Starting phenix.real_space_refine on Tue Feb 20 06:58:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gou_34181/02_2024/8gou_34181.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gou_34181/02_2024/8gou_34181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gou_34181/02_2024/8gou_34181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gou_34181/02_2024/8gou_34181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gou_34181/02_2024/8gou_34181.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gou_34181/02_2024/8gou_34181.pdb" } resolution = 3.7 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= 0.029 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 17316 2.51 5 N 4467 2.21 5 O 5202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" 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 TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 1041": "OD1" <-> "OD2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "B ARG 34": "NH1" <-> "NH2" 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 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 GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B ASP 1146": "OD1" <-> "OD2" 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 ARG 190": "NH1" <-> "NH2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" 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 PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" 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 "I GLU 89": "OE1" <-> "OE2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K ASP 84": "OD1" <-> "OD2" Residue "K ASP 87": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27108 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7754 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "C" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "J" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 798 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 798 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 13.87, per 1000 atoms: 0.51 Number of scatterers: 27108 At special positions: 0 Unit cell: (142.68, 200.9, 180.4, 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 5202 8.00 N 4467 7.00 C 17316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 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 I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.34 Conformation dependent library (CDL) restraints added in 5.2 seconds 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6554 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 56 sheets defined 22.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.654A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.516A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 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 801 through 805 removed outlier: 4.497A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.507A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.783A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.667A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) 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: 3.902A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.910A 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: 3.621A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.996A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.090A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 502 through 506 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 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.786A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.559A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) 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: 3.822A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.816A 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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.020A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.026A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.543A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.595A 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 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.574A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.699A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.565A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) 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: 3.502A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.092A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.880A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 81 through 85 