Starting phenix.real_space_refine on Sun Sep 29 09:39:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x80_38131/09_2024/8x80_38131.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x80_38131/09_2024/8x80_38131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x80_38131/09_2024/8x80_38131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x80_38131/09_2024/8x80_38131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x80_38131/09_2024/8x80_38131.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x80_38131/09_2024/8x80_38131.cif" } resolution = 3.88 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 14083 2.51 5 N 3557 2.21 5 O 4100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21890 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6162 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 47, 'TRANS': 715} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 2, 'PTRANS': 48, 'TRANS': 715} Chain breaks: 1 Chain: "E" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1124 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "D" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 809 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 2, 'PTRANS': 48, 'TRANS': 715} Chain breaks: 1 Chain: "F" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1124 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 16.49, per 1000 atoms: 0.75 Number of scatterers: 21890 At special positions: 0 Unit cell: (147.9, 147.05, 209.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4100 8.00 N 3557 7.00 C 14083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 413 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 498 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 674 " distance=2.03 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 117 " - pdb=" SG CYS D 167 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 352 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 413 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 488 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS F 117 " - pdb=" SG CYS F 167 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " BETA1-6 " NAG G 1 " - " FUC G 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG H 1 " - " FUC H 3 " " NAG I 1 " - " FUC I 3 " NAG-ASN " NAG A 901 " - " ASN A 750 " " NAG A 902 " - " ASN A 624 " " NAG A 903 " - " ASN A 397 " " NAG A 904 " - " ASN A 516 " " NAG A 905 " - " ASN A 728 " " NAG B 901 " - " ASN B 750 " " NAG B 902 " - " ASN B 624 " " NAG B 904 " - " ASN B 516 " " NAG B 905 " - " ASN B 728 " " NAG C 901 " - " ASN C 750 " " NAG C 902 " - " ASN C 624 " " NAG C 904 " - " ASN C 516 " " NAG C 905 " - " ASN C 728 " " NAG G 1 " - " ASN A 347 " " NAG H 1 " - " ASN B 347 " " NAG I 1 " - " ASN C 347 " Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 3.0 seconds 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5172 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 50 sheets defined 15.2% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.981A pdb=" N LYS A 109 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 123 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.675A pdb=" N GLN A 380 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.879A pdb=" N VAL A 535 " --> pdb=" O ASP A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'B' and resid 113 through 123 Processing helix chain 'B' and resid 201 through 207 removed outlier: 3.906A pdb=" N ASN B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 732 through 737 removed outlier: 3.855A pdb=" N SER B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 737 " --> pdb=" O TRP B 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 732 through 737' Processing helix chain 'E' and resid 23 through 43 removed outlier: 3.578A pdb=" N VAL E 27 " --> pdb=" O PRO E 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 32 " --> pdb=" O GLN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 88 removed outlier: 3.619A pdb=" N SER E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 115 removed outlier: 3.681A pdb=" N ILE E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN E 96 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE E 97 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 130 through 138 removed outlier: 4.056A pdb=" N VAL E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 162 removed outlier: 4.089A pdb=" N ASP E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 45 removed outlier: 4.007A pdb=" N ILE D 35 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D 40 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 89 removed outlier: 4.123A pdb=" N GLN D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 79 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 99 removed outlier: 3.911A pdb=" N GLN D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 115 Processing helix chain 'D' and resid 143 through 164 removed outlier: 3.783A pdb=" N GLN D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP D 156 " --> pdb=" O GLY D 152 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 163 " --> pdb=" O TRP D 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 