55.014 4544 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.01 % Favored : 93.97 % Rotamer: Outliers : 4.41 % Allowed : 17.44 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4094 helix: 0.22 (0.20), residues: 622 sheet: -0.55 (0.15), residues: 1213 loop : -1.33 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 105 HIS 0.010 0.002 HIS A 207 PHE 0.030 0.002 PHE C1121 TYR 0.036 0.002 TYR C 265 ARG 0.010 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 167 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6136 (mt-10) REVERT: A 1038 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6831 (mttm) REVERT: B 206 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6966 (tptt) REVERT: B 740 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6768 (ttt) REVERT: B 745 ASP cc_start: 0.4286 (OUTLIER) cc_final: 0.3787 (m-30) REVERT: B 1111 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6824 (tp30) REVERT: C 675 GLN cc_start: 0.5941 (OUTLIER) cc_final: 0.4665 (tm130) REVERT: C 740 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.6213 (ttt) REVERT: C 909 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6375 (pp) REVERT: G 32 MET cc_start: 0.1230 (mmt) cc_final: 0.0577 (ptm) REVERT: G 112 MET cc_start: 0.4384 (mmm) cc_final: 0.3747 (mmt) REVERT: H 4 MET cc_start: 0.2844 (tmt) cc_final: 0.1199 (pp-130) REVERT: M 32 MET cc_start: -0.0527 (mmm) cc_final: -0.1188 (tmm) REVERT: P 4 MET cc_start: 0.2352 (tpt) cc_final: 0.1151 (ttt) outliers start: 144 outliers final: 87 residues processed: 284 average time/residue: 0.8688 time to fit residues: 321.6073 Evaluate side-chains 249 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 153 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1057 PRO Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 2.9990 chunk 356 optimal weight: 40.0000 chunk 78 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 396 optimal weight: 5.9990 chunk 329 optimal weight: 50.0000 chunk 183 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 208 optimal weight: 50.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 360 ASN B 762 GLN B 978 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1101 HIS ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 32029 Z= 0.530 Angle : 0.762 10.717 43625 Z= 0.406 Chirality : 0.052 0.249 4921 Planarity : 0.006 0.088 5687 Dihedral : 5.922 57.237 4544 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.57 % Favored : 93.40 % Rotamer: Outliers : 5.18 % Allowed : 17.68 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4094 helix: -0.35 (0.20), residues: 623 sheet: -0.66 (0.15), residues: 1217 loop : -1.53 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 36 HIS 0.011 0.002 HIS C1048 PHE 0.034 0.003 PHE C1121 TYR 0.036 0.002 TYR C 265 ARG 0.013 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 159 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1038 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6850 (mttm) REVERT: B 206 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6960 (tptt) REVERT: B 740 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6731 (ttt) REVERT: B 1111 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.6875 (tp30) REVERT: C 461 LEU cc_start: -0.1290 (OUTLIER) cc_final: -0.1859 (mm) REVERT: C 675 GLN cc_start: 0.6059 (OUTLIER) cc_final: 0.4648 (tm130) REVERT: C 726 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7963 (mp) REVERT: C 740 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.6242 (ttt) REVERT: C 909 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6305 (pp) REVERT: N 72 ARG cc_start: -0.0345 (OUTLIER) cc_final: -0.1127 (mmt180) REVERT: G 32 MET cc_start: 0.1197 (mmt) cc_final: 0.0527 (ptm) REVERT: H 4 MET cc_start: 0.2686 (OUTLIER) cc_final: 0.1202 (pp-130) REVERT: M 32 MET cc_start: -0.0481 (mmm) cc_final: -0.1269 (tmm) REVERT: P 4 MET cc_start: 0.2390 (tpt) cc_final: 0.1109 (ttt) outliers start: 169 outliers final: 110 residues processed: 303 average time/residue: 0.9900 time to fit residues: 391.4785 Evaluate side-chains 267 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 146 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1057 PRO Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 382 optimal weight: 7.9990 chunk 44 optimal weight: 0.1980 chunk 226 optimal weight: 30.0000 chunk 289 optimal weight: 40.0000 chunk 224 optimal weight: 40.0000 chunk 333 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 395 optimal weight: 20.0000 chunk 247 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32029 Z= 0.330 Angle : 0.639 13.837 43625 