Starting phenix.real_space_refine on Fri Feb 23 16:41:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo8_33340/02_2024/7xo8_33340.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo8_33340/02_2024/7xo8_33340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo8_33340/02_2024/7xo8_33340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo8_33340/02_2024/7xo8_33340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo8_33340/02_2024/7xo8_33340.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo8_33340/02_2024/7xo8_33340.pdb" } resolution = 3.48 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= 0.023 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 S 192 5.16 5 Cl 3 4.86 5 C 25008 2.51 5 N 6444 2.21 5 O 7476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 589": "OE1" <-> "OE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 160": "OE1" <-> "OE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F GLU 208": "OE1" <-> "OE2" Residue "F ARG 245": "NH1" <-> "NH2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F GLU 310": "OE1" <-> "OE2" Residue "F GLU 430": "OE1" <-> "OE2" Residue "F GLU 479": "OE1" <-> "OE2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F ARG 518": "NH1" <-> "NH2" Residue "F GLU 527": "OE1" <-> "OE2" Residue "F ARG 559": "NH1" <-> "NH2" Residue "F GLU 589": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E GLU 310": "OE1" <-> "OE2" Residue "E GLU 430": "OE1" <-> "OE2" Residue "E GLU 479": "OE1" <-> "OE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E ARG 559": "NH1" <-> "NH2" Residue "E GLU 589": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39126 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "F" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 19.29, per 1000 atoms: 0.49 Number of scatterers: 39126 At special positions: 0 Unit cell: (160.68, 154.912, 240.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Cl 3 17.00 S 192 16.00 O 7476 8.00 N 6444 7.00 C 25008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 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=1.46 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.09 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 A1074 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 122 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 331 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 801 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 122 " " NAG C1310 " - " ASN C 331 " " NAG C1311 " - " ASN C 657 " " NAG D 903 " - " ASN D 546 " " NAG D 904 " - " ASN D 90 " " NAG E 903 " - " ASN E 546 " " NAG E 904 " - " ASN E 90 " " NAG F 903 " - " ASN F 546 " " NAG F 904 " - " ASN F 90 " Time building additional restraints: 16.09 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" NE2 HIS D 374 " pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 374 " pdb=" ZN F 902 " pdb="ZN ZN F 902 " - pdb=" NE2 HIS F 374 " 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9144 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 51 sheets defined 39.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.101A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.607A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.356A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.775A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.883A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.502A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 778 removed outlier: 3.865A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.693A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.013A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.628A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.504A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.813A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.607A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.356A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.775A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.884A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.502A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 778 removed outlier: 3.866A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.692A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.013A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.628A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1033 removed outlier: 3.504A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.605A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.356A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.776A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.832A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.716A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 778 removed outlier: 3.843A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 868 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.687A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.741A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 947 removed outlier: 4.503A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 959 Processing helix chain 'C' and resid 960 through 965 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.718A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 989 through 1033 removed outlier: 3.618A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.652A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.617A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.002A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.615A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.647A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.957A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.751A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.503A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.866A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.671A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.920A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 531 removed outlier: 3.542A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.743A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.598A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.653A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 81 Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.617A pdb=" N GLN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 4.001A pdb=" N SER F 106 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU F 108 " --> pdb=" O SER F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 108' Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 194 removed outlier: 3.616A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 3.649A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 252 removed outlier: 3.957A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.751A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 299 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.504A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 331 removed outlier: 3.868A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.671A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.920A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 531 removed outlier: 3.541A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.743A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 574 removed outlier: 3.595A pdb=" N VAL F 573 " --> pdb=" O ALA F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.652A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.616A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.001A pdb=" N SER E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 3.616A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.647A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.957A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.751A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.504A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.867A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.671A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.920A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 