Starting phenix.real_space_refine on Thu Mar 21 03:07:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yve_34124/03_2024/7yve_34124.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yve_34124/03_2024/7yve_34124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yve_34124/03_2024/7yve_34124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yve_34124/03_2024/7yve_34124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yve_34124/03_2024/7yve_34124.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yve_34124/03_2024/7yve_34124.pdb" } resolution = 3.4 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= 0.036 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 123 5.16 5 C 18542 2.51 5 N 4804 2.21 5 O 5540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ARG 66": "NH1" <-> "NH2" Residue "I ARG 68": "NH1" <-> "NH2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "K ARG 26": "NH1" <-> "NH2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "K ARG 62": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K GLU 82": "OE1" <-> "OE2" Residue "L ARG 13": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 66": "NH1" <-> "NH2" Residue "L ARG 68": "NH1" <-> "NH2" Residue "L ARG 100": "NH1" <-> "NH2" Residue "N ARG 26": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 62": "NH1" <-> "NH2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ARG 66": "NH1" <-> "NH2" Residue "O ARG 68": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29009 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "A" Number of atoms: 7725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7725 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "H" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "L" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "O" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 15.61, per 1000 atoms: 0.54 Number of scatterers: 29009 At special positions: 0 Unit cell: (167.28, 204.18, 177.94, 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 123 16.00 O 5540 8.00 N 4804 7.00 C 18542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.07 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 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=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 97 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.56 Conformation dependent library (CDL) restraints added in 5.4 seconds 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7014 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 55 sheets defined 22.1% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 368 removed outlier: 4.037A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.644A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.522A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 422' Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.678A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.573A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.578A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.859A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.579A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.158A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.694A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.671A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.132A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.925A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.984A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.604A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.602A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.106A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.685A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.105A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.874A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.526A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.204A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.515A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 4.030A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.570A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.570A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.017A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.603A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.935A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.891A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 4.013A pdb=" N ASP H 83 " --> pdb=" O ARG H 80 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU H 84 " --> pdb=" O SER H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 80 through 84' Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.503A pdb=" N THR I 92 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 removed