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.684A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.423A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.183A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.751A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.414A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.433A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.754A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.937A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.235A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.047A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.047A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.099A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.402A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 8.601A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.232A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.983A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.266A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.585A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.838A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.684A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.242A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.993A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.993A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.542A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.457A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.501A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.601A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.564A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.198A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AE2, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.421A pdb=" N LYS C 424 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.214A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.915A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.915A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.445A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.408A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 7 removed outlier: 5.148A pdb=" N GLY I 16 " --> pdb=" O SER I 85 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.155A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.281A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AF5, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.517A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.210A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.555A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AG2, first strand: chain 'K' and resid 18 through 23 1139 hydrogen bonds defined for protein. 3018 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: 14.18 Time building geometry restraints manager: 12.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8650 1.34 - 1.48: 7601 1.48 - 1.62: 11339 1.62 - 1.76: 8 1.76 - 1.90: 147 Bond restraints: 27745 Sorted by residual: bond pdb=" C PRO A 862 " pdb=" O PRO A 862 " ideal model delta sigma weight residual 1.240 1.205 0.035 1.12e-02 7.97e+03 9.86e+00 bond pdb=" N LEU A 117 " pdb=" CA LEU A 117 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.23e-02 6.61e+03 8.87e+00 bond pdb=" N GLU A 583 " pdb=" CA GLU A 583 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.69e+00 bond pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 1.808 1.900 -0.092 3.30e-02 9.18e+02 7.69e+00 bond pdb=" N PHE A 377 " pdb=" CA PHE A 377 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.08e-02 8.57e+03 7.19e+00 ... (remaining 27740 not shown) Histogram of bond angle deviations from ideal: 96.89 - 104.36: 479 104.36 - 111.83: 13376 111.83 - 119.30: 9181 119.30 - 126.77: 14530 126.77 - 134.25: 311 Bond angle restraints: 37877 Sorted by residual: angle pdb=" CA CYS B 538 " pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " ideal model delta sigma weight residual 114.40 127.02 -12.62 2.30e+00 1.89e-01 3.01e+01 angle pdb=" N TYR K 51 " pdb=" CA TYR K 51 " pdb=" C TYR K 51 " ideal model delta sigma weight residual 109.52 101.09 8.43 1.55e+00 4.16e-01 2.96e+01 angle pdb=" N ILE A 410 " pdb=" CA ILE A 410 " pdb=" C ILE A 410 " ideal model delta sigma weight residual 106.21 111.57 -5.36 1.07e+00 8.73e-01 2.51e+01 angle pdb=" N TYR J 51 " pdb=" CA TYR J 51 " pdb=" C TYR J 51 " ideal model delta sigma weight residual 109.52 101.84 7.68 1.55e+00 4.16e-01 2.45e+01 angle pdb=" C THR B 333 " pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 121.54 130.42 -8.88 1.91e+00 2.74e-01 2.16e+01 ... (remaining 37872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 15256 17.32 - 34.63: 1189 34.63 - 51.95: 285 51.95 - 69.27: 67 69.27 - 86.58: 24 Dihedral angle restraints: 16821 sinusoidal: 6604 harmonic: 10217 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 -2.60 -83.40 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.42 -81.58 1 1.00e+01 1.00e-02 8.19e+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 -4.48 -81.52 1 1.00e+01 1.00e-02 8.18e+01 ... (remaining 16818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4296 0.128 - 0.255: 115 0.255 - 0.383: 2 0.383 - 0.511: 0 0.511 - 0.638: 1 Chirality restraints: 4414 Sorted by residual: chirality pdb=" CB THR B 167 " pdb=" CA THR B 167 " pdb=" OG1 THR B 167 " pdb=" CG2 THR B 167 " both_signs ideal model delta sigma weight residual False 2.55 1.91 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CB ILE C 434 " pdb=" CA ILE C 434 " pdb=" CG1 ILE C 434 " pdb=" CG2 ILE C 434 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA CYS A 649 " pdb=" N CYS A 649 " pdb=" C CYS A 649 " pdb=" CB CYS A 649 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4411 not shown) Planarity restraints: 4856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.065 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO C 373 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " 0.063 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO B 373 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO C 330 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.047 5.00e-02 4.00e+02 ... (remaining 4853 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 642 2.66 - 3.22: 26611 3.22 - 3.78: 41095 3.78 - 4.34: 54564 4.34 - 4.90: 90672 Nonbonded interactions: 213584 Sorted by model distance: nonbonded pdb=" O PRO C 85 " pdb=" OH TYR C 269 " model vdw 2.098 2.440 nonbonded pdb=" ND2 ASN A 394 " pdb=" OH TYR B 200 " model vdw 2.104 2.520 nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.106 2.440 nonbonded pdb=" O ASN B 81 " pdb=" NE2 GLN B 239 " model vdw 2.125 2.520 nonbonded pdb=" O ASN C 978 " pdb=" OG SER C 982 " model vdw 2.125 2.440 ... (remaining 213579 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 370 or (resid 371 through 372 and (name N or na \ me CA or name C or name O or name CB )) or resid 373 through 414 or (resid 415 a \ nd (name N or name CA or name C or name O or name CB )) or resid 416 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 or (resid 421 and (name N or name CA or name C or name O or nam \ e CB )) or resid 422 through 426 or (resid 427 through 428 and (name N or name C \ A or name C or name O or name CB )) or resid 429 through 457 or (resid 458 and ( \ name N or name CA or name C or name O or name CB )) or resid 459 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 \ through 473 or (resid 474 through 475 and (name N or name CA or name C or name \ O or name CB )) or resid 476 through 477 or (resid 478 and (name N or name CA or \ name C or name O or name CB )) or resid 479 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 515 or (res \ id 516 and (name N or name CA or name C or name O or name CB )) or resid 517 thr \ ough 522 or (resid 523 and (name N or name CA or name C or name O or name CB )) \ or resid 524 through 1146 or resid 1301 through 1312)) selection = (chain 'B' and (resid 27 through 1146 or resid 1301 through 1312)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 10.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 28.930 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 78.470 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.008 0.139 27745 Z= 0.550 Angle : 0.972 12.618 37877 Z= 0.529 Chirality : 0.056 0.638 4414 Planarity : 0.005 0.101 4856 Dihedral : 13.468 86.582 10141 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.67 % Favored : 94.84 % Rotamer: Outliers : 1.54 % Allowed : 8.21 % Favored : 90.25 % 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: -1.86 (0.13), residues: 3472 helix: 0.26 (0.20), residues: 641 sheet: -0.86 (0.15), residues: 938 loop : -2.02 (0.12), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP H 110 HIS 0.007 0.002 HIS C1048 PHE 0.032 0.003 PHE A1089 TYR 0.039 0.003 TYR C 453 ARG 0.011 0.001 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7564 (m-80) cc_final: 0.7330 (m-10) REVERT: A 200 TYR cc_start: 0.9161 (m-80) cc_final: 0.8928 (m-80) REVERT: A 229 LEU cc_start: 0.9042 (mt) cc_final: 0.8833 (mt) REVERT: A 378 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8817 (mttt) REVERT: A 392 PHE cc_start: 0.8407 (m-80) cc_final: 0.8063 (m-10) REVERT: A 481 ASN cc_start: 0.9214 (m-40) cc_final: 0.8734 (p0) REVERT: A 516 GLU cc_start: 0.8254 (tt0) cc_final: 0.7888 (tm-30) REVERT: A 773 GLU cc_start: 0.7870 (tm-30) cc_final: 0.6950 (tm-30) REVERT: A 777 ASN cc_start: 0.8499 (m-40) cc_final: 0.7714 (m110) REVERT: A 780 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 983 ARG cc_start: 0.9010 (ptm-80) cc_final: 0.8769 (ttp80) REVERT: B 223 LEU cc_start: 0.9001 (mp) cc_final: 0.8642 (mt) REVERT: B 353 TRP cc_start: 0.7214 (p-90) cc_final: 0.6193 (p-90) REVERT: B 365 TYR cc_start: 0.8298 (m-80) cc_final: 0.7767 (m-80) REVERT: B 964 LYS