531 removed outlier: 3.542A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.742A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.598A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.644A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.607A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.799A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 4.338A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.757A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.539A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.601A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.639A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.767A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.644A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.562A pdb=" N LEU B 276 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.798A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 172 removed outlier: 4.337A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.757A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.539A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.601A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.085A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 714 removed outlier: 3.639A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.767A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.764A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.514A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 90 through 94 removed outlier: 4.265A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.114A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.614A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.540A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.603A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.047A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 714 removed outlier: 3.751A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.725A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 3.850A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.644A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.074A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.026A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 131 through 132 removed outlier: 3.645A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU F 142 " --> pdb=" O VAL F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.073A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.026A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.644A pdb=" N VAL E 132 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.074A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.026A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1623 hydrogen bonds defined for protein. 4521 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: 16.13 Time building geometry restraints manager: 17.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6687 1.32 - 1.45: 11258 1.45 - 1.58: 21880 1.58 - 1.70: 0 1.70 - 1.83: 279 Bond restraints: 40104 Sorted by residual: bond pdb=" C PRO B 337 " pdb=" N PHE B 338 " ideal model delta sigma weight residual 1.335 1.262 0.073 1.34e-02 5.57e+03 2.96e+01 bond pdb=" N THR C 208 " pdb=" CA THR C 208 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.78e+01 bond pdb=" N PRO C 295 " pdb=" CA PRO C 295 " ideal model delta sigma weight residual 1.469 1.416 0.053 1.28e-02 6.10e+03 1.70e+01 bond pdb=" N THR C 333 " pdb=" CA THR C 333 " ideal model delta sigma weight residual 1.453 1.501 -0.049 1.18e-02 7.18e+03 1.69e+01 bond pdb=" N LEU A 517 " pdb=" CA LEU A 517 " ideal model delta sigma weight residual 1.455 1.505 -0.050 1.25e-02 6.40e+03 1.61e+01 ... (remaining 40099 not shown) Histogram of bond angle deviations from ideal: 97.22 - 104.59: 694 104.59 - 111.96: 19173 111.96 - 119.33: 13360 119.33 - 126.70: 20676 126.70 - 134.07: 655 Bond angle restraints: 54558 Sorted by residual: angle pdb=" N SER C 530 " pdb=" CA SER C 530 " pdb=" C SER C 530 " ideal model delta sigma weight residual 108.23 122.42 -14.19 1.38e+00 5.25e-01 1.06e+02 angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 111.33 122.30 -10.97 1.43e+00 4.89e-01 5.88e+01 angle pdb=" CA PHE A 329 " pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 117.71 124.59 -6.88 9.20e-01 1.18e+00 5.59e+01 angle pdb=" N GLU A 340 " pdb=" CA GLU A 340 " pdb=" C GLU A 340 " ideal model delta sigma weight residual 114.39 103.95 10.44 1.45e+00 4.76e-01 5.18e+01 angle pdb=" CA PHE C 329 " pdb=" C PHE C 329 " pdb=" O PHE C 329 " ideal model delta sigma weight residual 120.41 111.98 8.43 1.19e+00 7.06e-01 5.02e+01 ... (remaining 54553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 22749 21.65 - 43.29: 1262 43.29 - 64.94: 185 64.94 - 86.59: 49 86.59 - 108.23: 16 Dihedral angle restraints: 24261 sinusoidal: 10056 harmonic: 14205 Sorted by residual: dihedral pdb=" C THR C 523 " pdb=" N THR C 523 " pdb=" CA THR C 523 " pdb=" CB THR C 523 " ideal model delta harmonic sigma weight residual -122.00 -149.28 27.28 0 2.50e+00 1.60e-01 1.19e+02 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -172.49 86.49 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" N THR C 523 " pdb=" C THR C 523 " pdb=" CA THR C 523 " pdb=" CB THR C 523 " ideal model delta harmonic sigma weight residual 123.40 146.10 -22.70 0 2.50e+00 1.60e-01 8.25e+01 ... (remaining 24258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.313: 6088 0.313 - 0.625: 21 0.625 - 0.938: 3 0.938 - 1.251: 2 1.251 - 1.563: 3 Chirality restraints: 6117 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.84 -1.56 2.00e-01 2.50e+01 6.11e+01 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.86 -1.54 2.00e-01 2.50e+01 5.95e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-01 2.50e+01 5.15e+01 ... (remaining 6114 not shown) Planarity restraints: 7044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG B1308 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1311 " 0.343 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG C1311 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C1311 " 0.082 2.00e-02 2.50e+03 pdb=" N2 NAG C1311 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG C1311 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.319 2.00e-02 2.50e+03 2.71e-01 9.17e+02 pdb=" C7 NAG A1306 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.472 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.051 2.00e-02 2.50e+03 ... (remaining 7041 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 7 2.00 - 2.72: 1920 2.72 - 3.45: 56090 3.45 - 4.17: 92360 4.17 - 4.90: 164857 Nonbonded interactions: 315234 Sorted by model distance: nonbonded pdb=" OG SER B 530 " pdb=" NE2 GLN B 580 " model vdw 1.275 2.520 nonbonded pdb=" OE1 GLU A 169 " pdb=" NH2 ARG B 357 " model vdw 1.298 2.520 nonbonded pdb=" CG2 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 1.466 3.460 nonbonded pdb=" OD1 ASN C 360 " pdb=" OG1 THR C 523 " model vdw 1.747 2.440 nonbonded pdb=" CB SER B 530 " pdb=" NE2 GLN B 580 " model vdw 1.758 3.520 ... (remaining 315229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 25.600 Check model and map are aligned: 0.720 Set scattering table: 0.390 Process input model: 109.220 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.260 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: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4584 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 : 0.004 0.073 40104 Z= 0.243 Angle : 0.714 14.187 54558 Z= 0.434 Chirality : 0.069 1.563 6117 Planarity : 0.013 0.299 7005 Dihedral : 13.521 108.234 15027 Min Nonbonded Distance : 1.275 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.56 % Favored : 96.28 % Rotamer: Outliers : 0.45 % Allowed : 9.72 % Favored : 89.83 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.11), residues: 4809 helix: -0.56 (0.11), residues: 1750 sheet: -1.76 (0.18), residues: 628 loop : -2.85 (0.11), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 165 HIS 0.002 0.000 HIS F 374 PHE 0.027 0.001 PHE C 329 TYR 0.023 0.001 TYR A 279 ARG 0.018 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 880 time to evaluate : 4.