450 through 455 removed outlier: 3.877A pdb=" N ILE C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 668 through 672 Processing helix chain 'C' and resid 733 through 737 Processing helix chain 'F' and resid 23 through 45 removed outlier: 3.606A pdb=" N ILE F 45 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 50 removed outlier: 3.915A pdb=" N GLN F 49 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER F 50 " --> pdb=" O HIS F 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 50' Processing helix chain 'F' and resid 71 through 89 removed outlier: 3.850A pdb=" N GLN F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET F 89 " --> pdb=" O ILE F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 115 Processing helix chain 'F' and resid 127 through 136 removed outlier: 3.600A pdb=" N GLU F 136 " --> pdb=" O GLY F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 164 Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.664A pdb=" N PHE A 33 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 34 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 164 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 212 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 162 " --> pdb=" O CYS A 212 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 216 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 158 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.664A pdb=" N PHE A 33 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 34 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 229 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 211 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 227 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.869A pdb=" N HIS A 244 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 256 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 253 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 295 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 271 Processing sheet with id=AA7, first strand: chain 'A' and resid 274 through 276 Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.709A pdb=" N ILE A 334 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 353 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE A 336 " --> pdb=" O HIS A 351 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 351 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.709A pdb=" N ILE A 334 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 353 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE A 336 " --> pdb=" O HIS A 351 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 351 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 348 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS A 352 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 389 " --> pdb=" O CYS A 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 339 through 343 removed outlier: 5.873A pdb=" N ILE A 340 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 428 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A 342 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 446 through 450 Processing sheet with id=AB3, first strand: chain 'A' and resid 462 through 465 removed outlier: 4.058A pdb=" N GLN A 463 " --> pdb=" O ARG A 514 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 462 through 465 removed outlier: 4.058A pdb=" N GLN A 463 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR A 509 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 527 " --> pdb=" O MET A 511 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 544 through 547 removed outlier: 3.874A pdb=" N VAL A 596 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 584 through 588 removed outlier: 3.587A pdb=" N TYR A 574 " --> pdb=" O LYS A 584 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 586 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 645 through 649 Processing sheet with id=AB8, first strand: chain 'A' and resid 691 through 694 removed outlier: 3.727A pdb=" N ARG A 678 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 682 " --> pdb=" O THR A 713 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A 710 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 731 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 729 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 748 through 750 removed outlier: 6.861A pdb=" N ILE A 755 " --> pdb=" O PRO A 748 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 753 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 756 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR A 795 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 784 through 789 removed outlier: 4.401A pdb=" N LYS A 784 " --> pdb=" O TRP A 774 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 786 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 772 " --> pdb=" O LEU A 786 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 182 through 186 removed outlier: 3.998A pdb=" N LYS B 34 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 33 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 129 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP B 127 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B 196 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 282 through 286 Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.606A pdb=" N VAL B 410 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 408 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.606A pdb=" N VAL B 410 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 408 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.724A pdb=" N VAL B 348 " --> pdb=" O PHE B 393 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 434 through 438 removed outlier: 4.246A pdb=" N SER B 435 " --> pdb=" O ARG B 448 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG B 448 " --> pdb=" O SER B 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 484 through 485 removed outlier: 3.613A pdb=" N GLU B 484 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 466 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR B 461 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 484 through 485 removed outlier: 3.613A pdb=" N GLU B 484 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 466 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR B 461 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 541 through 547 removed outlier: 6.214A pdb=" N SER B 542 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU B 559 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 544 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 584 through 588 removed outlier: 3.815A pdb=" N TYR B 574 " --> pdb=" O LYS B 584 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 570 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 612 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 645 through 649 removed outlier: 3.893A pdb=" N PHE B 701 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 679 through 684 removed outlier: 3.510A pdb=" N VAL B 680 " --> pdb=" O LEU B 715 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS B 710 " --> pdb=" O PHE B 731 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 741 through 750 removed outlier: 3.762A pdb=" N SER B 743 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 747 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYS B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 784 through 789 removed outlier: 3.790A pdb=" N LYS B 784 " --> pdb=" O TRP B 774 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP B 774 " --> pdb=" O LYS B 784 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 786 " --> pdb=" O ILE B 772 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 771 " --> pdb=" O TYR B 812 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE B 809 " --> pdb=" O ILE B 825 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 97 through 98 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 209 through 217 current: chain 'C' and resid 127 through 133 Processing sheet with id=AD8, first strand: chain 'C' and resid 182 through 186 removed outlier: 4.267A pdb=" N VAL C 159 " --> pdb=" O CYS C 186 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 210 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.577A pdb=" N TYR C 273 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 284 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 275 through 276 Processing sheet with id=AE2, first strand: chain 'C' and resid 333 through 335 Processing sheet with id=AE3, first strand: chain 'C' and resid 342 through 343 removed outlier: 6.689A pdb=" N THR C 342 " --> pdb=" O ILE C 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 347 through 350 Processing sheet with id=AE5, first strand: chain 'C' and resid 366 through 370 removed outlier: 3.576A pdb=" N VAL C 367 " --> pdb=" O CYS C 413 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 435 through 438 removed outlier: 4.472A pdb=" N SER C 435 " --> pdb=" O ARG C 448 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG C 448 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 445 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS C 447 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 498 " --> pdb=" O CYS C 447 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 484 through 486 removed outlier: 3.768A pdb=" N GLU C 484 " --> pdb=" O TYR C 466 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 464 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 461 " --> pdb=" O ASN C 516 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN C 463 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG C 465 " --> pdb=" O TRP C 512 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP C 512 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 484 through 486 removed outlier: 3.768A pdb=" N GLU C 484 " --> pdb=" O TYR C 466 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 464 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 461 " --> pdb=" O ASN C 516 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN C 463 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG C 465 " --> pdb=" O TRP C 512 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP C 512 