Starting phenix.real_space_refine on Tue Mar 19 18:41:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlz_32595/03_2024/7wlz_32595.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlz_32595/03_2024/7wlz_32595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlz_32595/03_2024/7wlz_32595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlz_32595/03_2024/7wlz_32595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlz_32595/03_2024/7wlz_32595.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlz_32595/03_2024/7wlz_32595.pdb" } resolution = 2.98 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= 0.024 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 111 5.16 5 C 16003 2.51 5 N 4132 2.21 5 O 4815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 847": "NH1" <-> "NH2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 30": "OD1" <-> "OD2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 1": "OD1" <-> "OD2" Residue "O TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 39": "OD1" <-> "OD2" Residue "O TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 86": "OE1" <-> "OE2" Residue "O PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25061 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8046 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 8 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8144 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 6692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 863, 6692 Classifications: {'peptide': 863} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 44, 'TRANS': 818} Chain breaks: 8 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Chain: "O" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 834 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.39, per 1000 atoms: 0.53 Number of scatterers: 25061 At special positions: 0 Unit cell: (135.876, 137.904, 203.814, 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 111 16.00 O 4815 8.00 N 4132 7.00 C 16003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.01 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.07 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 9.09 Conformation dependent library (CDL) restraints added in 4.4 seconds 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5942 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 51 sheets defined 24.6% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.962A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.867A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.894A pdb=" N SER A 637 " --> pdb=" O TRP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.666A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.592A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 removed outlier: 3.623A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.511A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.818A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.608A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.574A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.911A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.681A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.994A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 4.009A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.623A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.568A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 915 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.631A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.584A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.543A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.527A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.994A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 857 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.036A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1034 removed outlier: 3.510A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 removed outlier: 3.813A pdb=" N THR P 91 " --> pdb=" O ALA P 