outlier: 4.040A pdb=" N ASP K 83 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU K 84 " --> pdb=" O SER K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 84' Processing helix chain 'L' and resid 63 through 66 Processing helix chain 'L' and resid 75 through 77 No H-bonds generated for 'chain 'L' and resid 75 through 77' Processing helix chain 'L' and resid 88 through 92 Processing helix chain 'N' and resid 80 through 84 removed outlier: 3.868A pdb=" N ASP N 83 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU N 84 " --> pdb=" O SER N 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 80 through 84' Processing helix chain 'O' and resid 63 through 66 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 88 through 92 removed outlier: 3.640A pdb=" N THR O 92 " --> pdb=" O PRO O 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.533A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.551A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.553A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.664A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.588A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.595A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.990A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.161A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 6.801A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.495A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 788 through 789 removed outlier: 6.026A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.401A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.541A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.990A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.503A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.586A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.204A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.620A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.522A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.887A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.160A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 5.610A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.036A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.482A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.571A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 63 through 66 removed outlier: 3.548A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.797A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.471A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.847A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.921A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.119A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.018A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.018A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.509A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AE8, first strand: chain 'H' and resid 46 through 49 removed outlier: 6.800A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.944A pdb=" N THR I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.971A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 36 " --> pdb=" O ILE I 53 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE I 112 " --> pdb=" O HIS I 99 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.971A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 36 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AF4, first strand: chain 'K' and resid 46 through 49 removed outlier: 6.805A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA K 90 " --> pdb=" O TYR K 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER K 98 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AF6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.889A pdb=" N VAL L 36 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU L 52 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP L 38 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'N' and resid 34 through 36 Processing sheet with id=AF9, first strand: chain 'O' and resid 3 through 5 Processing sheet with id=AG1, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.151A pdb=" N ARG O 40 " --> pdb=" O TRP O 49 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP O 49 " --> pdb=" O ARG O 40 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 2958 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: 13.43 Time building geometry restraints manager: 12.