Z= 0.336 Chirality : 0.046 0.202 4921 Planarity : 0.005 0.078 5687 Dihedral : 5.434 56.792 4544 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.84 % Rotamer: Outliers : 4.26 % Allowed : 19.15 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 4094 helix: 0.18 (0.21), residues: 624 sheet: -0.69 (0.15), residues: 1222 loop : -1.44 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 105 HIS 0.006 0.001 HIS C1048 PHE 0.023 0.002 PHE C1121 TYR 0.028 0.002 TYR C 265 ARG 0.008 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 157 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5821 (mt-10) REVERT: B 1111 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6783 (tp30) REVERT: C 461 LEU cc_start: -0.1481 (OUTLIER) cc_final: -0.1935 (mm) REVERT: C 675 GLN cc_start: 0.6006 (OUTLIER) cc_final: 0.4619 (tm130) REVERT: C 740 MET cc_start: 0.6529 (OUTLIER) cc_final: 0.6281 (ttt) REVERT: C 909 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6259 (pp) REVERT: G 32 MET cc_start: 0.1169 (mmt) cc_final: 0.0325 (ptm) REVERT: G 112 MET cc_start: 0.4291 (mmm) cc_final: 0.3589 (mmt) REVERT: H 4 MET cc_start: 0.2627 (OUTLIER) cc_final: 0.2138 (pp-130) REVERT: M 32 MET cc_start: -0.0670 (mmm) cc_final: -0.1346 (tmm) outliers start: 139 outliers final: 94 residues processed: 274 average time/residue: 0.9133 time to fit residues: 327.4767 Evaluate side-chains 249 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 148 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1057 PRO Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 244 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 269 optimal weight: 0.7980 chunk 195 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 872 GLN B 895 GLN B 978 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32029 Z= 0.203 Angle : 0.582 15.309 43625 Z= 0.302 Chirality : 0.044 0.178 4921 Planarity : 0.005 0.067 5687 Dihedral : 5.088 56.759 4544 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 3.74 % Allowed : 19.71 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 4094 helix: 0.75 (0.21), residues: 623 sheet: -0.63 (0.15), residues: 1229 loop : -1.31 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 436 HIS 0.004 0.001 HIS I 104 PHE 0.034 0.001 PHE C 541 TYR 0.025 0.001 TYR C 265 ARG 0.004 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 161 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 567 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.6838 (mpp80) REVERT: C 598 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7377 (mt) REVERT: C 909 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6255 (pp) REVERT: E 93 CYS cc_start: 0.1984 (OUTLIER) cc_final: 0.0691 (t) REVERT: O 29 ILE cc_start: 0.0437 (OUTLIER) cc_final: -0.0399 (tt) REVERT: G 32 MET cc_start: 0.1134 (mmt) cc_final: 0.0312 (ptm) REVERT: G 112 MET cc_start: 0.4202 (mmm) cc_final: 0.3646 (mmt) REVERT: M 32 MET cc_start: -0.0662 (mmm) cc_final: -0.1464 (tmm) REVERT: M 94 VAL cc_start: -0.1606 (OUTLIER) cc_final: -0.2259 (t) REVERT: Q 83 MET cc_start: -0.1165 (OUTLIER) cc_final: -0.1805 (mmt) outliers start: 122 outliers final: 83 residues processed: 266 average time/residue: 0.8939 time to fit residues: 308.5553 Evaluate side-chains 241 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 151 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 93 CYS Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 359 optimal weight: 20.0000 chunk 378 optimal weight: 4.9990 chunk 345 optimal weight: 0.0970 chunk 368 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 160 optimal weight: 0.0470 chunk 289 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 332 optimal weight: 50.0000 chunk 348 optimal weight: 40.0000 chunk 366 optimal weight: 0.7980 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 872 GLN B 895 GLN B 978 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 895 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32029 Z= 0.177 Angle : 0.571 15.367 43625 Z= 0.294 Chirality : 0.043 0.201 4921 Planarity : 0.005 0.066 5687 Dihedral : 4.870 56.814 4544 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 2.91 % Allowed : 20.53 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4094 helix: 1.08 (0.21), residues: 624 sheet: -0.52 (0.15), residues: 1234 loop : -1.22 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 436 HIS 0.004 0.001 HIS C 207 PHE 0.035 0.001 PHE C 541 TYR 0.023 0.001 TYR C 265 ARG 0.005 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 159 time to evaluate : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8069 (mp) REVERT: B 489 