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 544 through 547 removed outlier: 3.558A pdb=" N VAL C 596 " --> pdb=" O ILE C 556 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 584 through 588 removed outlier: 3.590A pdb=" N PHE C 570 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 646 through 649 removed outlier: 3.578A pdb=" N PHE C 701 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 678 through 685 Processing sheet with id=AF4, first strand: chain 'C' and resid 741 through 747 removed outlier: 3.585A pdb=" N SER C 743 " --> pdb=" O ILE C 759 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 754 " --> pdb=" O ILE C 797 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 797 " --> pdb=" O VAL C 754 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 784 through 789 removed outlier: 3.719A pdb=" N LYS C 784 " --> pdb=" O TRP C 774 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 788 " --> pdb=" O PHE C 770 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR C 769 " --> pdb=" O ILE C 814 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1788 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: 12.72 Time building geometry restraints manager: 6.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6755 1.34 - 1.47: 5512 1.47 - 1.59: 9988 1.59 - 1.71: 1 1.71 - 1.83: 210 Bond restraints: 22466 Sorted by residual: bond pdb=" C1 NAG C 904 " pdb=" O5 NAG C 904 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.586 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 22461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 30420 3.63 - 7.25: 161 7.25 - 10.88: 13 10.88 - 14.51: 5 14.51 - 18.14: 2 Bond angle restraints: 30601 Sorted by residual: angle pdb=" CA GLU B 459 " pdb=" CB GLU B 459 " pdb=" CG GLU B 459 " ideal model delta sigma weight residual 114.10 126.21 -12.11 2.00e+00 2.50e-01 3.67e+01 angle pdb=" CA ARG A 678 " pdb=" CB ARG A 678 " pdb=" CG ARG A 678 " ideal model delta sigma weight residual 114.10 125.30 -11.20 2.00e+00 2.50e-01 3.14e+01 angle pdb=" CG ARG A 678 " pdb=" CD ARG A 678 " pdb=" NE ARG A 678 " ideal model delta sigma weight residual 112.00 123.33 -11.33 2.20e+00 2.07e-01 2.65e+01 angle pdb=" C GLN B 331 " pdb=" N ASP B 332 " pdb=" CA ASP B 332 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" CA LEU C 253 " pdb=" CB LEU C 253 " pdb=" CG LEU C 253 " ideal model delta sigma weight residual 116.30 132.46 -16.16 3.50e+00 8.16e-02 2.13e+01 ... (remaining 30596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.84: 12419 24.84 - 49.69: 1278 49.69 - 74.53: 151 74.53 - 99.38: 41 99.38 - 124.22: 10 Dihedral angle restraints: 13899 sinusoidal: 5934 harmonic: 7965 Sorted by residual: dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 447 " pdb=" CB CYS A 447 " ideal model delta sinusoidal sigma weight residual 93.00 4.46 88.54 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS A 488 " pdb=" SG CYS A 488 " pdb=" SG CYS A 498 " pdb=" CB CYS A 498 " ideal model delta sinusoidal sigma weight residual -86.00 0.01 -86.01 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CA GLN C 501 " pdb=" C GLN C 501 " pdb=" N PRO C 502 " pdb=" CA PRO C 502 " ideal model delta harmonic sigma weight residual -180.00 -139.85 -40.15 0 5.00e+00 4.00e-02 6.45e+01 ... (remaining 13896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3223 0.089 - 0.178: 306 0.178 - 0.267: 4 0.267 - 0.357: 3 0.357 - 0.446: 2 Chirality restraints: 3538 Sorted by residual: chirality pdb=" C1 NAG A 904 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 904 " pdb=" O5 NAG A 904 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" C1 NAG B 904 " pdb=" ND2 ASN B 516 " pdb=" C2 NAG B 904 " pdb=" O5 NAG B 904 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C4 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O4 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.24 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3535 not shown) Planarity restraints: 3806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 501 " -0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO C 502 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 502 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 502 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 600 " -0.054 5.00e-02 4.00e+02 7.90e-02 9.97e+00 pdb=" N PRO B 601 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 601 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 601 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 624 " -0.004 2.00e-02 2.50e+03 2.37e-02 7.00e+00 pdb=" CG ASN A 624 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 624 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 624 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " 0.027 2.00e-02 2.50e+03 ... (remaining 3803 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 372 2.65 - 3.22: 20155 3.22 - 3.78: 35021 3.78 - 4.34: 44916 4.34 - 4.90: 70931 Nonbonded interactions: 171395 Sorted by model distance: nonbonded pdb=" O VAL D 144 " pdb=" OG SER D 148 " model vdw 2.093 3.040 nonbonded pdb=" NZ LYS A 614 " pdb=" O ARG A 615 " model vdw 2.155 3.120 