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 8501 1.33 - 1.47: 9191 1.47 - 1.60: 11860 1.60 - 1.74: 14 1.74 - 1.88: 139 Bond restraints: 29705 Sorted by residual: bond pdb=" C PRO A 862 " pdb=" O PRO A 862 " ideal model delta sigma weight residual 1.240 1.196 0.044 1.12e-02 7.97e+03 1.54e+01 bond pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " ideal model delta sigma weight residual 1.808 1.690 0.118 3.30e-02 9.18e+02 1.28e+01 bond pdb=" C PRO B 862 " pdb=" O PRO B 862 " ideal model delta sigma weight residual 1.240 1.201 0.039 1.12e-02 7.97e+03 1.24e+01 bond pdb=" C PRO A 863 " pdb=" O PRO A 863 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " ideal model delta sigma weight residual 1.808 1.703 0.105 3.30e-02 9.18e+02 1.02e+01 ... (remaining 29700 not shown) Histogram of bond angle deviations from ideal: 94.30 - 102.27: 83 102.27 - 110.23: 8668 110.23 - 118.20: 14109 118.20 - 126.16: 17269 126.16 - 134.13: 438 Bond angle restraints: 40567 Sorted by residual: angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 111.26 122.06 -10.80 1.63e+00 3.76e-01 4.39e+01 angle pdb=" CA CYS C 538 " pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " ideal model delta sigma weight residual 114.40 129.19 -14.79 2.30e+00 1.89e-01 4.14e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 128.48 -14.08 2.30e+00 1.89e-01 3.75e+01 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 124.63 -12.29 2.04e+00 2.40e-01 3.63e+01 angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 128.02 -13.62 2.30e+00 1.89e-01 3.51e+01 ... (remaining 40562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 16472 18.05 - 36.09: 1198 36.09 - 54.14: 237 54.14 - 72.19: 68 72.19 - 90.24: 19 Dihedral angle restraints: 17994 sinusoidal: 7083 harmonic: 10911 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.27 -76.73 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 168.48 -75.48 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -11.47 -74.53 1 1.00e+01 1.00e-02 7.04e+01 ... (remaining 17991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3487 0.080 - 0.160: 1100 0.160 - 0.240: 128 0.240 - 0.320: 17 0.320 - 0.400: 3 Chirality restraints: 4735 Sorted by residual: chirality pdb=" CA CYS A 391 " pdb=" N CYS A 391 " pdb=" C CYS A 391 " pdb=" CB CYS A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA CYS A 760 " pdb=" N CYS A 760 " pdb=" C CYS A 760 " pdb=" CB CYS A 760 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA CYS C 379 " pdb=" N CYS C 379 " pdb=" C CYS C 379 " pdb=" CB CYS C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 4732 not shown) Planarity restraints: 5188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO B 527 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 377 " -0.032 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE C 377 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE C 377 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C 377 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 377 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 377 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 377 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 527 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.046 5.00e-02 4.00e+02 ... (remaining 5185 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 254 2.57 - 3.15: 24787 3.15 - 3.73: 40744 3.73 - 4.32: 57245 4.32 - 4.90: 99659 Nonbonded interactions: 222689 Sorted by model distance: nonbonded pdb=" OG1 THR K 5 " pdb=" OG SER K 23 " model vdw 1.983 2.440 nonbonded pdb=" O GLY I 33 " pdb=" NH1 ARG I 100 " model vdw 2.087 2.520 nonbonded pdb=" O6 NAG B1301 " pdb=" O6 NAG B1312 " model vdw 2.090 2.440 nonbonded pdb=" ND2 ASN B 450 " pdb=" OD2 ASP O 56 " model vdw 2.096 2.520 nonbonded pdb=" ND2 ASN C1134 " pdb=" O7 NAG C1304 " model vdw 2.102 2.520 ... (remaining 222684 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 1146 or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 1146 or resid 1301 through 1311)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.700 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: 0.030 Extract box with map and model: 28.470 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 80.070 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.210 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 : 0.017 0.132 29705 Z= 1.159 Angle : 1.236 14.792 40567 Z= 0.679 Chirality : 0.074 0.400 4735 Planarity : 0.007 0.105 5188 Dihedral : 13.192 90.236 10845 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.04 % Favored : 94.61 % Rotamer: Outliers : 1.49 % Allowed : 8.19 % Favored : 90.32 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.12), residues: 3708 helix: 0.03 (0.20), residues: 669 sheet: -1.26 (0.14), residues: 1054 loop : -2.34 (0.12), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP A1102 HIS 0.025 0.003 HIS N 50 PHE 0.070 0.005 PHE C 377 TYR 0.053 0.004 TYR C 495 ARG 0.027 0.002 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 272 time to evaluate : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 509 ARG cc_start: 0.6393 (mtt180) cc_final: 0.5805 (mtt180) REVERT: B 574 ASP cc_start: 0.8116 (t70) cc_final: 0.7902 (t0) REVERT: B 858 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9035 (mt) REVERT: A 102 ARG cc_start: 0.6713 (mtt180) cc_final: 0.6486 (mtt-85) REVERT: A 518 LEU cc_start: 0.2421 (OUTLIER) cc_final: 0.1862 (tp) REVERT: H 79 LEU cc_start: 0.5701 (OUTLIER) cc_final: 0.5349 (pp) REVERT: I 87 MET cc_start: 0.2361 (tpt) cc_final: -0.0337 (ptt) REVERT: K 63 PHE cc_start: 0.7782 (m-80) cc_final: 0.7479 (m-80) REVERT: L 38 TRP cc_start: 0.7443 (m100) cc_final: 0.7014 (m100) REVERT: L 53 ILE cc_start: 0.8695 (tt) cc_final: 0.8489 (tp) REVERT: L 61 TYR cc_start: 0.8105 (m-80) cc_final: 0.7642 (m-80) REVERT: L 62 ASN cc_start: 0.8245 (t0) cc_final: 0.7726 (t0) REVERT: L 73 LYS cc_start: 0.8674 (pttt) cc_final: 0.7986 (pttm) REVERT: L 111 GLU cc_start: 0.8556 (tp30) cc_final: 0.8271 (tp30) REVERT: N 96 LEU cc_start: 0.8950 (mm) cc_final: 0.8690 (mp) REVERT: N 106 LYS cc_start: 0.9020 (tppt) cc_final: 0.8714 (mmmt) outliers start: 45 outliers final: 20 residues processed: 311 average time/residue: 0.4684 time to fit residues: 219.5224 Evaluate side-chains 196 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain O residue 120 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 0.6980 chunk 284 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 340 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 544 ASN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 331 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 ASN B 755 GLN B 762 GLN B1074 ASN B1088 HIS B1134 ASN A 234 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 41 GLN L 86 ASN N 1 GLN N 6 GLN N 38 HIS N 54 GLN O 31 ASN O 41 GLN O 99 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29705 Z= 0.198 Angle : 0.614 10.354 40567 Z= 0.321 Chirality : 0.046 0.181 4735 Planarity : 0.004 0.054 5188 Dihedral : 7.093 57.886 4826 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.98 % Rotamer: Outliers : 2.05 % Allowed : 11.40 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3708 helix: 1.32 (0.21), residues: 669 sheet: -0.69 (0.15), residues: 1076 loop : -1.79 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 99 HIS 0.007 0.001 HIS O 104 PHE 0.017 0.001 PHE L 24 TYR 0.015 0.001 TYR A 265 ARG 0.005 0.001 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 242 time to evaluate : 5.386 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: C 375 PHE cc_start: 0.8084 (t80) cc_final: 0.7642 (t80) REVERT: C 509 ARG cc_start: 0.6028 (mtt180) cc_final: 0.5819 (ttm170) REVERT: C 754 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9383 (mm) REVERT: B 198 ASP cc_start: 0.7673 (t0) cc_final: 0.7437 (t0) REVERT: B 574 ASP cc_start: 0.8136 (t70) cc_final: 0.7863 (t0) REVERT: B 858 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8998 (mp) REVERT: B 950 ASP cc_start: 0.8092 (m-30) cc_final: 0.7883 (m-30) REVERT: A 135 PHE cc_start: 0.7804 (m-80) cc_final: 0.7578 (m-80) REVERT: A 1005 GLN cc_start: 0.8259 (tp40) cc_final: 0.7977 (tt0) REVERT: I 87 MET cc_start: 0.1933 (tpt) cc_final: -0.0439 (ptt) REVERT: K 55 ARG cc_start: 0.6785 (mtp-110) cc_final: 0.6233 (mtp180) REVERT: K 93 ASP cc_start: 0.8183 (t0) cc_final: 0.7878 (t70) REVERT: L 13 ARG cc_start: 0.8895 (mpp-170) cc_final: 0.8614 (mmt90) REVERT: L 38 TRP cc_start: 0.7509 (m100) cc_final: 0.6826 (m100) REVERT: L 40 ARG cc_start: 0.7591 (ptt180) cc_final: 0.7266 (ptm160) REVERT: L 61 TYR cc_start: 0.8234 (m-80) cc_final: 0.7831 (m-80) REVERT: L 62 ASN cc_start: 0.8486 (t0) cc_final: 0.8016 (t0) REVERT: L 86 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7932 (p0) REVERT: N 82 GLU cc_start: 0.8043 (pm20) cc_final: 0.7443 (pp20) REVERT: N 106 LYS cc_start: 0.8990 (tppt) cc_final: 0.8677 (mmmt) outliers start: 62 outliers final: 30 residues processed: 294 average time/residue: 0.4065 time to fit residues: 192.8714 Evaluate side-chains 227 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain O residue 99 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 231 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 341 optimal weight: 7.9990 chunk 368 optimal weight: 4.9990 chunk 303 optimal weight: 0.1980 chunk 338 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN L 99 HIS O 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29705 Z= 0.205 Angle : 0.571 11.481 40567 Z= 0.297 Chirality : 0.044 0.202 4735 Planarity : 0.004 0.051 5188 Dihedral : 6.301 54.649 4804 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.53 % Rotamer: Outliers : 3.24 % Allowed : 12.55 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 3708 helix: 1.84 (0.21), residues: 663 sheet: -0.28 (0.15), residues: 1068 loop : -1.59 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 92 HIS 0.007 0.001 HIS N 50 PHE 0.018 0.001 PHE B 375 TYR 0.019 0.001 TYR A 170 ARG 0.005 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 210 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9381 (mm) REVERT: B 198 ASP cc_start: 0.7742 (t0) cc_final: 0.7429 (t0) REVERT: B 574 ASP cc_start: 0.8135 (t70) cc_final: 0.7866 (t0) REVERT: B 950 ASP cc_start: 0.8073 (m-30) cc_final: 0.7844 (m-30) REVERT: A 619 GLU cc_start: 0.7513 (mp0) cc_final: 0.7293 (mp0) REVERT: A 902 MET cc_start: 0.8720 (tpt) cc_final: 0.8378 (mmt) REVERT: I 87 MET cc_start: 0.1921 (tpt) cc_final: -0.0440 (ptt) REVERT: I 121 VAL cc_start: 0.6364 (OUTLIER) cc_final: 0.5635 (p) REVERT: K 28 ASN cc_start: 0.7773 (p0) cc_final: 0.7383 (p0) REVERT: K 93 ASP cc_start: 0.8156 (t0) cc_final: 0.7908 (t70) REVERT: L 6 GLU cc_start: 0.7976 (mp0) cc_final: 0.7729 (mp0) REVERT: L 13 ARG cc_start: 0.8881 (mpp-170) cc_final: 0.8248 (tpp80) REVERT: L 38 TRP cc_start: 0.7420 (m100) cc_final: 0.6658 (m100) REVERT: L 61 TYR cc_start: 0.8285 (m-80) cc_final: 0.7997 (m-80) REVERT: L 62 ASN cc_start: 0.8554 (t0) cc_final: 0.8090 (t0) REVERT: L 79 GLN cc_start: 0.8207 (pt0) cc_final: 0.7789 (mt0) REVERT: L 87 MET cc_start: 0.6470 (mmm) cc_final: 0.6000 (mmm) REVERT: N 82 GLU cc_start: 0.7998 (pm20) cc_final: 0.7493 (pp20) REVERT: N 84 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7481 (mt-10) REVERT: N 106 LYS cc_start: 0.9013 (tppt) cc_final: 0.8651 (mmmt) REVERT: O 18 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7547 (mm) outliers start: 98 outliers final: 55 residues processed: 292 average time/residue: 0.3838 time to fit residues: 183.1381 Evaluate side-chains 253 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 195 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 99 HIS Chi-restraints excluded: chain O residue 121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 162 optimal weight: 0.4980 chunk 229 optimal weight: 5.9990 chunk 342 optimal weight: 1.9990 chunk 362 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 324 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 603 ASN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN A1005 GLN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN O 99 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29705 Z= 0.250 Angle : 0.570 15.006 40567 Z= 0.297 Chirality : 0.045 0.195 4735 Planarity : 0.004 0.049 5188 Dihedral : 5.959 54.798 4799 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 3.47 % Allowed : 13.91 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 3708 helix: 1.87 (0.21), residues: 669 sheet: -0.15 (0.15), residues: 1038 loop : -1.45 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.011 0.001 HIS O 99 PHE 0.026 0.001 PHE L 27 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 205 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9387 (mm) REVERT: B 198 ASP cc_start: 0.7746 (t0) cc_final: 0.7470 (t0) REVERT: B 574 ASP cc_start: 0.8128 (t70) cc_final: 0.7843 (t0) REVERT: B 950 ASP cc_start: 0.8088 (m-30) cc_final: 0.7865 (m-30) REVERT: I 87 MET cc_start: 0.1912 (tpt) cc_final: -0.0381 (ptt) REVERT: I 121 VAL cc_start: 0.5881 (OUTLIER) cc_final: 0.5631 (p) REVERT: K 28 ASN cc_start: 0.7701 (p0) cc_final: 0.7288 (p0) REVERT: K 93 ASP cc_start: 0.8127 (t0) cc_final: 0.7877 (t70) REVERT: L 6 GLU cc_start: 0.7904 (mp0) cc_final: 0.7685 (mp0) REVERT: L 13 ARG cc_start: 0.8882 (mpp-170) cc_final: 0.8220 (tpp80) REVERT: L 38 TRP cc_start: 0.7409 (m100) cc_final: 0.6617 (m100) REVERT: L 61 TYR cc_start: 0.8281 (m-80) cc_final: 0.7878 (m-80) REVERT: L 62 ASN cc_start: 0.8681 (t0) cc_final: 0.8138 (t0) REVERT: L 86 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7850 (p0) REVERT: N 82 GLU cc_start: 0.7994 (pm20) cc_final: 0.7593 (pp20) REVERT: N 84 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7566 (mt-10) REVERT: N 106 LYS cc_start: 0.9042 (tppt) cc_final: 0.8661 (mmmt) outliers start: 105 outliers final: 77 residues processed: 291 average time/residue: 0.4344 time to fit residues: 207.6128 Evaluate side-chains 274 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 194 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 99 HIS Chi-restraints excluded: chain O residue 121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 4.9990 chunk 205 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 269 optimal weight: 0.1980 chunk 149 optimal weight: 0.9990 chunk 309 optimal weight: 20.0000 chunk 250 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 325 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 HIS O 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 29705 Z= 0.319 