cc_start: 0.9375 (tptp) cc_final: 0.9028 (tppt) REVERT: B 1002 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 1005 GLN cc_start: 0.9345 (tp-100) cc_final: 0.8799 (tp-100) REVERT: C 360 ASN cc_start: 0.8967 (t0) cc_final: 0.8750 (p0) REVERT: C 779 GLN cc_start: 0.9237 (mm-40) cc_final: 0.9030 (tp40) REVERT: C 960 ASN cc_start: 0.9509 (t0) cc_final: 0.9106 (t0) REVERT: I 37 VAL cc_start: 0.7944 (t) cc_final: 0.7696 (t) REVERT: I 67 ARG cc_start: 0.7553 (ptt180) cc_final: 0.7146 (ptt180) REVERT: J 50 ILE cc_start: 0.9398 (mm) cc_final: 0.9132 (mm) outliers start: 43 outliers final: 18 residues processed: 255 average time/residue: 0.4657 time to fit residues: 182.1920 Evaluate side-chains 142 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 140 optimal weight: 20.0000 chunk 272 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 chunk 203 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 394 ASN A 414 GLN A 540 ASN A 657 ASN A 955 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN B 188 ASN B 409 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 354 ASN C 417 ASN C 505 HIS C 709 ASN C 762 GLN C 978 ASN C1088 HIS J 81 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27745 Z= 0.207 Angle : 0.624 9.009 37877 Z= 0.328 Chirality : 0.044 0.153 4414 Planarity : 0.005 0.051 4856 Dihedral : 6.858 58.039 4575 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 1.50 % Allowed : 11.64 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3472 helix: 1.28 (0.21), residues: 665 sheet: -0.33 (0.16), residues: 922 loop : -1.71 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.005 0.001 HIS A1088 PHE 0.026 0.001 PHE A 515 TYR 0.021 0.001 TYR J 88 ARG 0.008 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 4.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.9142 (m-80) cc_final: 0.8914 (m-80) REVERT: A 773 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6657 (tm-30) REVERT: A 777 ASN cc_start: 0.7647 (m-40) cc_final: 0.7350 (m110) REVERT: A 1029 MET cc_start: 0.9350 (tpp) cc_final: 0.8615 (tpp) REVERT: B 336 CYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7412 (m) REVERT: B 353 TRP cc_start: 0.6721 (p-90) cc_final: 0.5882 (p-90) REVERT: B 365 TYR cc_start: 0.8132 (m-80) cc_final: 0.7745 (m-80) REVERT: B 964 LYS cc_start: 0.9356 (tptp) cc_final: 0.8978 (tppt) REVERT: B 1005 GLN cc_start: 0.9276 (tp-100) cc_final: 0.8716 (tp-100) REVERT: C 229 LEU cc_start: 0.8759 (tp) cc_final: 0.8364 (tt) REVERT: C 282 ASN cc_start: 0.9301 (OUTLIER) cc_final: 0.9056 (m-40) REVERT: C 754 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9261 (mt) REVERT: C 960 ASN cc_start: 0.9501 (t0) cc_final: 0.9239 (m110) REVERT: J 50 ILE cc_start: 0.9233 (mm) cc_final: 0.8905 (mm) outliers start: 42 outliers final: 22 residues processed: 209 average time/residue: 0.4103 time to fit residues: 141.7284 Evaluate side-chains 146 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 615 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 780 GLU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 316 optimal weight: 20.0000 chunk 342 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 313 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 253 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 914 ASN ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1134 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.150 27745 Z= 0.570 Angle : 0.809 10.481 37877 Z= 0.417 Chirality : 0.047 0.226 4414 Planarity : 0.005 0.061 4856 Dihedral : 6.893 57.133 4562 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.39 % Favored : 94.50 % Rotamer: Outliers : 3.46 % Allowed : 13.11 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.17 (0.13), residues: 3472 helix: 0.87 (0.20), residues: 652 sheet: -0.48 (0.16), residues: 914 loop : -1.55 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 110 HIS 0.005 0.001 HIS A1083 PHE 0.035 0.003 PHE A 375 TYR 0.030 0.002 TYR B1067 ARG 0.017 0.001 ARG I 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 109 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.9293 (mmmm) cc_final: 0.9045 (pttt) REVERT: A 1029 MET cc_start: 0.9515 (tpp) cc_final: 0.8934 (tpp) REVERT: B 336 CYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7587 (m) REVERT: B 353 TRP cc_start: 0.6740 (p-90) cc_final: 0.6524 (p-90) REVERT: B 365 TYR cc_start: 0.8075 (m-80) cc_final: 0.7733 (m-80) REVERT: B 515 PHE cc_start: 0.8916 (p90) cc_final: 0.8669 (p90) REVERT: B 712 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9271 (mm) REVERT: B 791 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8875 (p) REVERT: B 904 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.8200 (m-10) REVERT: B 964 LYS cc_start: 0.9494 (tptp) cc_final: 0.9232 (tppt) REVERT: C 712 