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.4954 (OUTLIER) cc_final: 0.4657 (pt) REVERT: A 327 VAL cc_start: 0.8676 (t) cc_final: 0.8324 (p) REVERT: A 328 ARG cc_start: 0.7472 (mmm160) cc_final: 0.7038 (mtp85) REVERT: A 534 VAL cc_start: 0.8634 (t) cc_final: 0.8342 (m) REVERT: A 587 ILE cc_start: 0.7725 (mt) cc_final: 0.7441 (mt) REVERT: A 658 ASN cc_start: 0.7525 (p0) cc_final: 0.6387 (p0) REVERT: A 692 ILE cc_start: 0.8364 (mm) cc_final: 0.8164 (mt) REVERT: A 820 ASP cc_start: 0.7374 (t0) cc_final: 0.7074 (t0) REVERT: A 1073 LYS cc_start: 0.7519 (mtpp) cc_final: 0.7243 (mtpp) REVERT: A 1084 ASP cc_start: 0.7029 (m-30) cc_final: 0.6596 (t0) REVERT: A 1117 THR cc_start: 0.8027 (m) cc_final: 0.7797 (m) REVERT: B 190 ARG cc_start: 0.4855 (mtt180) cc_final: 0.3325 (mtt-85) REVERT: B 539 VAL cc_start: 0.6917 (m) cc_final: 0.6672 (m) REVERT: B 737 ASP cc_start: 0.6655 (t0) cc_final: 0.6440 (t0) REVERT: B 741 TYR cc_start: 0.7479 (t80) cc_final: 0.7018 (t80) REVERT: B 753 LEU cc_start: 0.7458 (tp) cc_final: 0.7206 (tp) REVERT: B 762 GLN cc_start: 0.7074 (tt0) cc_final: 0.6843 (tt0) REVERT: B 819 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6575 (mt-10) REVERT: B 858 LEU cc_start: 0.8027 (mp) cc_final: 0.7805 (mp) REVERT: B 1038 LYS cc_start: 0.7814 (mmmm) cc_final: 0.7401 (mmmm) REVERT: C 227 VAL cc_start: 0.7957 (m) cc_final: 0.7722 (t) REVERT: C 295 PRO cc_start: 0.8500 (Cg_exo) cc_final: 0.8121 (Cg_endo) REVERT: C 542 ASN cc_start: 0.7421 (t0) cc_final: 0.7116 (t0) REVERT: C 572 THR cc_start: 0.8058 (m) cc_final: 0.7831 (t) REVERT: C 587 ILE cc_start: 0.8513 (mp) cc_final: 0.8055 (mm) REVERT: C 655 TYR cc_start: 0.6571 (t80) cc_final: 0.6138 (t80) REVERT: C 692 ILE cc_start: 0.8657 (mm) cc_final: 0.8413 (mt) REVERT: C 737 ASP cc_start: 0.7068 (t0) cc_final: 0.6804 (t70) REVERT: C 1017 GLU cc_start: 0.6604 (tp30) cc_final: 0.6181 (tp30) REVERT: C 1108 ASN cc_start: 0.7327 (m-40) cc_final: 0.7124 (m-40) REVERT: D 355 ASP cc_start: 0.4204 (t0) cc_final: 0.3990 (t0) REVERT: F 117 ASN cc_start: 0.5784 (m-40) cc_final: 0.5279 (m-40) REVERT: F 119 ILE cc_start: 0.3092 (mt) cc_final: 0.2513 (tt) REVERT: F 558 LEU cc_start: 0.5242 (mt) cc_final: 0.4303 (mt) outliers start: 19 outliers final: 8 residues processed: 893 average time/residue: 0.5044 time to fit residues: 737.5893 Evaluate side-chains 745 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 736 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 534 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 9.9990 chunk 366 optimal weight: 7.9990 chunk 203 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 246 optimal weight: 0.0020 chunk 195 optimal weight: 0.9990 chunk 378 optimal weight: 4.9990 chunk 146 optimal weight: 30.0000 chunk 230 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 50.0000 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 188 ASN A 314 GLN A 360 ASN A 439 ASN A 474 GLN A 481 ASN A 563 GLN A 607 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 755 GLN A 895 GLN A 928 ASN A 935 GLN A 955 ASN A 957 GLN A 965 GLN A 978 ASN A1088 HIS B 125 ASN B 164 ASN B 188 ASN B 439 ASN B 474 GLN B 481 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 804 GLN B 895 GLN B 949 GLN B 955 ASN B 957 GLN B 978 ASN B1135 ASN C 52 GLN C 115 GLN C 125 ASN C 314 GLN C 317 ASN C 439 ASN C 481 ASN C 607 GLN C 784 GLN C 925 ASN C 955 ASN C 965 GLN C1119 ASN C1135 ASN D 51 ASN D 239 HIS D 330 ASN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN F 51 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 121 ASN F 322 ASN F 330 ASN F 345 HIS F 508 ASN F 578 ASN E 51 ASN E 58 ASN E 81 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 GLN E 505 HIS E 578 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5009 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40104 Z= 0.276 Angle : 0.683 16.273 54558 Z= 0.341 Chirality : 0.047 0.337 6117 Planarity : 0.005 0.056 7005 Dihedral : 5.899 91.264 6050 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.76 % Rotamer: Outliers : 3.37 % Allowed : 14.10 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.11), residues: 4809 helix: 0.46 (0.12), residues: 1755 sheet: -1.36 (0.20), residues: 595 loop : -2.20 (0.11), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 461 HIS 0.015 0.001 HIS B 207 PHE 0.031 0.002 PHE B 275 TYR 0.024 0.002 TYR D 41 ARG 0.011 0.001 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 826 time to evaluate : 3.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.6531 (tt0) cc_final: 0.6259 (tt0) REVERT: A 327 VAL cc_start: 0.8247 (t) cc_final: 0.8018 (p) REVERT: A 543 PHE cc_start: 0.6565 (m-10) cc_final: 0.6288 (m-80) REVERT: A 576 VAL cc_start: 0.7756 (p) cc_final: 0.7512 (m) REVERT: A 619 GLU cc_start: 0.5345 (pm20) cc_final: 0.3774 (mp0) REVERT: A 658 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7333 (p0) REVERT: A 660 TYR cc_start: 0.7455 (m-10) cc_final: 0.7072 (m-80) REVERT: A 737 ASP cc_start: 0.6313 (t0) cc_final: 0.6111 (t0) REVERT: A 774 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7463 (mp10) REVERT: A 787 GLN cc_start: 0.7925 (mt0) cc_final: 0.7724 (mt0) REVERT: A 790 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7372 (mtmm) REVERT: A 820 ASP cc_start: 0.7587 (t0) cc_final: 0.7322 (t0) REVERT: A 965 GLN cc_start: 0.7329 (tt0) cc_final: 0.6788 (tt0) REVERT: A 1136 THR cc_start: 0.7897 (t) cc_final: 0.7695 (t) REVERT: B 317 ASN cc_start: 0.7779 (m110) cc_final: 0.7434 (m-40) REVERT: B 670 ILE cc_start: 0.8645 (mp) cc_final: 0.8405 (mt) REVERT: B 698 SER cc_start: 0.7727 (t) cc_final: 0.7314 (p) REVERT: B 704 SER cc_start: 0.8385 (t) cc_final: 0.8036 (p) REVERT: B 720 ILE cc_start: 0.8549 (mm) cc_final: 0.8279 (mt) REVERT: B 761 THR cc_start: 0.7920 (t) cc_final: 0.7712 (m) REVERT: B 776 LYS cc_start: 0.8368 (tttt) cc_final: 0.8080 (ttpp) REVERT: B 786 LYS cc_start: 0.7266 (ptmm) cc_final: 0.7030 (ptmm) REVERT: B 895 GLN cc_start: 0.7555 (pt0) cc_final: 0.7339 (pt0) REVERT: B 933 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7645 (ttpp) REVERT: B 1019 ARG cc_start: 0.7107 (ttm110) cc_final: 0.6568 (ttp-110) REVERT: B 1038 LYS cc_start: 0.8009 (mmmm) cc_final: 0.7768 (mmmm) REVERT: B 1118 ASP cc_start: 0.7082 (t70) cc_final: 0.6823 (t0) REVERT: B 1130 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7983 (mt) REVERT: B 1139 ASP cc_start: 0.7927 (t0) cc_final: 0.7678 (t0) REVERT: C 51 THR cc_start: 0.6343 (OUTLIER) cc_final: 0.5338 (m) REVERT: C 104 TRP cc_start: 0.6577 (m-90) cc_final: 0.5572 (m-10) REVERT: C 227 VAL cc_start: 0.8094 (m) cc_final: 0.7840 (t) REVERT: C 308 VAL cc_start: 0.8715 (p) cc_final: 0.8305 (m) REVERT: C 572 THR cc_start: 0.8232 (m) cc_final: 0.7966 (t) REVERT: C 586 ASP cc_start: 0.6974 (m-30) cc_final: 0.6502 (m-30) REVERT: C 587 ILE cc_start: 0.8633 (mp) cc_final: 0.8156 (mm) REVERT: C 602 THR cc_start: 0.7776 (p) cc_final: 0.7564 (p) REVERT: C 673 SER cc_start: 0.8516 (p) cc_final: 0.8305 (t) REVERT: C 703 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7584 (p0) REVERT: C 822 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8364 (tp) REVERT: C 1005 GLN cc_start: 0.7901 (tp40) cc_final: 0.7605 (tp40) REVERT: C 1088 HIS cc_start: 0.7946 (m170) cc_final: 0.7697 (m170) REVERT: C 1092 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5759 (mm-30) REVERT: C 1097 SER cc_start: 0.8440 (t) cc_final: 0.8179 (p) REVERT: D 86 GLN cc_start: 0.2563 (OUTLIER) cc_final: 0.2259 (pm20) REVERT: D 270 MET cc_start: -0.0813 (mtt) cc_final: -0.1124 (ttm) outliers start: 143 outliers final: 64 residues processed: 914 average time/residue: 0.5304 time to fit residues: 800.3035 Evaluate side-chains 822 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 751 time to evaluate : 3.