nonbonded pdb=" O HIS B 800 " pdb=" ND1 HIS B 800 " model vdw 2.190 3.120 nonbonded pdb=" OD1 ASN A 371 " pdb=" OH TYR E 140 " model vdw 2.196 3.040 nonbonded pdb=" O ALA D 80 " pdb=" NE2 GLN D 84 " model vdw 2.197 3.120 ... (remaining 171390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 23 through 467 or (resid 468 and (name N or name CA or nam \ e C or name O or name CB )) or resid 469 through 829 or resid 901 through 905)) selection = (chain 'C' and (resid 23 through 467 or (resid 468 and (name N or name CA or nam \ e C or name O or name CB )) or resid 469 through 829 or resid 901 through 905)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.010 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: 0.010 Extract box with map and model: 0.900 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 58.610 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.220 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: 0.030 Load rotamer database and sin/cos tables:3.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 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 : 0.003 0.099 22466 Z= 0.214 Angle : 0.723 18.136 30601 Z= 0.354 Chirality : 0.047 0.446 3538 Planarity : 0.004 0.081 3790 Dihedral : 18.696 124.221 8610 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.12 % Favored : 95.73 % Rotamer: Outliers : 0.72 % Allowed : 36.82 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.19 (0.16), residues: 2672 helix: 1.11 (0.29), residues: 344 sheet: 0.03 (0.19), residues: 836 loop : -0.46 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 785 HIS 0.006 0.001 HIS F 47 PHE 0.017 0.001 PHE A 815 TYR 0.030 0.001 TYR B 354 ARG 0.015 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 437 time to evaluate : 2.188 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: A 348 VAL cc_start: 0.8187 (t) cc_final: 0.7700 (m) REVERT: A 634 MET cc_start: 0.6444 (ppp) cc_final: 0.6060 (ppp) REVERT: A 773 GLU cc_start: 0.7488 (pm20) cc_final: 0.7063 (pm20) REVERT: B 400 LYS cc_start: 0.8714 (mppt) cc_final: 0.8009 (mppt) REVERT: E 44 ASP cc_start: 0.7972 (t0) cc_final: 0.7754 (t0) REVERT: E 51 VAL cc_start: 0.8714 (m) cc_final: 0.8505 (t) REVERT: E 136 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6931 (tm-30) REVERT: C 640 MET cc_start: 0.6723 (pmm) cc_final: 0.6498 (pmm) REVERT: C 807 TYR cc_start: 0.6424 (m-10) cc_final: 0.5891 (m-10) REVERT: F 51 VAL cc_start: 0.8035 (m) cc_final: 0.7471 (t) REVERT: F 96 GLN cc_start: 0.7671 (tp40) cc_final: 0.7464 (tp40) outliers start: 18 outliers final: 14 residues processed: 443 average time/residue: 0.3420 time to fit residues: 236.0918 Evaluate side-chains 442 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 428 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 108 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 135 optimal weight: 0.5980 chunk 107 optimal weight: 0.0370 chunk 208 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 126 optimal weight: 0.0040 chunk 155 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 overall best weight: 0.4670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 ASN B 150 ASN B 182 GLN B 455 GLN B 698 HIS E 47 HIS E 109 HIS E 118 HIS E 151 GLN D 151 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22466 Z= 0.210 Angle : 0.663 13.504 30601 Z= 0.333 Chirality : 0.047 0.430 3538 Planarity : 0.004 0.087 3790 Dihedral : 9.936 120.710 3415 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.93 % Favored : 95.88 % Rotamer: Outliers : 4.38 % Allowed : 32.84 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.14 (0.17), residues: 2672 helix: 1.38 (0.28), residues: 335 sheet: -0.10 (0.18), residues: 874 loop : -0.36 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 121 HIS 0.009 0.001 HIS E 109 PHE 0.023 0.001 PHE A 815 TYR 0.018 0.001 TYR C 466 ARG 0.007 0.001 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 432 time to evaluate : 2.245 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: A 348 VAL cc_start: 0.8217 (t) cc_final: 0.7782 (m) REVERT: A 504 PHE cc_start: 0.6677 (m-80) cc_final: 0.6448 (m-80) REVERT: A 550 ASN cc_start: 0.7641 (m110) cc_final: 0.6908 (p0) REVERT: A 634 MET cc_start: 0.6483 (ppp) cc_final: 0.5910 (ppp) REVERT: B 362 PRO cc_start: 0.8516 (Cg_exo) cc_final: 0.8267 (Cg_endo) REVERT: B 410 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8202 (t) REVERT: B 459 GLU cc_start: 0.6929 (pp20) cc_final: 0.6688 (pp20) REVERT: B 507 SER cc_start: 0.8481 (m) cc_final: 0.7947 (p) REVERT: B 565 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7329 (mm-30) REVERT: B 584 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7676 (mtmm) REVERT: B 647 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7359 (tmt170) REVERT: E 44 ASP cc_start: 0.8010 (t0) cc_final: 0.7772 (t0) REVERT: E 51 VAL cc_start: 0.8746 (m) cc_final: 0.8537 (t) REVERT: E 61 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7719 (t0) REVERT: E 119 LEU cc_start: 0.8548 (mp) cc_final: 0.8190 (mp) REVERT: E 130 SER cc_start: 0.7448 (OUTLIER) cc_final: 0.7151 (p) REVERT: E 136 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6965 (tm-30) REVERT: D 84 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8356 (mm-40) REVERT: C 614 LYS cc_start: 0.7677 (tttm) cc_final: 0.6608 (tttm) REVERT: C 683 HIS cc_start: 0.6056 (OUTLIER) cc_final: 0.2030 (m-70) REVERT: C 745 SER cc_start: 0.7799 (p) cc_final: 0.7238 (t) REVERT: C 784 LYS cc_start: 0.8472 (mttp) cc_final: 0.8268 (mttp) REVERT: C 807 TYR cc_start: 0.6521 (m-10) cc_final: 0.5959 (m-10) REVERT: F 51 VAL cc_start: 0.8117 (m) cc_final: 0.7595 (t) REVERT: F 77 GLN cc_start: 0.8188 (tp40) cc_final: 0.7729 (tp40) outliers start: 110 outliers final: 62 residues processed: 498 average time/residue: 0.3211 time to fit residues: 250.4637 Evaluate side-chains 479 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 411 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 109 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 215 optimal weight: 0.0040 chunk 239 optimal weight: 0.0040 chunk 82 optimal weight: 20.0000 chunk 194 optimal weight: 0.9980 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 150 ASN B 351 HIS B 397 ASN B 491 GLN B 739 ASN B 742 GLN E 109 HIS E 118 HIS E 151 GLN D 151 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 ASN C 684 HIS ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 49 GLN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22466 Z= 0.198 Angle : 0.643 11.607 30601 Z= 0.317 Chirality : 0.047 0.395 3538 Planarity : 0.004 0.095 3790 Dihedral : 9.370 120.545 3395 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.97 % Favored : 95.85 % Rotamer: Outliers : 5.21 % Allowed : 33.04 % Favored : 61.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.18 (0.16), residues: 2672 helix: 1.41 (0.28), residues: 331 sheet: -0.09 (0.18), residues: 871 loop : -0.42 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 121 HIS 0.015 0.001 HIS F 109 PHE 0.016 0.001 PHE C 394 TYR 0.015 0.001 TYR B 411 ARG 0.012 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 423 time to evaluate : 2.286 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: A 348 VAL cc_start: 0.8260 (t) cc_final: 0.7804 (m) REVERT: A 550 ASN cc_start: 0.7665 (m110) cc_final: 0.6806 (p0) REVERT: A 614 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6785 (tptt) REVERT: A 634 MET cc_start: 0.6518 (ppp) cc_final: 0.5833 (ppp) REVERT: A 768 MET cc_start: 0.6442 (pmm) cc_final: 0.6030 (pmm) REVERT: B 271 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7923 (m) REVERT: B 362 PRO cc_start: 0.8573 (Cg_exo) cc_final: 0.8160 (Cg_endo) REVERT: B 365 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6786 (mt-10) REVERT: B 400 LYS cc_start: 0.8754 (mptt) cc_final: 0.8403 (mptt) REVERT: B 410 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8160 (t) REVERT: B 507 SER cc_start: 0.8521 (m) cc_final: 0.7940 (p) REVERT: B 584 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7773 (mtmm) REVERT: B 647 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7222 (tmt170) REVERT: B 768 MET cc_start: 0.7303 (mpp) cc_final: 0.7066 (mpp) REVERT: E 44 ASP cc_start: 0.8022 (t0) cc_final: 0.7759 (t0) REVERT: E 51 VAL cc_start: 0.8740 (m) cc_final: 0.8536 (t) REVERT: E 119 LEU cc_start: 0.8654 (mp) cc_final: 0.8204 (mp) REVERT: E 130 SER cc_start: 0.7463 (OUTLIER) cc_final: 0.7151 (p) REVERT: C 614 LYS cc_start: 0.7698 (tttm) cc_final: 0.6625 (tttm) REVERT: C 615 ARG cc_start: 0.8015 (mtp180) cc_final: 0.7796 (mtp180) REVERT: C 683 HIS cc_start: 0.5900 (OUTLIER) cc_final: 0.1795 (m-70) REVERT: C 745 SER cc_start: 0.7756 (p) cc_final: 0.7364 (t) REVERT: C 750 ASN cc_start: 0.5974 (t0) cc_final: 0.5429 (t0) REVERT: F 51 VAL cc_start: 0.8279 (m) cc_final: 0.7777 (t) REVERT: F 77 GLN cc_start: 0.8190 (tp40) cc_final: 0.7714 (tp40) REVERT: F 96 GLN cc_start: 0.7835 (tp40) cc_final: 0.7575 (tp40) outliers start: 131 outliers final: 78 residues processed: 511 average time/residue: 0.3211 time to fit residues: 257.9945 Evaluate side-chains 491 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 405 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 742 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 801 PHE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 115 optimal weight: 0.0070 chunk 162 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 257 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 chunk 230 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN B 150 ASN B 455 GLN B 742 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS E 151 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 670 ASN ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 55 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN F 109 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22466 Z= 0.212 Angle : 0.651 14.465 30601 Z= 0.321 Chirality : 0.047 0.386 3538 Planarity : 0.004 0.097 3790 Dihedral : 9.021 120.326 3392 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.51 % Rotamer: Outliers : 5.93 % Allowed : 33.04 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.19 (0.16), residues: 2672 helix: 1.47 (0.28), residues: 331 sheet: -0.12 (0.18), residues: 885 loop : -0.44 