Angle : 0.588 14.130 40567 Z= 0.307 Chirality : 0.045 0.196 4735 Planarity : 0.004 0.051 5188 Dihedral : 5.877 55.430 4798 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.07 % Rotamer: Outliers : 3.77 % Allowed : 14.47 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3708 helix: 1.85 (0.21), residues: 668 sheet: -0.11 (0.16), residues: 1034 loop : -1.40 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 55 HIS 0.008 0.001 HIS O 99 PHE 0.021 0.002 PHE L 27 TYR 0.021 0.001 TYR B1067 ARG 0.007 0.000 ARG K 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 197 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8130 (pt) REVERT: C 754 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9389 (mm) REVERT: B 198 ASP cc_start: 0.7765 (t0) cc_final: 0.7442 (t0) REVERT: B 574 ASP cc_start: 0.8153 (t70) cc_final: 0.7873 (t0) REVERT: B 950 ASP cc_start: 0.8091 (m-30) cc_final: 0.7853 (m-30) REVERT: I 87 MET cc_start: 0.1933 (tpt) cc_final: -0.0393 (ptt) REVERT: I 121 VAL cc_start: 0.5941 (OUTLIER) cc_final: 0.5707 (p) REVERT: K 55 ARG cc_start: 0.6534 (mtp-110) cc_final: 0.5933 (mtp180) REVERT: L 6 GLU cc_start: 0.7910 (mp0) cc_final: 0.7677 (mp0) REVERT: L 13 ARG cc_start: 0.8888 (mpp-170) cc_final: 0.8157 (tpp80) REVERT: L 38 TRP cc_start: 0.7412 (m100) cc_final: 0.6613 (m100) REVERT: L 61 TYR cc_start: 0.8257 (m-80) cc_final: 0.7697 (m-80) REVERT: L 68 ARG cc_start: 0.7023 (ttt180) cc_final: 0.6409 (ttt180) REVERT: L 86 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.7999 (p0) REVERT: N 13 THR cc_start: 0.8323 (t) cc_final: 0.7980 (p) REVERT: N 82 GLU cc_start: 0.7999 (pm20) cc_final: 0.7612 (pp20) REVERT: N 84 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7620 (mt-10) REVERT: N 106 LYS cc_start: 0.9065 (tppt) cc_final: 0.8697 (mmmt) outliers start: 114 outliers final: 86 residues processed: 291 average time/residue: 0.3856 time to fit residues: 184.1189 Evaluate side-chains 279 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 189 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 99 HIS Chi-restraints excluded: chain O residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 2.9990 chunk 326 optimal weight: 10.0000 chunk 71 optimal weight: 0.0050 chunk 212 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 362 optimal weight: 5.9990 chunk 301 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 30.0000 chunk 190 optimal weight: 1.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 957 GLN C1005 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29705 Z= 0.315 Angle : 0.584 13.405 40567 Z= 0.305 Chirality : 0.045 0.193 4735 Planarity : 0.004 0.053 5188 Dihedral : 5.821 55.459 4796 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.09 % Rotamer: Outliers : 3.77 % Allowed : 15.13 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 3708 helix: 1.86 (0.21), residues: 669 sheet: -0.10 (0.16), residues: 1037 loop : -1.38 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS L 99 PHE 0.024 0.002 PHE L 112 TYR 0.020 0.001 TYR B1067 ARG 0.010 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 196 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8116 (pt) REVERT: C 394 ASN cc_start: 0.5526 (OUTLIER) cc_final: 0.5306 (t0) REVERT: C 754 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9377 (mm) REVERT: B 198 ASP cc_start: 0.7862 (t0) cc_final: 0.7471 (t0) REVERT: B 574 ASP cc_start: 0.8151 (t70) cc_final: 0.7863 (t0) REVERT: B 950 ASP cc_start: 0.8090 (m-30) cc_final: 0.7887 (m-30) REVERT: B 990 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: I 87 MET cc_start: 0.1855 (tpt) cc_final: -0.0305 (ptt) REVERT: I 121 VAL cc_start: 0.5918 (OUTLIER) cc_final: 0.5693 (p) REVERT: K 28 ASN cc_start: 0.7613 (p0) cc_final: 0.7015 (p0) REVERT: K 93 ASP cc_start: 0.8230 (t0) cc_final: 0.7934 (t70) REVERT: L 6 GLU cc_start: 0.7876 (mp0) cc_final: 0.7653 (mp0) REVERT: L 13 ARG cc_start: 0.8873 (mpp-170) cc_final: 0.8140 (tpp80) REVERT: L 38 TRP cc_start: 0.7416 (m100) cc_final: 0.6615 (m100) REVERT: L 61 TYR cc_start: 0.8227 (m-80) cc_final: 0.7656 (m-80) REVERT: N 82 GLU cc_start: 0.8025 (pm20) cc_final: 0.7699 (pp20) REVERT: N 106 LYS cc_start: 0.9054 (tppt) cc_final: 0.8688 (mmmt) outliers start: 114 outliers final: 90 residues processed: 290 average time/residue: 0.3987 time to fit residues: 189.7191 Evaluate side-chains 284 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 189 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 99 HIS Chi-restraints excluded: chain O residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 264 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 305 optimal weight: 0.0170 chunk 202 optimal weight: 5.9990 chunk 361 optimal weight: 4.9990 chunk 226 optimal weight: 0.5980 