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 10.0000 chunk 136 optimal weight: 30.0000 chunk 365 optimal weight: 5.9990 chunk 298 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 chunk 439 optimal weight: 0.8980 chunk 474 optimal weight: 40.0000 chunk 391 optimal weight: 7.9990 chunk 435 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 352 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 644 GLN A 751 ASN A 949 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 544 ASN B 895 GLN C 804 GLN C 954 HIS C 955 ASN D 63 ASN D 81 GLN D 374 HIS D 378 HIS ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS F 322 ASN F 345 HIS F 505 HIS F 522 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5113 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40104 Z= 0.216 Angle : 0.588 9.324 54558 Z= 0.298 Chirality : 0.044 0.241 6117 Planarity : 0.004 0.054 7005 Dihedral : 5.366 101.698 6042 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 3.30 % Allowed : 17.04 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4809 helix: 0.84 (0.13), residues: 1751 sheet: -1.06 (0.19), residues: 614 loop : -1.91 (0.11), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 461 HIS 0.013 0.001 HIS F 345 PHE 0.035 0.002 PHE B 192 TYR 0.025 0.001 TYR C 369 ARG 0.012 0.001 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 808 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 VAL cc_start: 0.3994 (OUTLIER) cc_final: 0.3689 (t) REVERT: A 542 ASN cc_start: 0.7397 (t0) cc_final: 0.7150 (t0) REVERT: A 543 PHE cc_start: 0.6835 (m-10) cc_final: 0.6429 (m-80) REVERT: A 576 VAL cc_start: 0.8188 (p) cc_final: 0.7811 (m) REVERT: A 619 GLU cc_start: 0.5450 (pm20) cc_final: 0.4880 (mp0) REVERT: A 658 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7803 (p0) REVERT: A 737 ASP cc_start: 0.6114 (t0) cc_final: 0.5858 (t0) REVERT: A 790 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7483 (mtmm) REVERT: A 819 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6694 (mt-10) REVERT: A 820 ASP cc_start: 0.7543 (t0) cc_final: 0.7278 (t0) REVERT: A 824 ASN cc_start: 0.8078 (m-40) cc_final: 0.7512 (m110) REVERT: A 922 LEU cc_start: 0.9048 (tp) cc_final: 0.8820 (tt) REVERT: A 1073 LYS cc_start: 0.7708 (ttmm) cc_final: 0.7481 (ttmm) REVERT: A 1075 PHE cc_start: 0.8071 (m-80) cc_final: 0.7792 (m-80) REVERT: A 1084 ASP cc_start: 0.7603 (t0) cc_final: 0.7231 (t0) REVERT: A 1130 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8262 (mt) REVERT: B 317 ASN cc_start: 0.7574 (m110) cc_final: 0.7086 (m-40) REVERT: B 692 ILE cc_start: 0.8675 (mm) cc_final: 0.8409 (mt) REVERT: B 698 SER cc_start: 0.8041 (t) cc_final: 0.7656 (p) REVERT: B 704 SER cc_start: 0.8523 (t) cc_final: 0.8159 (p) REVERT: B 720 ILE cc_start: 0.8565 (mm) cc_final: 0.8262 (mt) REVERT: B 776 LYS cc_start: 0.8321 (tttt) cc_final: 0.8043 (ttpp) REVERT: B 786 LYS cc_start: 0.7290 (ptmm) cc_final: 0.7043 (ptmm) REVERT: B 1019 ARG cc_start: 0.7011 (ttm110) cc_final: 0.6557 (ttp-170) REVERT: B 1031 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6929 (mt-10) REVERT: B 1091 ARG cc_start: 0.7819 (tpp-160) cc_final: 0.7465 (tpp80) REVERT: B 1118 ASP cc_start: 0.7060 (t70) cc_final: 0.6760 (t0) REVERT: B 1130 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8209 (mt) REVERT: C 51 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6313 (m) REVERT: C 104 TRP cc_start: 0.6946 (m-90) cc_final: 0.5834 (m-90) REVERT: C 227 VAL cc_start: 0.8062 (m) cc_final: 0.7827 (t) REVERT: C 287 ASP cc_start: 0.6131 (t0) cc_final: 0.5906 (t0) REVERT: C 306 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7401 (t80) REVERT: C 308 VAL cc_start: 0.8752 (p) cc_final: 0.8346 (m) REVERT: C 556 ASN cc_start: 0.7389 (p0) cc_final: 0.7169 (p0) REVERT: C 572 THR cc_start: 0.8231 (m) cc_final: 0.7996 (t) REVERT: C 587 ILE cc_start: 0.8646 (mp) cc_final: 0.8391 (mt) REVERT: C 615 VAL cc_start: 0.6432 (OUTLIER) cc_final: 0.5214 (t) REVERT: C 643 PHE cc_start: 0.8038 (t80) cc_final: 0.7767 (t80) REVERT: C 822 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8309 (tp) REVERT: C 916 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7733 (tp) REVERT: C 1005 GLN cc_start: 0.7747 (tp40) cc_final: 0.7490 (tp40) REVERT: C 1028 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7700 (mttm) REVERT: C 1051 SER cc_start: 0.8155 (t) cc_final: 0.7930 (m) REVERT: C 1088 HIS cc_start: 0.8281 (m170) cc_final: 0.7943 (m170) REVERT: C 1092 GLU cc_start: 0.6261 (mm-30) cc_final: 0.6041 (mm-30) REVERT: C 1097 SER cc_start: 0.8483 (t) cc_final: 0.8118 (p) REVERT: C 1122 VAL cc_start: 0.8163 (t) cc_final: 0.7832 (m) REVERT: C 1141 LEU cc_start: 0.7695 (tt) cc_final: 0.7438 (tp) REVERT: D 86 GLN cc_start: 0.2533 (OUTLIER) cc_final: 0.2233 (pm20) REVERT: D 249 MET cc_start: 0.2149 (tpp) cc_final: 0.1884 (tpp) REVERT: D 270 MET cc_start: -0.0834 (mtt) cc_final: -0.1189 (ttm) REVERT: F 244 VAL cc_start: 0.2898 (m) cc_final: 0.1915 (t) REVERT: F 315 PHE cc_start: 0.4649 (m-80) cc_final: 0.3624 (m-80) REVERT: F 332 MET cc_start: 0.0681 (tmm) cc_final: 0.0153 (tpp) REVERT: F 587 TYR cc_start: 0.3536 (t80) cc_final: 0.3211 (t80) outliers start: 140 outliers final: 74 residues processed: 889 average time/residue: 0.5099 time to fit residues: 743.2031 Evaluate side-chains 854 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 769 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 409 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 209 optimal weight: 0.0870 chunk 295 optimal weight: 1.9990 chunk 440 optimal weight: 3.9990 chunk 466 optimal weight: 0.4980 chunk 230 optimal weight: 2.9990 chunk 417 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 644 GLN A 774 GLN A 787 GLN A 949 GLN A 955 ASN A 965 GLN A1083 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 755 GLN C 804 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5219 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 40104 Z= 0.245 Angle : 0.591 11.796 54558 Z= 0.301 Chirality : 0.044 0.255 6117 Planarity : 0.004 0.059 7005 Dihedral : 5.296 106.694 6040 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.86 % Rotamer: Outliers : 3.48 % Allowed : 18.97 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4809 helix: 1.05 (0.13), residues: 1741 sheet: -1.03 (0.20), residues: 601 loop : -1.72 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 461 HIS 0.011 0.001 HIS C1083 PHE 0.039 0.002 PHE A 497 TYR 0.030 0.002 TYR F 279 ARG 0.006 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 837 time to evaluate : 4.