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9062 (mm) REVERT: C 754 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9208 (mt) REVERT: C 902 MET cc_start: 0.9289 (tpp) cc_final: 0.9066 (tpt) REVERT: C 960 ASN cc_start: 0.9538 (t0) cc_final: 0.9146 (t0) REVERT: J 50 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9175 (mm) outliers start: 97 outliers final: 53 residues processed: 195 average time/residue: 0.3693 time to fit residues: 119.3275 Evaluate side-chains 159 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 99 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 212 optimal weight: 7.9990 chunk 317 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 301 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 506 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 439 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 282 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS C 965 GLN I 84 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27745 Z= 0.180 Angle : 0.569 9.101 37877 Z= 0.299 Chirality : 0.043 0.175 4414 Planarity : 0.004 0.058 4856 Dihedral : 6.072 59.070 4561 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 2.89 % Allowed : 14.82 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.68 (0.14), residues: 3472 helix: 1.73 (0.21), residues: 638 sheet: -0.24 (0.16), residues: 916 loop : -1.36 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS A1088 PHE 0.020 0.001 PHE A 375 TYR 0.015 0.001 TYR I 80 ARG 0.003 0.000 ARG I 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 127 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8165 (t) REVERT: A 392 PHE cc_start: 0.8424 (m-80) cc_final: 0.8120 (m-10) REVERT: A 523 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8684 (t) REVERT: A 1029 MET cc_start: 0.9338 (tpp) cc_final: 0.8567 (tpp) REVERT: B 81 ASN cc_start: 0.6361 (OUTLIER) cc_final: 0.5559 (t0) REVERT: B 242 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8720 (mt) REVERT: B 336 CYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7252 (m) REVERT: B 353 TRP cc_start: 0.6622 (p-90) cc_final: 0.6313 (p-90) REVERT: B 365 TYR cc_start: 0.7920 (m-80) cc_final: 0.7565 (m-80) REVERT: B 515 PHE cc_start: 0.8883 (p90) cc_final: 0.8599 (p90) REVERT: B 712 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9214 (mm) REVERT: B 855 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6201 (m-80) REVERT: B 904 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7689 (m-10) REVERT: B 964 LYS cc_start: 0.9430 (tptp) cc_final: 0.9091 (tppt) REVERT: B 1005 GLN cc_start: 0.9277 (tp-100) cc_final: 0.8698 (tp-100) REVERT: C 712 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8957 (mm) REVERT: C 960 ASN cc_start: 0.9519 (t0) cc_final: 0.9117 (t0) outliers start: 81 outliers final: 43 residues processed: 203 average time/residue: 0.3639 time to fit residues: 122.2150 Evaluate side-chains 161 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 109 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 250 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 287 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 27745 Z= 0.290 Angle : 0.592 7.708 37877 Z= 0.310 Chirality : 0.043 0.193 4414 Planarity : 0.004 0.053 4856 Dihedral : 5.927 57.973 4561 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 3.29 % Allowed : 15.54 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3472 helix: 1.63 (0.21), residues: 650 sheet: -0.26 (0.16), residues: 928 loop : -1.30 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.002 0.001 HIS A1083 PHE 0.020 0.001 PHE A 375 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 118 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8232 (t) REVERT: A 392 PHE cc_start: 0.8469 (m-80) cc_final: 0.8141 (m-10) REVERT: A 773 GLU cc_start: 0.8812 (tt0) cc_final: 0.8388 (tm-30) REVERT: B 81 ASN cc_start: 0.6526 (OUTLIER) cc_final: 0.5559 (t0) REVERT: B 336 CYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7187 (m) REVERT: B 353 TRP cc_start: 0.6668 (p-90) cc_final: 0.6317 (p-90) REVERT: B 365 TYR cc_start: 0.7909 (m-80) cc_final: 0.7535 (m-80) REVERT: B 515 PHE cc_start: 0.8904 (p90) cc_final: 0.8666 (p90) REVERT: B 712 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9223 (mm) REVERT: B 855 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6110 (m-80) REVERT: B 904 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7811 (m-10) REVERT: B 960 ASN cc_start: 0.9433 (t0) cc_final: 0.9062 (t0) REVERT: B 964 LYS cc_start: 0.9461 (tptp) cc_final: 0.9129 (tppt) REVERT: B 1005 GLN cc_start: 0.9318 (tp-100) cc_final: 0.8710 (tp-100) REVERT: C 282 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8857 (m-40) REVERT: C 712 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9001 (mm) REVERT: C 960 ASN cc_start: 0.9529 (t0) cc_final: 0.9131 (t0) REVERT: J 49 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.6006 (ptt) outliers start: 92 outliers final: 51 residues processed: 201 average time/residue: 0.3620 time to fit residues: 122.3854 Evaluate side-chains 161 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 101 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.9990 chunk 302 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 197 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 336 optimal weight: 20.0000 chunk 279 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 111 optimal weight: 0.3980 chunk 176 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 81 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN H 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27745 Z= 0.143 Angle : 0.547 9.092 37877 Z= 0.284 Chirality : 0.043 0.282 4414 Planarity : 0.004 0.058 4856 Dihedral : 5.583 59.941 4561 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 3.04 % Allowed : 16.36 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.44 (0.14), residues: 3472 helix: 1.65 (0.21), residues: 674 sheet: -0.12 (0.16), residues: 955 loop : -1.14 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 436 HIS 0.003 0.000 HIS A 519 PHE 0.028 0.001 PHE I 107 TYR 0.015 0.001 TYR B1067 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 122 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.8084 (t) REVERT: A 392 PHE cc_start: 0.8373 (m-80) cc_final: 0.8008 (m-10) REVERT: A 523 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8605 (t) REVERT: A 1029 MET cc_start: 0.9325 (tpp) cc_final: 0.8545 (tpp) REVERT: B 81 ASN cc_start: 0.6235 (OUTLIER) cc_final: 0.5373 (t0) REVERT: B 242 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8686 (mt) REVERT: B 333 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7954 (m) REVERT: B 336 CYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6963 (m) REVERT: B 353 TRP cc_start: 0.6674 (p-90) cc_final: 0.6391 (p-90) REVERT: B 365 TYR cc_start: 0.7887 (m-80) cc_final: 0.7497 (m-10) REVERT: B 515 PHE cc_start: 0.8948 (p90) cc_final: 0.8636 (p90) REVERT: B 712 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9177 (mm) REVERT: B 855 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6073 (m-80) REVERT: B 904 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: B 960 ASN cc_start: 0.9386 (t0) cc_final: 0.9023 (t0) REVERT: B 964 LYS cc_start: 0.9412 (tptp) cc_final: 0.9007 (tppt) REVERT: C 282 ASN cc_start: 0.9284 (OUTLIER) cc_final: 0.8889 (m-40) REVERT: C 712 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8942 (mm) REVERT: C 960 ASN cc_start: 0.9512 (t0) cc_final: 0.9100 (t0) REVERT: H 34 MET cc_start: 0.3761 (mmt) cc_final: 0.3383 (tmm) outliers start: 85 outliers final: 58 residues processed: 199 average time/residue: 0.3608 time to fit residues: 121.9385 Evaluate side-chains 177 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 108 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 50.0000 chunk 37 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 245 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 283 optimal weight: 0.5980 chunk 188 optimal weight: 0.8980 chunk 335 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 154 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27745 Z= 0.142 Angle : 0.536 10.391 37877 Z= 0.277 Chirality : 0.043 0.225 4414 Planarity : 0.004 0.059 4856 Dihedral : 5.320 58.122 4561 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 2.82 % Allowed : 17.14 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.36 (0.14), residues: 3472 helix: 1.66 (0.21), residues: 674 sheet: -0.01 (0.16), residues: 949 loop : -1.09 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.003 0.000 HIS A 519 PHE 0.023 0.001 PHE I 107 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 117 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8011 (t) REVERT: A 392 PHE cc_start: 0.8441 (m-80) cc_final: 0.8083 (m-10) REVERT: A 523 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8573 (t) REVERT: A 1002 GLN cc_start: 0.8914 (tp40) cc_final: 0.8486 (tp-100) REVERT: A 1029 MET cc_start: 0.9355 (tpp) cc_final: 0.8605 (tpp) REVERT: A 1031 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: B 81 ASN cc_start: 0.6069 (OUTLIER) cc_final: 0.5301 (t0) REVERT: B 242 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8677 (mt) REVERT: B 333 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7949 (m) REVERT: B 336 CYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6946 (m) REVERT: B 353 TRP cc_start: 0.6765 (p-90) cc_final: 0.6458 (p-90) REVERT: B 365 TYR cc_start: 0.7896 (m-80) cc_final: 0.7479 (m-10) REVERT: B 515 PHE cc_start: 0.8956 (p90) cc_final: 0.8657 (p90) REVERT: B 712 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9151 (mm) REVERT: B 855 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6085 (m-80) REVERT: B 904 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: B 960 ASN cc_start: 0.9385 (t0) cc_final: 0.9020 (t0) REVERT: B 964 LYS cc_start: 0.9399 (tptp) cc_final: 0.8981 (tppt) REVERT: C 712 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8898 (mm) REVERT: C 904 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8323 (m-10) REVERT: C 960 ASN cc_start: 0.9507 (t0) cc_final: 0.9240 (m110) REVERT: I 67 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7311 (ptt-90) REVERT: J 8 ARG cc_start: 0.8171 (mmp-170) cc_final: 0.7859 (mmp-170) REVERT: H 34 MET cc_start: 0.3634 (mmt) cc_final: 0.3278 (tmm) outliers start: 79 outliers final: 55 residues processed: 185 average time/residue: 0.3654 time to fit residues: 114.4642 Evaluate side-chains 178 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 110 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.142 27745 Z= 0.522 Angle : 0.739 11.844 37877 Z= 0.381 Chirality : 0.046 0.450 4414 Planarity : 0.005 0.059 4856 Dihedral : 6.086 57.679 4559 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 3.18 % Allowed : 17.46 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3472 helix: 1.25 (0.21), residues: 656 sheet: -0.33 (0.16), residues: 928 loop : -1.23 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 110 HIS 0.005 0.001 HIS A1083 PHE 0.025 0.002 PHE A1089 TYR 0.032 0.002 TYR B1067 ARG 0.006 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 108 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8310 (t) REVERT: A 392 PHE cc_start: 0.8529 (m-80) cc_final: 0.8193 (m-10) REVERT: A 523 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8711 (t) REVERT: A 697 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8700 (ttp) REVERT: A 773 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 1002 GLN cc_start: 0.9090 (tp40) cc_final: 0.8771 (tp-100) REVERT: A 1029 MET cc_start: 0.9463 (tpp) cc_final: 0.8800 (tpp) REVERT: A 1031 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: B 81 ASN cc_start: 0.6499 (OUTLIER) cc_final: 0.5679 (t0) REVERT: B 333 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7968 (m) REVERT: B 336 CYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7164 (m) REVERT: B 353 TRP cc_start: 0.6889 (p-90) cc_final: 0.6471 (p-90) REVERT: B 365 TYR cc_start: 0.7966 (m-80) cc_final: 0.7530 (m-10) REVERT: B 712 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9246 (mm) REVERT: B 904 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7985 (m-10) REVERT: B 964 LYS cc_start: 0.9509 (tptp) cc_final: 0.9224 (tppt) REVERT: B 1005 GLN cc_start: 0.9381 (tp40) cc_final: 0.8848 (tp-100) REVERT: C 282 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8852 (m-40) REVERT: C 712 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9089 (mm) REVERT: C 960 ASN cc_start: 0.9536 (t0) cc_final: 0.9136 (t0) REVERT: H 34 MET cc_start: 0.3686 (mmt) cc_final: 0.3206 (tmm) outliers start: 89 outliers final: 62 residues processed: 187 average time/residue: 0.3502 time to fit residues: 110.6765 Evaluate side-chains 173 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 100 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 0.7980 chunk 321 optimal weight: 20.0000 chunk 293 optimal weight: 1.9990 chunk 312 optimal weight: 0.0050 chunk 188 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 245 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 311 optimal weight: 9.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 81 ASN C 239 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27745 Z= 0.160 Angle : 0.564 11.555 37877 Z= 0.292 Chirality : 0.043 0.345 4414 Planarity : 0.004 0.061 4856 Dihedral : 5.575 59.536 4558 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.61 % Allowed : 18.50 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.38 (0.14), residues: 3472 helix: 1.67 (0.21), residues: 670 sheet: -0.14 (0.16), residues: 947 loop : -1.04 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP I 110 HIS 0.003 0.001 HIS A1088 PHE 0.026 0.001 PHE I 107 TYR 0.014 0.001 TYR B1067 ARG 0.004 0.000 ARG I 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 111 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8100 (t) REVERT: A 392 PHE cc_start: 0.8381 (m-80) cc_final: 0.7980 (m-10) REVERT: A 523 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8632 (t) REVERT: A 773 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7534 (tm-30) REVERT: A 904 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.7258 (m-10) REVERT: A 1002 GLN cc_start: 0.8970 (tp40) cc_final: 0.8544 (tp-100) REVERT: A 1029 MET cc_start: 0.9337 (tpp) cc_final: 0.8495 (tpp) REVERT: A 1031 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: B 242 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8661 (mt) REVERT: B 336 CYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6975 (m) REVERT: B 353 TRP cc_start: 0.6926 (p-90) cc_final: 0.6554 (p-90) REVERT: B 365 TYR cc_start: 0.7884 (m-80) cc_final: 0.7465 (m-10) REVERT: B 712 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9176 (mm) REVERT: B 904 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7706 (m-10) REVERT: B 960 ASN cc_start: 0.9401 (t0) cc_final: 0.9050 (t0) REVERT: B 964 LYS cc_start: 0.9426 (tptp) cc_final: 0.9068 (tppt) REVERT: C 282 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.8781 (m110) REVERT: C 712 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8998 (mm) REVERT: C 960 ASN cc_start: 0.9518 (t0) cc_final: 0.9103 (t0) REVERT: I 67 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7260 (ptt-90) REVERT: H 34 MET cc_start: 0.3487 (mmt) cc_final: 0.3065 (tmm) outliers start: 73 outliers final: 50 residues processed: 177 average time/residue: 0.3637 time to fit residues: 108.3015 Evaluate side-chains 165 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 104 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 1.9990 chunk 330 optimal weight: 30.0000 chunk 201 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 229 optimal weight: 0.9990 chunk 346 optimal weight: 40.0000 chunk 319 optimal weight: 8.9990 chunk 276 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 27745 Z= 0.290 Angle : 0.602 10.905 37877 Z= 0.311 Chirality : 0.044 0.415 4414 Planarity : 0.004 0.060 4856 Dihedral : 5.592 58.227 4556 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.43 % Allowed : 18.79 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.45 (0.14), residues: 3472 helix: 1.50 (0.21), residues: 675 sheet: -0.17 (0.16), residues: 928 loop : -1.04 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 110 HIS 0.002 0.001 HIS C1083 PHE 0.020 0.001 PHE I 107 TYR 0.021 0.001 TYR B1067 ARG 0.003 0.000 ARG I 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 106 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8212 (t) REVERT: A 392 PHE cc_start: 0.8491 (m-80) cc_final: 0.8117 (m-10) REVERT: A 523 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8639 (t) REVERT: A 773 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 904 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7476 (m-10) REVERT: A 1002 GLN cc_start: 0.9012 (tp40) cc_final: 0.8633 (tp-100) REVERT: A 1029 MET cc_start: 0.9389 (tpp) cc_final: 0.8631 (tpp) REVERT: A 1031 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: B 242 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8763 (mt) REVERT: B 336 CYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7025 (m) REVERT: B 353 TRP cc_start: 0.6930 (p-90) cc_final: 0.6516 (p-90) REVERT: B 365 TYR cc_start: 0.7945 (m-80) cc_final: 0.7533 (m-10) REVERT: B 712 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9201 (mm) REVERT: B 904 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7781 (m-10) REVERT: B 960 ASN cc_start: 0.9425 (t0) cc_final: 0.9068 (t0) REVERT: B 964 LYS cc_start: 0.9462 (tptp) cc_final: 0.9142 (tppt) REVERT: C 282 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8796 (m-40) REVERT: C 712 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9000 (mm) REVERT: C 960 ASN cc_start: 0.9526 (t0) cc_final: 0.9117 (t0) REVERT: H 34 MET cc_start: 0.3578 (mmt) cc_final: 0.3137 (tmm) outliers start: 68 outliers final: 54 residues processed: 168 average time/residue: 0.3568 time to fit residues: 101.2338 Evaluate side-chains 170 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 106 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 276 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 81 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.088077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053799 restraints weight = 120943.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.055422 restraints weight = 57318.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056445 restraints weight = 35748.383| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27745 Z= 0.178 Angle : 0.553 10.493 37877 Z= 0.286 Chirality : 0.043 0.377 4414 Planarity : 0.004 0.059 4856 Dihedral : 5.373 59.859 4556 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.43 % Allowed : 19.00 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.31 (0.14), residues: 3472 helix: 1.64 (0.21), residues: 675 sheet: -0.11 (0.16), residues: 943 loop : -0.94 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 110 HIS 0.003 0.001 HIS A1088 PHE 0.022 0.001 PHE B 238 TYR 0.016 0.001 TYR B1067 ARG 0.003 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4868.99 seconds wall clock time: 90 minutes 39.19 seconds (5439.19 seconds total)