chunk 220 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 506 GLN ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN N 16 GLN O 99 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29705 Z= 0.228 Angle : 0.557 13.746 40567 Z= 0.290 Chirality : 0.044 0.192 4735 Planarity : 0.004 0.054 5188 Dihedral : 5.575 56.222 4796 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 3.83 % Allowed : 15.66 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3708 helix: 2.03 (0.21), residues: 662 sheet: -0.00 (0.16), residues: 1038 loop : -1.33 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS H 38 PHE 0.020 0.001 PHE L 112 TYR 0.016 0.001 TYR B1067 ARG 0.006 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 200 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8059 (pt) REVERT: C 394 ASN cc_start: 0.6039 (OUTLIER) cc_final: 0.5800 (t0) REVERT: C 754 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9353 (mm) REVERT: B 198 ASP cc_start: 0.7888 (t0) cc_final: 0.7497 (t0) REVERT: B 574 ASP cc_start: 0.8140 (t70) cc_final: 0.7850 (t0) REVERT: B 950 ASP cc_start: 0.8041 (m-30) cc_final: 0.7821 (m-30) REVERT: A 238 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7213 (p90) REVERT: I 87 MET cc_start: 0.1809 (tpt) cc_final: -0.0485 (ptp) REVERT: K 93 ASP cc_start: 0.8256 (t0) cc_final: 0.7756 (t0) REVERT: L 13 ARG cc_start: 0.8860 (mpp-170) cc_final: 0.8125 (tpp80) REVERT: L 38 TRP cc_start: 0.7381 (m100) cc_final: 0.6559 (m100) REVERT: L 61 TYR cc_start: 0.8168 (m-80) cc_final: 0.7448 (m-80) REVERT: N 82 GLU cc_start: 0.8007 (pm20) cc_final: 0.7720 (pp20) REVERT: N 106 LYS cc_start: 0.9050 (tppt) cc_final: 0.8661 (mmmt) outliers start: 116 outliers final: 92 residues processed: 296 average time/residue: 0.3832 time to fit residues: 187.7186 Evaluate side-chains 284 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 188 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 98 THR Chi-restraints excluded: chain O residue 99 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 0.2980 chunk 70 optimal weight: 0.0020 chunk 229 optimal weight: 0.0030 chunk 246 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 ASN L 79 GLN O 99 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 29705 Z= 0.145 Angle : 0.533 13.336 40567 Z= 0.277 Chirality : 0.043 0.183 4735 Planarity : 0.004 0.053 5188 Dihedral : 5.207 59.307 4796 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 3.17 % Allowed : 16.58 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3708 helix: 2.13 (0.21), residues: 660 sheet: 0.11 (0.16), residues: 1028 loop : -1.18 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS O 99 PHE 0.019 0.001 PHE B 375 TYR 0.012 0.001 TYR A 170 ARG 0.013 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 208 time to evaluate : 3.374 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: C 754 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9322 (mm) REVERT: B 198 ASP cc_start: 0.7817 (t0) cc_final: 0.7461 (t0) REVERT: B 574 ASP cc_start: 0.8124 (t70) cc_final: 0.7840 (t0) REVERT: A 238 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7250 (p90) REVERT: K 93 ASP cc_start: 0.8271 (t0) cc_final: 0.8043 (t70) REVERT: L 13 ARG cc_start: 0.8854 (mpp-170) cc_final: 0.8120 (tpp80) REVERT: L 38 TRP cc_start: 0.7367 (m100) cc_final: 0.6475 (m100) REVERT: L 61 TYR cc_start: 0.8378 (m-80) cc_final: 0.7575 (m-80) REVERT: L 62 ASN cc_start: 0.8893 (t0) cc_final: 0.8510 (t0) REVERT: L 68 ARG cc_start: 0.6690 (ttt180) cc_final: 0.5796 (ttt180) REVERT: L 86 ASN cc_start: 0.8646 (m-40) cc_final: 0.8277 (p0) REVERT: N 82 GLU cc_start: 0.7993 (pm20) cc_final: 0.7784 (pp20) REVERT: N 106 LYS cc_start: 0.9029 (tppt) cc_final: 0.8692 (mmmt) outliers start: 96 outliers final: 79 residues processed: 284 average time/residue: 0.3813 time to fit residues: 178.0742 Evaluate side-chains 278 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 197 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 99 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 315 optimal weight: 2.9990 chunk 336 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 304 optimal weight: 0.0070 chunk 318 optimal weight: 20.0000 chunk 335 optimal weight: 6.