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7935 (mp) REVERT: A 542 ASN cc_start: 0.7640 (t0) cc_final: 0.7372 (t0) REVERT: A 552 LEU cc_start: 0.7944 (mt) cc_final: 0.7724 (mt) REVERT: A 615 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7094 (p) REVERT: A 619 GLU cc_start: 0.5734 (pm20) cc_final: 0.5219 (mp0) REVERT: A 658 ASN cc_start: 0.8260 (p0) cc_final: 0.7814 (p0) REVERT: A 692 ILE cc_start: 0.9005 (mm) cc_final: 0.8795 (mt) REVERT: A 824 ASN cc_start: 0.8022 (m-40) cc_final: 0.7555 (m-40) REVERT: A 825 LYS cc_start: 0.8134 (tptp) cc_final: 0.7758 (tttp) REVERT: A 922 LEU cc_start: 0.8945 (tp) cc_final: 0.8732 (tt) REVERT: A 995 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6400 (ttm-80) REVERT: A 1072 GLU cc_start: 0.8205 (pm20) cc_final: 0.7803 (pm20) REVERT: A 1084 ASP cc_start: 0.7565 (t0) cc_final: 0.7044 (t0) REVERT: A 1130 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8354 (mt) REVERT: B 88 ASP cc_start: 0.6778 (m-30) cc_final: 0.6556 (m-30) REVERT: B 317 ASN cc_start: 0.7625 (m110) cc_final: 0.7022 (m-40) REVERT: B 692 ILE cc_start: 0.8752 (mm) cc_final: 0.8508 (mt) REVERT: B 698 SER cc_start: 0.8155 (t) cc_final: 0.7876 (p) REVERT: B 704 SER cc_start: 0.8576 (t) cc_final: 0.8268 (p) REVERT: B 720 ILE cc_start: 0.8553 (mm) cc_final: 0.8295 (mt) REVERT: B 776 LYS cc_start: 0.8317 (tttt) cc_final: 0.8057 (ttpp) REVERT: B 786 LYS cc_start: 0.7286 (ptmm) cc_final: 0.7034 (ptmm) REVERT: B 791 THR cc_start: 0.7703 (OUTLIER) cc_final: 0.7449 (p) REVERT: B 1019 ARG cc_start: 0.7010 (ttm110) cc_final: 0.6800 (ttp-170) REVERT: B 1038 LYS cc_start: 0.8009 (mmmm) cc_final: 0.7666 (mmmm) REVERT: B 1072 GLU cc_start: 0.7922 (pm20) cc_final: 0.7633 (pm20) REVERT: B 1118 ASP cc_start: 0.7058 (t70) cc_final: 0.6848 (t70) REVERT: B 1127 ASP cc_start: 0.6759 (t0) cc_final: 0.6400 (t0) REVERT: C 51 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7426 (p) REVERT: C 227 VAL cc_start: 0.8151 (m) cc_final: 0.7788 (t) REVERT: C 240 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.6459 (p) REVERT: C 298 GLU cc_start: 0.7419 (tp30) cc_final: 0.7213 (tt0) REVERT: C 316 SER cc_start: 0.8190 (t) cc_final: 0.7808 (p) REVERT: C 317 ASN cc_start: 0.7602 (m-40) cc_final: 0.7292 (m-40) REVERT: C 513 LEU cc_start: 0.6933 (mm) cc_final: 0.6694 (mt) REVERT: C 542 ASN cc_start: 0.7480 (t0) cc_final: 0.7195 (t0) REVERT: C 558 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7726 (mmmt) REVERT: C 572 THR cc_start: 0.8278 (m) cc_final: 0.8030 (t) REVERT: C 587 ILE cc_start: 0.8608 (mp) cc_final: 0.8393 (mt) REVERT: C 615 VAL cc_start: 0.6981 (OUTLIER) cc_final: 0.6101 (t) REVERT: C 954 HIS cc_start: 0.7315 (m-70) cc_final: 0.7062 (m170) REVERT: C 1005 GLN cc_start: 0.7865 (tp40) cc_final: 0.7500 (tp40) REVERT: C 1075 PHE cc_start: 0.7737 (m-80) cc_final: 0.7401 (m-80) REVERT: C 1097 SER cc_start: 0.8425 (t) cc_final: 0.8106 (p) REVERT: C 1122 VAL cc_start: 0.8226 (t) cc_final: 0.8015 (m) REVERT: C 1141 LEU cc_start: 0.7847 (tt) cc_final: 0.7551 (tp) REVERT: D 152 MET cc_start: 0.1425 (ttp) cc_final: 0.0981 (ttp) REVERT: D 270 MET cc_start: -0.0973 (mtt) cc_final: -0.1182 (ttm) REVERT: D 293 VAL cc_start: 0.2961 (p) cc_final: 0.2155 (m) REVERT: D 325 GLN cc_start: 0.4201 (tm-30) cc_final: 0.3970 (tm-30) REVERT: F 22 GLU cc_start: 0.4022 (tt0) cc_final: 0.3804 (tt0) outliers start: 148 outliers final: 79 residues processed: 928 average time/residue: 0.5044 time to fit residues: 770.8724 Evaluate side-chains 875 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 788 time to evaluate : 4.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 20.0000 chunk 265 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 192 optimal weight: 0.5980 chunk 398 optimal weight: 7.9990 chunk 322 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 419 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 957 GLN A 965 GLN B 66 HIS B 282 ASN B 703 ASN C 207 HIS C 774 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN F 305 GLN F 493 HIS ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 40104 Z= 0.423 Angle : 0.734 14.224 54558 Z= 0.378 Chirality : 0.049 0.373 6117 Planarity : 0.005 0.073 7005 Dihedral : 5.840 99.614 6040 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.18 % Favored : 94.80 % Rotamer: Outliers : 4.50 % Allowed : 19.35 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.95 (0.12), residues: 4809 helix: 0.91 (0.13), residues: 1737 sheet: -1.03 (0.20), residues: 593 loop : -1.70 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 461 HIS 0.019 0.002 HIS C1064 PHE 0.035 0.003 PHE A 192 TYR 0.037 0.002 TYR C 204 ARG 0.013 0.001 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 863 time to evaluate : 4.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7986 (mt) REVERT: A 293 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7809 (pp) REVERT: A 534 VAL cc_start: 0.8693 (t) cc_final: 0.8462 (p) REVERT: A 537 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7705 (mtmt) REVERT: A 542 ASN cc_start: 0.8137 (t0) cc_final: 0.7724 (t0) REVERT: A 612 TYR cc_start: 0.8179 (m-80) cc_final: 0.7953 (m-80) REVERT: A 619 GLU cc_start: 0.6472 (pm20) cc_final: 0.5709 (mp0) REVERT: A 824 ASN cc_start: 0.7957 (m-40) cc_final: 0.7580 (m-40) REVERT: A 995 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6945 (ttm-80) REVERT: A 1066 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.7930 (p) REVERT: A 1072 GLU cc_start: 0.8172 (pm20) cc_final: 0.7876 (pm20) REVERT: A 1084 ASP cc_start: 0.7482 (t0) cc_final: 0.7058 (t0) REVERT: A 1130 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8517 (mt) REVERT: B 54 LEU cc_start: 0.7924 (mt) cc_final: 0.7700 (mt) REVERT: B 239 GLN cc_start: 0.7447 (pm20) cc_final: 0.6830 (pm20) REVERT: B 317 ASN cc_start: 0.7455 (m110) cc_final: 0.7060 (m-40) REVERT: B 551 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8242 (p) REVERT: B 693 ILE cc_start: 0.8375 (pt) cc_final: 0.8166 (mt) REVERT: B 699 LEU cc_start: 0.8654 (mt) cc_final: 0.8359 (mp) REVERT: B 720 ILE cc_start: 0.8574 (mm) cc_final: 0.8325 (mt) REVERT: B 776 LYS cc_start: 0.8300 (tttt) cc_final: 0.8009 (ttpp) REVERT: B 786 LYS cc_start: 0.7318 (ptmm) cc_final: 0.7108 (ptmm) REVERT: B 947 LYS cc_start: 0.7773 (mttt) cc_final: 0.7491 (mttp) REVERT: B 995 ARG cc_start: 0.7380 (ttp-170) cc_final: 0.7089 (mtp180) REVERT: B 998 THR cc_start: 0.8324 (p) cc_final: 0.7951 (m) REVERT: B 1067 TYR cc_start: 0.8505 (t80) cc_final: 0.7987 (t80) REVERT: B 1118 ASP cc_start: 0.7120 (t70) cc_final: 0.6913 (t70) REVERT: B 1127 ASP cc_start: 0.7043 (t0) cc_final: 0.6680 (t0) REVERT: B 1129 VAL cc_start: 0.8791 (t) cc_final: 0.8394 (m) REVERT: B 1139 ASP cc_start: 0.7869 (t0) cc_final: 0.7666 (t0) REVERT: C 36 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8555 (p) REVERT: C 45 SER cc_start: 0.8256 (t) cc_final: 0.7822 (p) REVERT: C 54 LEU cc_start: 0.7655 (mp) cc_final: 0.7249 (mp) REVERT: C 193 VAL cc_start: 0.7704 (t) cc_final: 0.7381 (t) REVERT: C 231 ILE cc_start: 0.2685 (OUTLIER) cc_final: 0.2305 (pt) REVERT: C 306 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7633 (t80) REVERT: C 307 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7549 (p) REVERT: C 308 VAL cc_start: 0.8816 (p) cc_final: 0.8320 (m) REVERT: C 317 ASN cc_start: 0.7803 (m-40) cc_final: 0.7443 (m-40) REVERT: C 369 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6102 (p90) REVERT: C 542 ASN cc_start: 0.7795 (t0) cc_final: 0.7428 (t0) REVERT: C 558 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7764 (mmmt) REVERT: C 572 THR cc_start: 0.8458 (m) cc_final: 0.8112 (p) REVERT: C 604 THR cc_start: 0.8021 (p) cc_final: 0.7805 (m) REVERT: C 642 VAL cc_start: 0.8733 (t) cc_final: 0.8484 (p) REVERT: C 768 THR cc_start: 0.8471 (t) cc_final: 0.8194 (m) REVERT: C 796 TYR cc_start: 0.7494 (t80) cc_final: 0.7269 (t80) REVERT: C 954 HIS cc_start: 0.7353 (m-70) cc_final: 0.7129 (m-70) REVERT: C 1002 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 1005 GLN cc_start: 0.7979 (tp40) cc_final: 0.7551 (tp40) REVERT: C 1136 THR cc_start: 0.8454 (t) cc_final: 0.8185 (p) REVERT: C 1141 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7796 (tp) REVERT: D 152 MET cc_start: 0.1490 (ttp) cc_final: 0.1086 (ttp) REVERT: D 249 MET cc_start: 0.2419 (tpp) cc_final: 0.2147 (tpp) REVERT: D 270 MET cc_start: -0.0726 (mtt) cc_final: -0.0996 (ttm) REVERT: D 293 VAL cc_start: 0.3130 (p) cc_final: 0.2339 (m) REVERT: D 325 GLN cc_start: 0.4342 (tm-30) cc_final: 0.4069 (tm-30) REVERT: E 86 GLN cc_start: 0.3522 (OUTLIER) cc_final: 0.3204 (pm20) outliers start: 191 outliers final: 105 residues processed: 981 average time/residue: 0.5130 time to fit residues: 834.8293 Evaluate side-chains 928 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 810 time to evaluate : 4.