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.552A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.635A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.537A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.791A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.516A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.731A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.982A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.837A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.169A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.840A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.901A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.304A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.609A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.097A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.481A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.704A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.585A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.020A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.960A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.625A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.635A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.617A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 722 removed outlier: 6.751A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.359A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD6, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AD7, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.584A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.792A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 55 removed outlier: 4.369A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.556A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.574A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 194 through 197 removed outlier: 5.096A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.533A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.961A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.146A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.466A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF1, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.664A pdb=" N THR P 124 " --> pdb=" O TYR P 94 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR P 94 " --> pdb=" O THR P 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL P 126 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.560A pdb=" N LEU O 11 " --> pdb=" O LYS O 108 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP O 110 " --> pdb=" O LEU O 11 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2508 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: 11.03 Time building geometry restraints manager: 10.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4613 1.33 - 1.45: 7067 1.45 - 1.58: 13804 1.58 - 1.71: 0 1.71 - 1.84: 143 Bond restraints: 25627 Sorted by residual: bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta sigma weight residual 1.456 1.489 -0.032 9.40e-03 1.13e+04 1.16e+01 bond pdb=" N VAL O 88 " pdb=" CA VAL O 88 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" N LEU B 492 " pdb=" CA LEU B 492 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.18e-02 7.18e+03 1.13e+01 ... (remaining 25622 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.17: 706 106.17 - 113.22: 13871 113.22 - 120.27: 9362 120.27 - 127.32: 10708 127.32 - 134.37: 217 Bond angle restraints: 34864 Sorted by residual: angle pdb=" N LEU B 368 " pdb=" CA LEU B 368 " pdb=" C LEU B 368 " ideal model delta sigma weight residual 113.41 101.76 11.65 1.22e+00 6.72e-01 9.12e+01 angle pdb=" N GLY B 404 " pdb=" CA GLY B 404 " pdb=" C GLY B 404 " ideal model delta sigma weight residual 112.49 121.41 -8.92 1.21e+00 6.83e-01 5.44e+01 angle pdb=" C VAL B 367 " pdb=" CA VAL B 367 " pdb=" CB VAL B 367 " ideal model delta sigma weight residual 112.14 103.43 8.71 1.35e+00 5.49e-01 4.16e+01 angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 110.62 116.55 -5.93 1.02e+00 9.61e-01 3.38e+01 angle pdb=" CA ILE B 410 " pdb=" C ILE B 410 " pdb=" O ILE B 410 " ideal model delta sigma weight residual 122.63 117.93 4.70 8.70e-01 1.32e+00 2.92e+01 ... (remaining 34859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.88: 14756 22.88 - 45.76: 750 45.76 - 68.64: 94 68.64 - 91.52: 32 91.52 - 114.40: 3 Dihedral angle restraints: 15635 sinusoidal: 6415 harmonic: 9220 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.66 -88.34 1 1.00e+01 1.00e-02 9.32e+01 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 -171.58 85.58 1 1.00e+01 1.00e-02 8.86e+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 -171.09 85.09 1 1.00e+01 1.00e-02 8.78e+01 ... (remaining 15632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 3977 0.160 - 0.319: 63 0.319 - 0.479: 4 0.479 - 0.639: 0 0.639 - 0.798: 1 Chirality restraints: 4045 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 4042 not shown) Planarity