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 29705 Z= 0.267 Angle : 0.566 14.530 40567 Z= 0.293 Chirality : 0.044 0.186 4735 Planarity : 0.004 0.054 5188 Dihedral : 5.255 59.678 4795 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.26 % Rotamer: Outliers : 3.60 % Allowed : 16.58 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3708 helix: 2.06 (0.21), residues: 660 sheet: 0.09 (0.16), residues: 1033 loop : -1.21 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS L 99 PHE 0.019 0.001 PHE B 375 TYR 0.018 0.001 TYR B1067 ARG 0.008 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 201 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 501 TYR cc_start: 0.4969 (OUTLIER) cc_final: 0.4101 (m-10) REVERT: C 754 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9345 (mm) REVERT: B 198 ASP cc_start: 0.7929 (t0) cc_final: 0.7540 (t0) REVERT: B 574 ASP cc_start: 0.8150 (t70) cc_final: 0.7863 (t0) REVERT: A 238 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7243 (p90) REVERT: A 979 ASP cc_start: 0.8053 (t70) cc_final: 0.7652 (t0) REVERT: A 983 ARG cc_start: 0.7892 (ptt-90) cc_final: 0.7614 (ptt-90) REVERT: K 93 ASP cc_start: 0.8234 (t0) cc_final: 0.8009 (t70) REVERT: L 13 ARG cc_start: 0.8866 (mpp-170) cc_final: 0.8120 (tpp80) REVERT: L 38 TRP cc_start: 0.7408 (m100) cc_final: 0.6441 (m100) REVERT: L 62 ASN cc_start: 0.8932 (t0) cc_final: 0.8530 (t0) REVERT: L 68 ARG cc_start: 0.6745 (ttt180) cc_final: 0.5966 (ttt180) REVERT: L 86 ASN cc_start: 0.8688 (m-40) cc_final: 0.8326 (p0) REVERT: N 82 GLU cc_start: 0.8002 (pm20) cc_final: 0.7784 (pp20) REVERT: N 106 LYS cc_start: 0.9052 (tppt) cc_final: 0.8744 (mmmt) outliers start: 109 outliers final: 96 residues processed: 292 average time/residue: 0.3742 time to fit residues: 181.7439 Evaluate side-chains 293 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 194 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain O residue 98 THR Chi-restraints excluded: chain O residue 99 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 1.9990 chunk 356 optimal weight: 0.6980 chunk 217 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 373 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29705 Z= 0.259 Angle : 0.565 13.261 40567 Z= 0.293 Chirality : 0.044 0.185 4735 Planarity : 0.004 0.054 5188 Dihedral : 5.273 59.875 4795 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 3.57 % Allowed : 16.85 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3708 helix: 2.04 (0.21), residues: 659 sheet: 0.12 (0.16), residues: 1028 loop : -1.19 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS L 99 PHE 0.018 0.001 PHE B 375 TYR 0.017 0.001 TYR B1067 ARG 0.016 0.000 ARG B 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 191 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 501 TYR cc_start: 0.5055 (OUTLIER) cc_final: 0.3976 (m-10) REVERT: C 506 GLN cc_start: 0.6089 (pm20) cc_final: 0.5753 (mp10) REVERT: C 754 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9337 (mm) REVERT: B 198 ASP cc_start: 0.7901 (t0) cc_final: 0.7528 (t0) REVERT: B 574 ASP cc_start: 0.8166 (t70) cc_final: 0.7884 (t0) REVERT: A 238 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7239 (p90) REVERT: A 979 ASP cc_start: 0.8023 (t70) cc_final: 0.7575 (t0) REVERT: A 983 ARG cc_start: 0.7907 (ptt-90) cc_final: 0.7626 (ptt-90) REVERT: K 93 ASP cc_start: 0.8219 (t0) cc_final: 0.7973 (t70) REVERT: L 13 ARG cc_start: 0.8861 (mpp-170) cc_final: 0.8404 (mpp-170) REVERT: L 38 TRP cc_start: 0.7404 (m100) cc_final: 0.6468 (m100) REVERT: L 61 TYR cc_start: 0.8258 (m-10) cc_final: 0.7745 (m-80) REVERT: L 68 ARG cc_start: 0.6754 (ttt180) cc_final: 0.5984 (ttt180) REVERT: L 86 ASN cc_start: 0.8662 (m-40) cc_final: 0.8325 (p0) REVERT: N 106 LYS cc_start: 0.9063 (tppt) cc_final: 0.8701 (mmmt) outliers start: 108 outliers final: 97 residues processed: 282 average time/residue: 0.3558 time to fit residues: 166.5477 Evaluate side-chains 287 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 187 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain O residue 98 THR Chi-restraints excluded: chain O residue 99 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 2.9990 chunk 316 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 82 optimal weight: 0.4980 chunk 297 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 305 optimal weight: 0.0570 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.120607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.081434 restraints weight = 67462.595| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.50 r_work: 0.3161 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29705 Z= 0.193 Angle : 0.544 13.019 40567 Z= 0.282 Chirality : 0.044 0.180 4735 Planarity : 0.004 0.059 5188 Dihedral : 5.054 57.843 4795 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 3.20 % Allowed : 17.34 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3708 helix: 2.16 (0.21), residues: 654 sheet: 0.19 (0.16), residues: 1020 loop : -1.11 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.012 0.001 HIS O 99 PHE 0.018 0.001 PHE B 375 TYR 0.013 0.001 TYR B1067 ARG 0.014 0.000 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6256.78 seconds wall clock time: 114 minutes 7.38 seconds (6847.38 seconds total)