TYR cc_start: 0.3257 (OUTLIER) cc_final: 0.2985 (p90) REVERT: C 567 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.6804 (mpp80) REVERT: C 909 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6327 (pp) REVERT: E 93 CYS cc_start: 0.2021 (OUTLIER) cc_final: 0.0645 (t) REVERT: O 29 ILE cc_start: 0.0582 (OUTLIER) cc_final: -0.0252 (tt) REVERT: G 32 MET cc_start: 0.1264 (mmt) cc_final: 0.0287 (ptm) REVERT: G 112 MET cc_start: 0.4530 (mmm) cc_final: 0.4055 (mmt) REVERT: H 4 MET cc_start: 0.2261 (ppp) cc_final: 0.1002 (ppp) REVERT: M 32 MET cc_start: -0.0670 (mmm) cc_final: -0.1460 (tmm) REVERT: M 94 VAL cc_start: -0.1692 (OUTLIER) cc_final: -0.2327 (t) REVERT: Q 83 MET cc_start: -0.1169 (mmp) cc_final: -0.1802 (mmt) outliers start: 95 outliers final: 69 residues processed: 241 average time/residue: 0.9163 time to fit residues: 287.2849 Evaluate side-chains 229 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 153 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 93 CYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 241 optimal weight: 2.9990 chunk 389 optimal weight: 50.0000 chunk 237 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 270 optimal weight: 0.6980 chunk 408 optimal weight: 40.0000 chunk 375 optimal weight: 50.0000 chunk 325 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 251 optimal weight: 0.7980 chunk 199 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 872 GLN B 895 GLN B 978 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Q 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32029 Z= 0.167 Angle : 0.557 14.928 43625 Z= 0.286 Chirality : 0.043 0.170 4921 Planarity : 0.004 0.063 5687 Dihedral : 4.698 56.771 4544 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.01 % Favored : 94.97 % Rotamer: Outliers : 2.48 % Allowed : 20.90 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 4094 helix: 1.25 (0.21), residues: 624 sheet: -0.45 (0.15), residues: 1235 loop : -1.16 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 436 HIS 0.004 0.001 HIS C 207 PHE 0.034 0.001 PHE C 541 TYR 0.021 0.001 TYR C 265 ARG 0.003 0.000 ARG N 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 165 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 489 TYR cc_start: 0.3272 (OUTLIER) cc_final: 0.2992 (p90) REVERT: C 567 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6897 (mpp80) REVERT: C 909 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6340 (pp) REVERT: E 93 CYS cc_start: 0.2013 (OUTLIER) cc_final: 0.0631 (t) REVERT: O 29 ILE cc_start: 0.0435 (OUTLIER) cc_final: -0.0400 (tt) REVERT: G 32 MET cc_start: 0.1383 (mmt) cc_final: 0.0327 (ptm) REVERT: G 112 MET cc_start: 0.4550 (mmm) cc_final: 0.4106 (mmt) REVERT: M 32 MET cc_start: -0.0747 (mmm) cc_final: -0.1484 (tmm) REVERT: M 94 VAL cc_start: -0.1753 (OUTLIER) cc_final: -0.2373 (t) REVERT: Q 83 MET cc_start: -0.1006 (mmp) cc_final: -0.1646 (mmt) outliers start: 81 outliers final: 66 residues processed: 235 average time/residue: 0.9522 time to fit residues: 297.4935 Evaluate side-chains 228 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 155 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 93 CYS Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 258 optimal weight: 2.9990 chunk 346 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 299 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 325 optimal weight: 40.0000 chunk 136 optimal weight: 0.3980 chunk 334 optimal weight: 40.0000 chunk 41 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN B 895 GLN B 978 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.260983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.214485 restraints weight = 44856.330| |-----------------------------------------------------------------------------| r_work (start): 0.4536 rms_B_bonded: 2.80 r_work: 0.4294 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.4229 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32029 Z= 0.259 Angle : 0.594 14.244 43625 Z= 0.308 Chirality : 0.044 0.206 4921 Planarity : 0.005 0.064 5687 Dihedral : 4.868 56.091 4544 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 2.64 % Allowed : 20.84 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4094 helix: 0.85 (0.21), residues: 628 sheet: -0.47 (0.15), residues: 1252 loop : -1.22 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 436 HIS 0.006 0.001 HIS C1048 PHE 0.023 0.002 PHE C1121 TYR 0.023 0.001 TYR C 265 ARG 0.003 0.000 ARG B 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7960.24 seconds wall clock time: 144 minutes 35.39 seconds (8675.39 seconds total)