restraints: 4495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B1308 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.085 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " -0.333 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG B1306 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " 0.514 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.331 2.00e-02 2.50e+03 2.82e-01 9.97e+02 pdb=" C7 NAG A1301 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.497 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.077 2.00e-02 2.50e+03 ... (remaining 4492 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2942 2.75 - 3.29: 25168 3.29 - 3.82: 39860 3.82 - 4.36: 47193 4.36 - 4.90: 83220 Nonbonded interactions: 198383 Sorted by model distance: nonbonded pdb=" O TRP B 633 " pdb=" OG SER B 637 " model vdw 2.212 2.440 nonbonded pdb=" O THR C 747 " pdb=" OG SER C 750 " model vdw 2.218 2.440 nonbonded pdb=" OE1 GLU B 819 " pdb=" OG SER B1055 " model vdw 2.240 2.440 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.265 2.440 ... (remaining 198378 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 101 or (resid 102 and (name N or name CA or nam \ e C or name O or name CB )) or resid 103 through 118 or (resid 119 and (name N o \ r name CA or name C or name O or name CB )) or resid 120 through 209 or (resid 2 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 212 through \ 228 or (resid 229 and (name N or name CA or name C or name O or name CB )) or r \ esid 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) \ or resid 232 through 333 or (resid 334 and (name N or name CA or name C or name \ O or name CB )) or resid 335 through 461 or (resid 462 and (name N or name CA or \ name C or name O or name CB )) or resid 463 through 502 or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or resid 504 through 556 or (res \ id 557 through 558 and (name N or name CA or name C or name O or name CB )) or r \ esid 559 through 622 or resid 632 through 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 27 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 429 or (resid 430 and (name N o \ r name CA or name C or name O or name CB )) or resid 431 through 468 or resid 49 \ 2 through 536 or (resid 537 and (name N or name CA or name C or name O or name C \ B )) or resid 538 through 562 or (resid 563 and (name N or name CA or name C or \ name O or name CB )) or resid 564 through 579 or (resid 580 and (name N or name \ CA or name C or name O or name CB )) or resid 581 through 1147 or resid 1301 thr \ ough 1309)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 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: 13.110 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 68.870 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.006 0.078 25627 Z= 0.387 Angle : 0.899 12.485 34864 Z= 0.571 Chirality : 0.059 0.798 4045 Planarity : 0.012 0.294 4468 Dihedral : 13.186 114.395 9585 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.15 % Allowed : 1.83 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.14), residues: 3111 helix: 0.42 (0.20), residues: 688 sheet: -1.78 (0.18), residues: 745 loop : -2.30 (0.13), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 633 HIS 0.006 0.001 HIS C 49 PHE 0.031 0.002 PHE A 906 TYR 0.016 0.001 TYR B1067 ARG 0.008 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 2.824 Fit side-chains revert: symmetry clash REVERT: A 577 ARG cc_start: 0.6871 (ttp-170) cc_final: 0.6646 (ttm-80) REVERT: A 886 TRP cc_start: 0.8100 (p90) cc_final: 0.7548 (p90) REVERT: B 88 ASP cc_start: 0.7513 (m-30) cc_final: 0.7053 (p0) REVERT: B 544 ASN cc_start: 0.6982 (m-40) cc_final: 0.6704 (m-40) REVERT: B 1010 GLN cc_start: 0.7916 (mp10) cc_final: 0.7493 (mp10) REVERT: C 44 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7404 (mtt90) REVERT: P 102 MET cc_start: 0.6143 (mtm) cc_final: 0.5934 (mpm) REVERT: O 7 SER cc_start: 0.6280 (m) cc_final: 0.6015 (p) outliers start: 4 outliers final: 0 residues processed: 246 average time/residue: 1.2222 time to fit residues: 352.3771 Evaluate side-chains 155 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 286 optimal weight: 0.0980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 134 GLN A 164 ASN A 314 GLN A 370 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 542 ASN A 607 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 919 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1119 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 