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 86 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 0.0470 chunk 420 optimal weight: 0.0670 chunk 92 optimal weight: 0.6980 chunk 274 optimal weight: 0.3980 chunk 115 optimal weight: 0.6980 chunk 467 optimal weight: 9.9990 chunk 387 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 762 GLN A 957 GLN A 965 GLN A1106 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 957 GLN C 218 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN F 394 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40104 Z= 0.179 Angle : 0.599 12.632 54558 Z= 0.303 Chirality : 0.044 0.443 6117 Planarity : 0.004 0.065 7005 Dihedral : 5.527 103.762 6040 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.81 % Favored : 96.17 % Rotamer: Outliers : 3.11 % Allowed : 22.43 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.65 (0.12), residues: 4809 helix: 1.24 (0.13), residues: 1741 sheet: -1.13 (0.20), residues: 607 loop : -1.52 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 461 HIS 0.007 0.001 HIS F 374 PHE 0.039 0.002 PHE A 497 TYR 0.026 0.001 TYR C1110 ARG 0.006 0.000 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 825 time to evaluate : 4.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8199 (mt) cc_final: 0.7947 (mt) REVERT: A 542 ASN cc_start: 0.8031 (t0) cc_final: 0.7714 (t0) REVERT: A 619 GLU cc_start: 0.5716 (pm20) cc_final: 0.4956 (mp0) REVERT: A 824 ASN cc_start: 0.7869 (m-40) cc_final: 0.7535 (m-40) REVERT: A 957 GLN cc_start: 0.7764 (tt0) cc_final: 0.6737 (tt0) REVERT: A 995 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6539 (ttm-80) REVERT: A 1002 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6859 (tm-30) REVERT: A 1066 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.7859 (p) REVERT: A 1130 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 54 LEU cc_start: 0.7764 (mt) cc_final: 0.7412 (mt) REVERT: B 196 ASN cc_start: 0.8282 (t0) cc_final: 0.8082 (t0) REVERT: B 239 GLN cc_start: 0.7265 (pm20) cc_final: 0.6994 (pm20) REVERT: B 278 LYS cc_start: 0.8341 (ptmt) cc_final: 0.8086 (tttt) REVERT: B 317 ASN cc_start: 0.7470 (m110) cc_final: 0.7027 (m-40) REVERT: B 671 CYS cc_start: 0.5350 (m) cc_final: 0.4991 (m) REVERT: B 699 LEU cc_start: 0.8556 (mt) cc_final: 0.8178 (mp) REVERT: B 704 SER cc_start: 0.8562 (t) cc_final: 0.8264 (p) REVERT: B 737 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6457 (t0) REVERT: B 776 LYS cc_start: 0.8269 (tttt) cc_final: 0.7977 (ttpp) REVERT: B 786 LYS cc_start: 0.7308 (ptmm) cc_final: 0.7062 (ptmm) REVERT: B 998 THR cc_start: 0.8152 (p) cc_final: 0.7886 (m) REVERT: B 1019 ARG cc_start: 0.7180 (ttp-110) cc_final: 0.6889 (ttp-170) REVERT: B 1038 LYS cc_start: 0.8100 (mmmm) cc_final: 0.7808 (mmmm) REVERT: B 1067 TYR cc_start: 0.8503 (t80) cc_final: 0.8028 (t80) REVERT: B 1127 ASP cc_start: 0.6986 (t0) cc_final: 0.6622 (t0) REVERT: B 1129 VAL cc_start: 0.8753 (t) cc_final: 0.8305 (m) REVERT: B 1139 ASP cc_start: 0.7786 (t0) cc_final: 0.7563 (t0) REVERT: B 1141 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7058 (tt) REVERT: C 45 SER cc_start: 0.8201 (t) cc_final: 0.7767 (p) REVERT: C 307 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7806 (p) REVERT: C 308 VAL cc_start: 0.8758 (p) cc_final: 0.8377 (m) REVERT: C 317 ASN cc_start: 0.7859 (m-40) cc_final: 0.7493 (m-40) REVERT: C 369 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.5983 (p90) REVERT: C 542 ASN cc_start: 0.7504 (t0) cc_final: 0.7185 (t0) REVERT: C 558 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7739 (mmmt) REVERT: C 572 THR cc_start: 0.8364 (m) cc_final: 0.8032 (p) REVERT: C 642 VAL cc_start: 0.8834 (t) cc_final: 0.8547 (p) REVERT: C 656 VAL cc_start: 0.8349 (t) cc_final: 0.8081 (p) REVERT: C 658 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7448 (p0) REVERT: C 726 ILE cc_start: 0.8568 (mp) cc_final: 0.8338 (mt) REVERT: C 748 GLU cc_start: 0.8009 (pm20) cc_final: 0.7517 (pm20) REVERT: C 768 THR cc_start: 0.8302 (t) cc_final: 0.8074 (m) REVERT: C 902 MET cc_start: 0.7960 (tpp) cc_final: 0.7612 (mmt) REVERT: C 954 HIS cc_start: 0.7260 (m-70) cc_final: 0.7051 (m-70) REVERT: C 1005 GLN cc_start: 0.7776 (tp40) cc_final: 0.7382 (tp40) REVERT: C 1141 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7721 (tp) REVERT: D 152 MET cc_start: 0.1468 (ttp) cc_final: 0.1085 (ttp) REVERT: D 249 MET cc_start: 0.2175 (tpp) cc_final: 0.1918 (tpp) REVERT: F 587 TYR cc_start: 0.3952 (t80) cc_final: 0.3407 (t80) REVERT: E 82 MET cc_start: 0.1585 (mtt) cc_final: 0.1377 (mtt) REVERT: E 86 GLN cc_start: 0.3557 (OUTLIER) cc_final: 0.3208 (pm20) outliers start: 132 outliers final: 87 residues processed: 895 average time/residue: 0.4852 time to fit residues: 714.5382 Evaluate side-chains 900 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 803 time to evaluate : 4.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 266 optimal weight: 0.9980 chunk 341 optimal weight: 9.9990 chunk 264 optimal weight: 3.9990 chunk 393 optimal weight: 3.9990 chunk 260 optimal weight: 0.6980 chunk 465 optimal weight: 8.9990 chunk 291 optimal weight: 3.9990 chunk 283 optimal weight: 0.0970 chunk 214 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN C 505 HIS C 949 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5395 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40104 Z= 0.254 Angle : 0.616 15.819 54558 Z= 0.313 Chirality : 0.045 0.409 6117 Planarity : 0.004 0.059 7005 Dihedral : 5.362 101.913 6038 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 3.72 % Allowed : 22.15 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 4809 helix: 1.30 (0.13), residues: 1746 sheet: -1.05 (0.20), residues: 574 loop : -1.46 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 461 HIS 0.012 0.001 HIS D 373 PHE 0.036 0.002 PHE C1075 TYR 0.024 0.001 TYR C 369 ARG 0.007 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 802 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8261 (mt) cc_final: 0.7986 (mt) REVERT: A 293 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7910 (pp) REVERT: A 619 GLU cc_start: 0.5932 (pm20) cc_final: 0.4647 (mp0) REVERT: A 790 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7609 (mtmt) REVERT: A 824 ASN cc_start: 0.7919 (m-40) cc_final: 0.7575 (m-40) REVERT: A 957 GLN cc_start: 0.7518 (tt0) cc_final: 0.6551 (tt0) REVERT: A 995 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6659 (ttm-80) REVERT: A 1002 GLN cc_start: 0.7181 (tm-30) cc_final: 0.6882 (tm-30) REVERT: A 1066 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7853 (p) REVERT: A 1122 VAL cc_start: 0.8533 (p) cc_final: 0.8281 (m) REVERT: A 1130 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8493 (mt) REVERT: B 54 LEU cc_start: 0.7850 (mt) cc_final: 0.7632 (mt) REVERT: B 58 PHE cc_start: 0.8496 (m-10) cc_final: 0.8213 (m-80) REVERT: B 196 ASN cc_start: 0.8409 (t0) cc_final: 0.8204 (t0) REVERT: B 239 GLN cc_start: 0.7326 (pm20) cc_final: 0.7061 (pm20) REVERT: B 317 ASN cc_start: 0.7473 (m110) cc_final: 0.7022 (m-40) REVERT: B 699 LEU cc_start: 0.8496 (mt) cc_final: 0.8225 (mm) REVERT: B 737 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6470 (t0) REVERT: B 776 LYS cc_start: 0.8252 (tttt) cc_final: 0.7960 (ttpp) REVERT: B 786 LYS cc_start: 0.7251 (ptmm) cc_final: 0.7004 (ptmm) REVERT: B 998 THR cc_start: 0.8203 (p) cc_final: 0.7936 (m) REVERT: B 1019 ARG cc_start: 0.7170 (ttp-110) cc_final: 0.6795 (ttp-170) REVERT: B 1127 ASP cc_start: 0.7075 (t0) cc_final: 0.6713 (t0) REVERT: B 1129 VAL cc_start: 0.8762 (t) cc_final: 0.8318 (m) REVERT: C 45 SER cc_start: 0.8231 (t) cc_final: 0.7805 (p) REVERT: C 307 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7861 (p) REVERT: C 308 VAL cc_start: 0.8760 (p) cc_final: 0.8409 (m) REVERT: C 369 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.5985 (p90) REVERT: C 542 ASN cc_start: 0.7525 (t0) cc_final: 0.7262 (t0) REVERT: C 558 