317 ASN B 448 ASN B 450 ASN B 606 ASN B 804 GLN B 957 GLN B 960 ASN B1002 GLN C 121 ASN C 271 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 751 ASN C 965 GLN P 13 GLN P 39 GLN O 31 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25627 Z= 0.255 Angle : 0.667 13.584 34864 Z= 0.334 Chirality : 0.047 0.307 4045 Planarity : 0.005 0.065 4468 Dihedral : 7.557 97.331 3954 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.64 % Allowed : 8.84 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3111 helix: 1.11 (0.20), residues: 692 sheet: -1.37 (0.18), residues: 785 loop : -2.06 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 633 HIS 0.007 0.001 HIS P 35 PHE 0.024 0.002 PHE A 168 TYR 0.024 0.001 TYR C1067 ARG 0.006 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 175 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8370 (m-80) cc_final: 0.8159 (m-80) REVERT: A 542 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7076 (t0) REVERT: A 976 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8279 (m) REVERT: A 1010 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: B 88 ASP cc_start: 0.7600 (m-30) cc_final: 0.7221 (p0) REVERT: B 226 LEU cc_start: 0.8440 (tp) cc_final: 0.8121 (pp) REVERT: B 278 LYS cc_start: 0.8153 (tttt) cc_final: 0.7809 (ttpp) REVERT: B 544 ASN cc_start: 0.6956 (m-40) cc_final: 0.6724 (m-40) REVERT: B 979 ASP cc_start: 0.8012 (t0) cc_final: 0.7566 (t0) REVERT: B 983 ARG cc_start: 0.8486 (ttp80) cc_final: 0.7885 (ptt90) REVERT: C 65 PHE cc_start: 0.7630 (m-10) cc_final: 0.7202 (m-10) REVERT: O 4 MET cc_start: 0.4803 (mpp) cc_final: 0.2682 (pmm) outliers start: 45 outliers final: 12 residues processed: 205 average time/residue: 1.0798 time to fit residues: 266.3273 Evaluate side-chains 158 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain O residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 238 optimal weight: 0.0980 chunk 194 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 286 optimal weight: 0.4980 chunk 309 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 chunk 229 optimal weight: 5.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 542 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1119 ASN B 49 HIS B 505 HIS B1002 GLN C 280 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25627 Z= 0.169 Angle : 0.608 11.215 34864 Z= 0.302 Chirality : 0.045 0.284 4045 Planarity : 0.004 0.047 4468 Dihedral : 6.965 91.667 3954 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.42 % Allowed : 11.68 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 3111 helix: 1.37 (0.20), residues: 696 sheet: -1.06 (0.18), residues: 779 loop : -1.93 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 633 HIS 0.008 0.001 HIS A 66 PHE 0.026 0.001 PHE A 133 TYR 0.022 0.001 TYR C 91 ARG 0.004 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 2.711 Fit side-chains revert: symmetry clash REVERT: A 886 TRP cc_start: 0.8045 (p90) cc_final: 0.7561 (p90) REVERT: A 976 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8187 (m) REVERT: B 88 ASP cc_start: 0.7416 (m-30) cc_final: 0.6984 (p0) REVERT: B 278 LYS cc_start: 0.8105 (tttt) cc_final: 0.7785 (ttpp) REVERT: B 979 ASP cc_start: 0.8042 (t0) cc_final: 0.7537 (t0) REVERT: B 983 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7823 (ptt90) REVERT: C 65 PHE cc_start: 0.7442 (m-10) cc_final: 0.7021 (m-10) REVERT: C 762 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7875 (mp10) REVERT: P 34 MET cc_start: 0.3328 (mmm) cc_final: 0.2298 (mtp) REVERT: P 65 LYS cc_start: -0.1282 (OUTLIER) cc_final: -0.2154 (mmmt) REVERT: O 4 MET cc_start: 0.4721 (mpp) cc_final: 0.2811 (pmm) outliers start: 39 outliers final: 15 residues processed: 193 average time/residue: 1.0748 time to fit residues: 250.1998 Evaluate side-chains 169 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain P residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 136 optimal weight: 0.0670 chunk 192 optimal weight: 3.9990 chunk 287 optimal weight: 0.5980 chunk 304 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 272 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1119 ASN B 564 GLN B1088 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 25627 Z= 0.340 Angle : 0.644 10.439 34864 Z= 0.323 Chirality : 0.047 0.305 4045 Planarity : 0.004 0.046 4468 Dihedral : 6.810 90.765 3954 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.67 % Allowed : 12.27 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 3111 helix: 1.33 (0.20), residues: 687 sheet: -0.95 (0.19), residues: 765 loop : -1.87 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 886 HIS 0.005 0.001 HIS B1048 PHE 0.027 0.002 PHE A 133 TYR 0.023 0.001 TYR C1067 ARG 0.005 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 160 time to evaluate : 2.588 Fit side-chains revert: symmetry clash REVERT: A 976 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8247 (m) REVERT: A 1010 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: B 88 ASP cc_start: 0.7530 (m-30) cc_final: 0.7214 (p0) REVERT: B 177 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6474 (tpt) REVERT: C 65 PHE cc_start: 0.7584 (m-10) cc_final: 0.7135 (m-10) REVERT: C 739 THR cc_start: 0.9038 (m) cc_final: 0.8796 (p) REVERT: C 990 GLU cc_start: 0.8070 (pp20) cc_final: 0.7790 (pp20) REVERT: O 4 MET cc_start: 0.4676 (mpp) cc_final: 0.2885 (pmm) outliers start: 73 outliers final: 34 residues processed: 214 average time/residue: 1.0155 time to fit residues: 265.4116 Evaluate side-chains 185 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 259 optimal weight: 0.9990 chunk 210 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 273 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25627 Z= 0.185 Angle : 0.603 11.900 34864 Z= 0.296 Chirality : 0.045 0.279 4045 Planarity : 0.004 0.046 4468 Dihedral : 6.244 77.637 3954 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.01 % Allowed : 14.20 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3111 helix: 1.51 (0.20), residues: 696 sheet: -0.78 (0.19), residues: 736 loop : -1.73 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 633 HIS 0.024 0.001 HIS A 66 PHE 0.027 0.001 PHE A 133 TYR 0.021 0.001 TYR C1067 ARG 0.006 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 166 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8498 (mtt) REVERT: A 886 TRP cc_start: 0.8062 (p90) cc_final: 0.7588 (p90) REVERT: A 976 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8225 (m) REVERT: A 1010 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: B 88 ASP cc_start: 0.7492 (m-30) cc_final: 0.7024 (p0) REVERT: B 177 MET cc_start: 0.7343 (pmt) cc_final: 0.6638 (tpt) REVERT: B 979 ASP cc_start: 0.8024 (t0) cc_final: 0.7593 (t0) REVERT: B 983 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8027 (ptt90) REVERT: C 65 PHE cc_start: 0.7464 (m-10) cc_final: 0.6999 (m-10) REVERT: C 739 THR cc_start: 0.8888 (m) cc_final: 0.8622 (p) REVERT: C 990 GLU cc_start: 0.8212 (pp20) cc_final: 0.7845 (pp20) REVERT: C 992 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: O 4 MET cc_start: 0.4680 (mpp) cc_final: 0.2862 (pmm) outliers start: 55 outliers final: 25 residues processed: 205 average time/residue: 0.9952 time to fit residues: 249.3495 Evaluate side-chains 185 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 304 optimal weight: 8.9990 chunk 253 optimal weight: 0.9980 chunk 141 optimal weight: 40.0000 chunk 25 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 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 66 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1119 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25627 Z= 0.232 Angle : 0.611 11.035 34864 Z= 0.300 Chirality : 0.045 0.288 4045 Planarity : 0.004 0.047 4468 Dihedral : 5.931 69.211 3954 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.56 % Allowed : 15.01 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.15), residues: 3111 helix: 1.49 (0.20), residues: 697 sheet: -0.76 (0.19), residues: 757 loop : -1.71 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 886 HIS 0.005 0.001 HIS C 49 PHE 0.028 0.001 PHE A 133 TYR 0.024 0.001 TYR B 170 ARG 0.005 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 156 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 TRP cc_start: 0.8112 (p90) cc_final: 0.7588 (p90) REVERT: A 976 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8220 (m) REVERT: A 1010 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: B 88 ASP cc_start: 0.7445 (m-30) cc_final: 0.7132 (p0) REVERT: B 170 TYR cc_start: 0.8608 (t80) cc_final: 0.8330 (t80) REVERT: B 177 MET cc_start: 0.7389 (pmt) cc_final: 0.6639 (tpt) REVERT: B 979 ASP cc_start: 0.8071 (t0) cc_final: 0.7416 (t0) REVERT: B 983 ARG cc_start: 0.8509 (ttp80) cc_final: 0.7971 (ptt90) REVERT: C 65 PHE cc_start: 0.7411 (m-10) cc_final: 0.6923 (m-10) REVERT: C 649 CYS cc_start: 0.6374 (OUTLIER) cc_final: 0.6149 (p) REVERT: C 739 THR cc_start: 0.8894 (m) cc_final: 0.8622 (p) REVERT: C 992 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: P 65 LYS cc_start: -0.0706 (OUTLIER) cc_final: -0.2278 (tttt) REVERT: O 4 MET cc_start: 0.4697 (mpp) cc_final: 0.2881 (pmm) outliers start: 70 outliers final: 37 residues processed: 208 average time/residue: 1.0344 time to fit residues: 260.6348 Evaluate side-chains 193 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 65 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 40.0000 chunk 34 optimal weight: 30.0000 chunk 173 optimal weight: 0.4980 chunk 222 optimal weight: 0.3980 chunk 172 optimal weight: 0.9990 chunk 256 optimal weight: 0.5980 chunk 170 optimal weight: 0.3980 chunk 303 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 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 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1119 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25627 Z= 0.162 Angle : 0.589 12.667 34864 Z= 0.287 Chirality : 0.044 0.273 4045 Planarity : 0.004 0.052 4468 Dihedral : 5.525 55.031 3954 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.08 % Allowed : 15.77 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3111 helix: 1.63 (0.20), residues: 698 sheet: -0.69 (0.19), residues: 727 loop : -1.58 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.028 0.001 HIS A 66 PHE 0.029 0.001 PHE C 192 TYR 0.019 0.001 TYR B 170 ARG 0.005 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 165 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 TRP cc_start: 0.8074 (p90) cc_final: 0.7583 (p90) REVERT: A 976 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8201 (m) REVERT: A 990 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7688 (mp0) REVERT: B 88 ASP cc_start: 0.7468 (m-30) cc_final: 0.7005 (p0) REVERT: B 177 MET cc_start: 0.7381 (pmt) cc_final: 0.6645 (tpt) REVERT: B 194 PHE cc_start: 0.7958 (m-80) cc_final: 0.7742 (m-10) REVERT: B 979 ASP cc_start: 0.8079 (t0) cc_final: 0.7766 (t0) REVERT: C 65 PHE cc_start: 0.7327 (m-10) cc_final: 0.6834 (m-10) REVERT: C 649 CYS cc_start: 0.6290 (OUTLIER) cc_final: 0.6064 (p) REVERT: C 739 THR cc_start: 0.8797 (m) cc_final: 0.8529 (p) REVERT: C 992 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: O 4 MET cc_start: 0.4683 (mpp) cc_final: 0.2858 (pmm) outliers start: 57 outliers final: 25 residues processed: 212 average time/residue: 0.9762 time to fit residues: 254.8974 Evaluate side-chains 180 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 238 optimal weight: 0.0070 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1119 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25627 Z= 0.266 Angle : 0.618 11.624 34864 Z= 0.305 Chirality : 0.046 0.296 4045 Planarity : 0.004 0.056 4468 Dihedral : 5.436 55.456 3954 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.30 % Allowed : 15.41 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3111 helix: 1.54 (0.20), residues: 686 sheet: -0.69 (0.19), residues: 728 loop : -1.58 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 886 HIS 0.011 0.001 HIS C 49 PHE 0.028 0.001 PHE A 133 TYR 0.025 0.001 TYR A 904 ARG 0.009 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 158 time to evaluate : 2.956 Fit side-chains revert: symmetry clash REVERT: A 976 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8252 (m) REVERT: A 985 ASP cc_start: 0.7457 (p0) cc_final: 0.6203 (p0) REVERT: A 1010 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: B 177 MET cc_start: 0.7438 (pmt) cc_final: 0.6673 (tpt) REVERT: B 983 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8128 (ttp80) REVERT: C 65 PHE cc_start: 0.7451 (m-10) cc_final: 0.6982 (m-10) REVERT: C 193 VAL cc_start: 0.7752 (t) cc_final: 0.7489 (t) REVERT: C 649 CYS cc_start: 0.6547 (OUTLIER) cc_final: 0.6284 (p) REVERT: C 739 THR cc_start: 0.8809 (m) cc_final: 0.8539 (p) REVERT: C 990 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: P 34 MET cc_start: 0.2801 (mmt) cc_final: 0.0948 (mtp) REVERT: P 65 LYS cc_start: -0.0732 (OUTLIER) cc_final: -0.2284 (tttt) REVERT: O 4 MET cc_start: 0.4645 (mpp) cc_final: 0.2821 (pmm) outliers start: 63 outliers final: 35 residues processed: 207 average time/residue: 0.9541 time to fit residues: 242.0674 Evaluate side-chains 188 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 265 optimal weight: 0.9980 chunk 282 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 123 optimal weight: 0.3980 chunk 222 optimal weight: 0.0670 chunk 86 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 267 optimal weight: 0.2980 chunk 281 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN A1119 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25627 Z= 0.162 Angle : 0.592 12.532 34864 Z= 0.288 Chirality : 0.044 0.273 4045 Planarity : 0.004 0.050 4468 Dihedral : 5.202 54.641 3954 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.61 % Allowed : 16.50 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3111 helix: 1.64 (0.21), residues: 686 sheet: -0.63 (0.19), residues: 734 loop : -1.45 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.006 0.001 HIS C 49 PHE 0.031 0.001 PHE C 192 TYR 0.019 0.001 TYR A 904 ARG 0.008 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 886 TRP cc_start: 0.8051 (p90) cc_final: 0.7600 (p90) REVERT: A 976 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8244 (m) REVERT: A 1010 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7760 (mp10) REVERT: B 177 MET cc_start: 0.7452 (pmt) cc_final: 0.6700 (tpt) REVERT: B 226 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8190 (mm) REVERT: B 983 ARG cc_start: 0.8322 (ttp80) cc_final: 0.8114 (ttp80) REVERT: C 65 PHE cc_start: 0.7353 (m-10) cc_final: 0.6895 (m-10) REVERT: C 193 VAL cc_start: 0.7609 (t) cc_final: 0.7356 (t) REVERT: C 649 CYS cc_start: 0.6471 (OUTLIER) cc_final: 0.6208 (p) REVERT: C 739 THR cc_start: 0.8600 (m) cc_final: 0.8334 (p) REVERT: C 934 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8088 (mt) REVERT: O 4 MET cc_start: 0.4596 (mpp) cc_final: 0.2844 (pmm) REVERT: O 52 LEU cc_start: 0.4427 (tm) cc_final: 0.3920 (tt) outliers start: 44 outliers final: 29 residues processed: 195 average time/residue: 0.9843 time to fit residues: 236.3078 Evaluate side-chains 185 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 0.6980 chunk 299 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 313 optimal weight: 6.9990 chunk 288 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25627 Z= 0.225 Angle : 0.613 14.806 34864 Z= 0.300 Chirality : 0.045 0.290 4045 Planarity : 0.004 0.050 4468 Dihedral : 5.205 54.959 3954 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.57 % Allowed : 16.72 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3111 helix: 1.61 (0.20), residues: 686 sheet: -0.63 (0.19), residues: 738 loop : -1.44 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.005 0.001 HIS A 66 PHE 0.029 0.001 PHE A 168 TYR 0.027 0.001 TYR A 904 ARG 0.008 0.000 ARG B 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 976 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8271 (m) REVERT: A 1010 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: B 170 TYR cc_start: 0.8827 (t80) cc_final: 0.8595 (t80) REVERT: B 177 MET cc_start: 0.7480 (pmt) cc_final: 0.6713 (tpt) REVERT: B 226 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8209 (mm) REVERT: B 983 ARG cc_start: 0.8332 (ttp80) cc_final: 0.8119 (ttp80) REVERT: C 65 PHE cc_start: 0.7451 (m-10) cc_final: 0.7026 (m-10) REVERT: C 193 VAL cc_start: 0.7621 (t) cc_final: 0.7374 (t) REVERT: C 649 CYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6351 (p) REVERT: C 739 THR cc_start: 0.8678 (m) cc_final: 0.8406 (p) REVERT: P 34 MET cc_start: 0.2571 (mmt) cc_final: 0.0880 (ptp) REVERT: O 4 MET cc_start: 0.4627 (mpp) cc_final: 0.2858 (pmm) REVERT: O 52 LEU cc_start: 0.4415 (tm) cc_final: 0.3900 (tt) outliers start: 43 outliers final: 36 residues processed: 186 average time/residue: 1.0142 time to fit residues: 231.5785 Evaluate side-chains 192 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 36 optimal weight: 30.0000 chunk 69 optimal weight: 0.5980 chunk 250 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 257 optimal weight: 0.0980 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.172612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.105822 restraints weight = 46023.886| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.88 r_work: 0.3260 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25627 Z= 0.200 Angle : 0.615 14.501 34864 Z= 0.298 Chirality : 0.045 0.286 4045 Planarity : 0.004 0.052 4468 Dihedral : 5.153 54.781 3954 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.79 % Allowed : 16.76 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 3111 helix: 1.62 (0.20), residues: 686 sheet: -0.61 (0.19), residues: 738 loop : -1.41 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.010 0.001 HIS A 66 PHE 0.033 0.001 PHE C 192 TYR 0.025 0.001 TYR A 904 ARG 0.012 0.000 ARG C 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7226.12 seconds wall clock time: 129 minutes 55.08 seconds (7795.08 seconds total)