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7743 (mmmt) REVERT: C 572 THR cc_start: 0.8406 (m) cc_final: 0.8067 (p) REVERT: C 591 SER cc_start: 0.7787 (m) cc_final: 0.7445 (m) REVERT: C 642 VAL cc_start: 0.8840 (t) cc_final: 0.8511 (p) REVERT: C 726 ILE cc_start: 0.8585 (mp) cc_final: 0.8262 (mt) REVERT: C 768 THR cc_start: 0.8420 (t) cc_final: 0.8091 (m) REVERT: C 796 TYR cc_start: 0.7221 (t80) cc_final: 0.6994 (t80) REVERT: C 1005 GLN cc_start: 0.7865 (tp40) cc_final: 0.7559 (tp40) REVERT: C 1017 GLU cc_start: 0.7077 (tp30) cc_final: 0.6638 (tp30) REVERT: C 1141 LEU cc_start: 0.8068 (tt) cc_final: 0.7749 (tp) REVERT: D 152 MET cc_start: 0.1511 (ttp) cc_final: 0.1070 (ttp) REVERT: D 249 MET cc_start: 0.2331 (tpp) cc_final: 0.2102 (tpp) REVERT: D 529 LEU cc_start: 0.6620 (mt) cc_final: 0.6381 (mt) REVERT: E 86 GLN cc_start: 0.3499 (OUTLIER) cc_final: 0.3137 (pm20) REVERT: E 366 MET cc_start: 0.3286 (mpp) cc_final: 0.3040 (mpp) outliers start: 158 outliers final: 111 residues processed: 888 average time/residue: 0.4863 time to fit residues: 709.6628 Evaluate side-chains 903 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 783 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 140 optimal weight: 30.0000 chunk 91 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 295 optimal weight: 1.9990 chunk 317 optimal weight: 20.0000 chunk 230 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 365 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40104 Z= 0.217 Angle : 0.615 13.808 54558 Z= 0.311 Chirality : 0.044 0.363 6117 Planarity : 0.004 0.060 7005 Dihedral : 5.303 101.534 6038 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.97 % Favored : 96.01 % Rotamer: Outliers : 3.44 % Allowed : 22.98 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.12), residues: 4809 helix: 1.35 (0.13), residues: 1736 sheet: -1.01 (0.20), residues: 579 loop : -1.41 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 594 HIS 0.024 0.001 HIS C 505 PHE 0.036 0.002 PHE C1075 TYR 0.024 0.001 TYR C 369 ARG 0.012 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 792 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8248 (mt) cc_final: 0.8028 (mt) REVERT: A 293 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7883 (pp) REVERT: A 306 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: A 619 GLU cc_start: 0.5837 (pm20) cc_final: 0.4274 (mp0) REVERT: A 790 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7628 (mtmt) REVERT: A 824 ASN cc_start: 0.7913 (m-40) cc_final: 0.7615 (m-40) REVERT: A 957 GLN cc_start: 0.7201 (tt0) cc_final: 0.6592 (tt0) REVERT: A 995 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6680 (ttm-80) REVERT: A 1002 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6857 (tm-30) REVERT: A 1066 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 1130 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8471 (mt) REVERT: B 54 LEU cc_start: 0.7844 (mt) cc_final: 0.7641 (mt) REVERT: B 196 ASN cc_start: 0.8394 (t0) cc_final: 0.8188 (t0) REVERT: B 239 GLN cc_start: 0.7302 (pm20) cc_final: 0.7000 (pm20) REVERT: B 278 LYS cc_start: 0.8352 (ptmt) cc_final: 0.8078 (tttt) REVERT: B 317 ASN cc_start: 0.7482 (m110) cc_final: 0.7032 (m-40) REVERT: B 699 LEU cc_start: 0.8449 (mt) cc_final: 0.8173 (mm) REVERT: B 776 LYS cc_start: 0.8185 (tttt) cc_final: 0.7906 (ttpp) REVERT: B 786 LYS cc_start: 0.7445 (ptmm) cc_final: 0.7189 (ptmm) REVERT: B 998 THR cc_start: 0.8186 (p) cc_final: 0.7954 (m) REVERT: B 1019 ARG cc_start: 0.7160 (ttp-110) cc_final: 0.6783 (ttp-170) REVERT: B 1075 PHE cc_start: 0.8220 (m-80) cc_final: 0.7985 (m-80) REVERT: B 1129 VAL cc_start: 0.8751 (t) cc_final: 0.8285 (m) REVERT: C 45 SER cc_start: 0.8199 (t) cc_final: 0.7762 (p) REVERT: C 204 TYR cc_start: 0.6752 (m-80) cc_final: 0.6371 (m-80) REVERT: C 307 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7877 (p) REVERT: C 308 VAL cc_start: 0.8757 (p) cc_final: 0.8401 (m) REVERT: C 369 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.6152 (p90) REVERT: C 542 ASN cc_start: 0.7498 (t0) cc_final: 0.7207 (t0) REVERT: C 558 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7755 (mmmt) REVERT: C 572 THR cc_start: 0.8392 (m) cc_final: 0.8044 (p) REVERT: C 726 ILE cc_start: 0.8580 (mp) cc_final: 0.8252 (mt) REVERT: C 748 GLU cc_start: 0.8371 (pm20) cc_final: 0.7490 (pm20) REVERT: C 765 ARG cc_start: 0.7073 (ttm-80) cc_final: 0.6796 (ttm-80) REVERT: C 768 THR cc_start: 0.8350 (t) cc_final: 0.8037 (m) REVERT: C 796 TYR cc_start: 0.7182 (t80) cc_final: 0.6940 (t80) REVERT: C 1005 GLN cc_start: 0.7840 (tp40) cc_final: 0.7500 (tp40) REVERT: C 1017 GLU cc_start: 0.7045 (tp30) cc_final: 0.6619 (tp30) REVERT: C 1141 LEU cc_start: 0.8062 (tt) cc_final: 0.7737 (tp) REVERT: D 152 MET cc_start: 0.1561 (ttp) cc_final: 0.1163 (ttp) REVERT: D 360 MET cc_start: 0.0605 (tpp) cc_final: 0.0352 (tpp) REVERT: D 529 LEU cc_start: 0.6481 (mt) cc_final: 0.6261 (mt) REVERT: E 86 GLN cc_start: 0.3496 (OUTLIER) cc_final: 0.3113 (pm20) REVERT: E 366 MET cc_start: 0.3354 (mpp) cc_final: 0.3064 (mpp) outliers start: 146 outliers final: 112 residues processed: 868 average time/residue: 0.5050 time to fit residues: 718.9203 Evaluate side-chains 896 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 775 time to evaluate : 4.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 322 ASN Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 40.0000 chunk 445 optimal weight: 10.0000 chunk 406 optimal weight: 3.9990 chunk 433 optimal weight: 30.0000 chunk 261 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 340 optimal weight: 0.3980 chunk 133 optimal weight: 0.3980 chunk 392 optimal weight: 0.2980 chunk 410 optimal weight: 0.6980 chunk 432 optimal weight: 50.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 907 ASN C 505 HIS ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5426 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 40104 Z= 0.261 Angle : 0.640 13.429 54558 Z= 0.323 Chirality : 0.045 0.327 6117 Planarity : 0.004 0.056 7005 Dihedral : 5.348 99.553 6038 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.60 % Favored : 95.38 % Rotamer: Outliers : 3.20 % Allowed : 23.56 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 4809 helix: 1.37 (0.13), residues: 1726 sheet: -0.92 (0.20), residues: 570 loop : -1.39 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 258 HIS 0.011 0.001 HIS A1083 PHE 0.039 0.002 PHE C1075 TYR 0.024 0.002 TYR C 170 ARG 0.008 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 794 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7950 (pp) REVERT: A 619 GLU cc_start: 0.6069 (pm20) cc_final: 0.5363 (mp0) REVERT: A 790 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7496 (mtmm) REVERT: A 824 ASN cc_start: 0.7960 (m-40) cc_final: 0.7677 (m-40) REVERT: A 922 LEU cc_start: 0.8746 (tp) cc_final: 0.8516 (tt) REVERT: A 957 GLN cc_start: 0.7244 (tt0) cc_final: 0.6862 (tt0) REVERT: A 969 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7988 (ptmt) REVERT: A 995 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6728 (ttm-80) REVERT: A 1002 GLN cc_start: 0.7149 (tm-30) cc_final: 0.6852 (tm-30) REVERT: A 1066 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.7846 (p) REVERT: A 1130 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8476 (mt) REVERT: B 54 LEU cc_start: 0.7902 (mt) cc_final: 0.7685 (mt) REVERT: B 87 ASN cc_start: 0.7105 (OUTLIER) cc_final: 0.6857 (p0) REVERT: B 239 GLN cc_start: 0.7331 (pm20) cc_final: 0.6946 (pm20) REVERT: B 278 LYS cc_start: 0.8384 (ptmt) cc_final: 0.8112 (tttt) REVERT: B 317 ASN cc_start: 0.7521 (m110) cc_final: 0.7063 (m-40) REVERT: B 325 SER cc_start: 0.8315 (t) cc_final: 0.8031 (p) REVERT: B 671 CYS cc_start: 0.5569 (m) cc_final: 0.5313 (m) REVERT: B 699 LEU cc_start: 0.8440 (mt) cc_final: 0.8184 (mm) REVERT: B 776 LYS cc_start: 0.8204 (tttt) cc_final: 0.7908 (ttpp) REVERT: B 786 LYS cc_start: 0.7346 (ptmm) cc_final: 0.7080 (ptmm) REVERT: B 998 THR cc_start: 0.8214 (p) cc_final: 0.7968 (m) REVERT: B 1019 ARG cc_start: 0.7142 (ttp-110) cc_final: 0.6913 (ttp-170) REVERT: B 1072 GLU cc_start: 0.8031 (pm20) cc_final: 0.7712 (pm20) REVERT: B 1075 PHE cc_start: 0.8146 (m-80) cc_final: 0.7882 (m-80) REVERT: C 45 SER cc_start: 0.8187 (t) cc_final: 0.7748 (p) REVERT: C 204 TYR cc_start: 0.7069 (m-80) cc_final: 0.6533 (m-80) REVERT: C 306 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7447 (t80) REVERT: C 307 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7910 (p) REVERT: C 308 VAL cc_start: 0.8741 (p) cc_final: 0.8389 (m) REVERT: C 369 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6166 (p90) REVERT: C 429 PHE cc_start: 0.6533 (t80) cc_final: 0.6033 (t80) REVERT: C 542 ASN cc_start: 0.7579 (t0) cc_final: 0.7319 (t0) REVERT: C 558 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7768 (mmmt) REVERT: C 572 THR cc_start: 0.8411 (m) cc_final: 0.8081 (p) REVERT: C 722 VAL cc_start: 0.8948 (m) cc_final: 0.8298 (p) REVERT: C 726 ILE cc_start: 0.8611 (mp) cc_final: 0.8336 (mt) REVERT: C 765 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.6849 (ttm-80) REVERT: C 796 TYR cc_start: 0.7186 (t80) cc_final: 0.6768 (t80) REVERT: C 934 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8554 (tp) REVERT: C 974 SER cc_start: 0.7468 (m) cc_final: 0.7247 (t) REVERT: C 1002 GLN cc_start: 0.7454 (tm-30) cc_final: 0.7242 (tm-30) REVERT: C 1005 GLN cc_start: 0.7867 (tp40) cc_final: 0.7590 (tp40) REVERT: C 1017 GLU cc_start: 0.7025 (tp30) cc_final: 0.6781 (tp30) REVERT: C 1136 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8056 (p) REVERT: C 1141 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7754 (tp) REVERT: D 293 VAL cc_start: 0.3206 (p) cc_final: 0.2457 (m) REVERT: E 86 GLN cc_start: 0.3470 (OUTLIER) cc_final: 0.3074 (pm20) REVERT: E 366 MET cc_start: 0.3389 (mpp) cc_final: 0.3037 (mpp) outliers start: 136 outliers final: 98 residues processed: 869 average time/residue: 0.5126 time to fit residues: 729.5898 Evaluate side-chains 896 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 785 time to evaluate : 4.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 0.9990 chunk 458 optimal weight: 20.0000 chunk 279 optimal weight: 0.4980 chunk 217 optimal weight: 1.9990 chunk 318 optimal weight: 7.9990 chunk 481 optimal weight: 40.0000 chunk 442 optimal weight: 5.9990 chunk 383 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 295 optimal weight: 0.9980 chunk 234 optimal weight: 0.0020 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS F 305 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5433 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40104 Z= 0.249 Angle : 0.636 13.569 54558 Z= 0.322 Chirality : 0.045 0.361 6117 Planarity : 0.004 0.085 7005 Dihedral : 5.366 98.656 6038 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.76 % Rotamer: Outliers : 2.82 % Allowed : 24.34 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 4809 helix: 1.39 (0.13), residues: 1736 sheet: -0.83 (0.21), residues: 546 loop : -1.36 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 353 HIS 0.010 0.001 HIS A1083 PHE 0.038 0.002 PHE C1075 TYR 0.028 0.002 TYR B 904 ARG 0.009 0.000 ARG C1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 791 time to evaluate : 4.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7916 (pp) REVERT: A 824 ASN cc_start: 0.7983 (m-40) cc_final: 0.7681 (m-40) REVERT: A 957 GLN cc_start: 0.7199 (tt0) cc_final: 0.6805 (tt0) REVERT: A 969 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7966 (ptmt) REVERT: A 995 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6615 (ttm-80) REVERT: A 1002 GLN cc_start: 0.7128 (tm-30) cc_final: 0.6823 (tm-30) REVERT: A 1066 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7832 (p) REVERT: A 1130 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (mt) REVERT: B 54 LEU cc_start: 0.7923 (mt) cc_final: 0.7702 (mt) REVERT: B 87 ASN cc_start: 0.7133 (OUTLIER) cc_final: 0.6852 (p0) REVERT: B 239 GLN cc_start: 0.7316 (pm20) cc_final: 0.6854 (pm20) REVERT: B 278 LYS cc_start: 0.8392 (ptmt) cc_final: 0.8106 (tttt) REVERT: B 317 ASN cc_start: 0.7501 (m110) cc_final: 0.7056 (m-40) REVERT: B 558 LYS cc_start: 0.7682 (mmmm) cc_final: 0.7472 (mmmt) REVERT: B 671 CYS cc_start: 0.5534 (m) cc_final: 0.5279 (m) REVERT: B 699 LEU cc_start: 0.8418 (mt) cc_final: 0.8158 (mm) REVERT: B 776 LYS cc_start: 0.8205 (tttt) cc_final: 0.7920 (ttpp) REVERT: B 786 LYS cc_start: 0.7336 (ptmm) cc_final: 0.7115 (ptmm) REVERT: B 998 THR cc_start: 0.8221 (p) cc_final: 0.7946 (m) REVERT: B 1072 GLU cc_start: 0.8032 (pm20) cc_final: 0.7698 (pm20) REVERT: C 45 SER cc_start: 0.8127 (t) cc_final: 0.7742 (p) REVERT: C 204 TYR cc_start: 0.7189 (m-80) cc_final: 0.6646 (m-80) REVERT: C 307 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7927 (p) REVERT: C 308 VAL cc_start: 0.8750 (p) cc_final: 0.8380 (m) REVERT: C 369 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6100 (p90) REVERT: C 542 ASN cc_start: 0.7549 (t0) cc_final: 0.7266 (t0) REVERT: C 558 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7770 (mmmt) REVERT: C 572 THR cc_start: 0.8396 (m) cc_final: 0.8073 (p) REVERT: C 722 VAL cc_start: 0.8973 (m) cc_final: 0.8336 (p) REVERT: C 726 ILE cc_start: 0.8615 (mp) cc_final: 0.8335 (mt) REVERT: C 745 ASP cc_start: 0.7651 (p0) cc_final: 0.7322 (p0) REVERT: C 748 GLU cc_start: 0.8556 (pm20) cc_final: 0.8119 (pm20) REVERT: C 768 THR cc_start: 0.8401 (t) cc_final: 0.8077 (m) REVERT: C 934 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8548 (tp) REVERT: C 974 SER cc_start: 0.7500 (m) cc_final: 0.7276 (t) REVERT: C 1005 GLN cc_start: 0.7851 (tp40) cc_final: 0.7551 (tp40) REVERT: C 1136 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8048 (p) REVERT: C 1141 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7756 (tp) REVERT: D 208 GLU cc_start: 0.7098 (pt0) cc_final: 0.6401 (tt0) REVERT: D 293 VAL cc_start: 0.3195 (p) cc_final: 0.2428 (m) REVERT: D 360 MET cc_start: 0.0848 (tpp) cc_final: 0.0605 (tpt) REVERT: E 86 GLN cc_start: 0.3501 (OUTLIER) cc_final: 0.3095 (pm20) REVERT: E 366 MET cc_start: 0.3426 (mpp) cc_final: 0.3092 (mpp) outliers start: 120 outliers final: 96 residues processed: 852 average time/residue: 0.5262 time to fit residues: 732.1313 Evaluate side-chains 889 residues out of total 4269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 782 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 0.8980 chunk 408 optimal weight: 2.9990 chunk 117 optimal weight: 0.0970 chunk 353 optimal weight: 0.0170 chunk 56 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 383 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 394 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 955 ASN B1106 GLN C 505 HIS ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 GLN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.228158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.167956 restraints weight = 69098.816| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.82 r_work: 0.3547 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40104 Z= 0.183 Angle : 0.622 13.357 54558 Z= 0.314 Chirality : 0.044 0.354 6117 Planarity : 0.004 0.069 7005 Dihedral : 5.237 98.932 6037 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 2.52 % Allowed : 25.02 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.12), residues: 4809 helix: 1.42 (0.13), residues: 1746 sheet: -0.73 (0.21), residues: 553 loop : -1.33 (0.12), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 353 HIS 0.009 0.001 HIS A1083 PHE 0.036 0.001 PHE A 497 TYR 0.037 0.001 TYR F 521 ARG 0.012 0.000 ARG B1014 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12594.83 seconds wall clock time: 228 minutes 52.46 seconds (13732.46 seconds total)