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 664 HIS 0.010 0.001 HIS E 109 PHE 0.016 0.001 PHE C 394 TYR 0.016 0.001 TYR B 411 ARG 0.009 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 405 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 PHE cc_start: 0.7390 (t80) cc_final: 0.7063 (t80) REVERT: A 348 VAL cc_start: 0.8331 (t) cc_final: 0.7876 (m) REVERT: A 364 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7836 (ptpp) REVERT: A 422 TYR cc_start: 0.8522 (p90) cc_final: 0.8139 (p90) REVERT: A 550 ASN cc_start: 0.7741 (m110) cc_final: 0.6954 (p0) REVERT: A 585 MET cc_start: 0.6419 (tpt) cc_final: 0.6135 (tpt) REVERT: A 621 TYR cc_start: 0.6565 (m-80) cc_final: 0.6284 (m-80) REVERT: A 634 MET cc_start: 0.6479 (ppp) cc_final: 0.5724 (ppp) REVERT: B 271 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7893 (m) REVERT: B 331 GLN cc_start: 0.7434 (pm20) cc_final: 0.7188 (pm20) REVERT: B 355 LYS cc_start: 0.7989 (tppt) cc_final: 0.7316 (tptm) REVERT: B 400 LYS cc_start: 0.8762 (mptt) cc_final: 0.8412 (mptt) REVERT: B 410 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8121 (t) REVERT: B 506 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7878 (mp) REVERT: B 584 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7774 (mtmm) REVERT: B 647 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7222 (tmt170) REVERT: B 713 THR cc_start: 0.8434 (m) cc_final: 0.8111 (p) REVERT: B 717 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7326 (tt) REVERT: B 764 ASP cc_start: 0.8242 (p0) cc_final: 0.7917 (p0) REVERT: B 768 MET cc_start: 0.7557 (mpp) cc_final: 0.7261 (mpp) REVERT: E 43 ASN cc_start: 0.8011 (t0) cc_final: 0.7378 (m-40) REVERT: E 44 ASP cc_start: 0.8064 (t0) cc_final: 0.7768 (t0) REVERT: E 51 VAL cc_start: 0.8747 (m) cc_final: 0.8542 (t) REVERT: E 61 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7711 (t0) REVERT: E 119 LEU cc_start: 0.8668 (mp) cc_final: 0.8126 (mp) REVERT: E 130 SER cc_start: 0.7522 (OUTLIER) cc_final: 0.7296 (p) REVERT: E 136 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7027 (tm-30) REVERT: E 151 GLN cc_start: 0.7953 (tt0) cc_final: 0.7742 (tt0) REVERT: C 196 CYS cc_start: -0.0143 (OUTLIER) cc_final: -0.0413 (t) REVERT: C 493 ASP cc_start: 0.8428 (p0) cc_final: 0.8127 (p0) REVERT: C 614 LYS cc_start: 0.7748 (tttm) cc_final: 0.6656 (tttm) REVERT: C 665 LYS cc_start: 0.8401 (mmtm) cc_final: 0.8159 (mmtm) REVERT: C 745 SER cc_start: 0.7815 (p) cc_final: 0.7386 (t) REVERT: F 51 VAL cc_start: 0.8342 (m) cc_final: 0.7903 (t) REVERT: F 96 GLN cc_start: 0.7962 (tp40) cc_final: 0.7692 (tp40) outliers start: 149 outliers final: 103 residues processed: 507 average time/residue: 0.3165 time to fit residues: 250.4842 Evaluate side-chains 507 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 394 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 109 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 3 optimal weight: 50.0000 chunk 191 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 219 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 chunk 0 optimal weight: 100.0000 chunk 131 optimal weight: 0.0970 chunk 230 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN B 182 GLN B 742 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 ASN ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 109 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22466 Z= 0.201 Angle : 0.645 15.328 30601 Z= 0.316 Chirality : 0.047 0.384 3538 Planarity : 0.004 0.097 3790 Dihedral : 8.708 120.035 3392 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 5.89 % Allowed : 33.12 % Favored : 60.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.22 (0.16), residues: 2672 helix: 1.49 (0.28), residues: 331 sheet: -0.15 (0.18), residues: 872 loop : -0.45 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 664 HIS 0.013 0.001 HIS F 109 PHE 0.016 0.001 PHE C 394 TYR 0.016 0.001 TYR B 411 ARG 0.006 0.000 ARG C 678 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 407 time to evaluate : 2.281 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: A 328 PHE cc_start: 0.7447 (t80) cc_final: 0.7124 (t80) REVERT: A 330 THR cc_start: 0.7177 (p) cc_final: 0.6329 (m) REVERT: A 348 VAL cc_start: 0.8343 (t) cc_final: 0.7891 (m) REVERT: A 364 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7855 (ptpp) REVERT: A 422 TYR cc_start: 0.8483 (p90) cc_final: 0.8166 (p90) REVERT: A 550 ASN cc_start: 0.7749 (m110) cc_final: 0.6976 (p0) REVERT: A 634 MET cc_start: 0.6498 (ppp) cc_final: 0.5718 (ppp) REVERT: B 271 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7859 (m) REVERT: B 355 LYS cc_start: 0.8008 (tppt) cc_final: 0.7436 (tptm) REVERT: B 400 LYS cc_start: 0.8774 (mptt) cc_final: 0.8414 (mptt) REVERT: B 410 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8071 (t) REVERT: B 506 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7945 (mp) REVERT: B 507 SER cc_start: 0.8509 (m) cc_final: 0.7973 (p) REVERT: B 584 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7804 (mtmm) REVERT: B 647 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7186 (tmt170) REVERT: B 713 THR cc_start: 0.8463 (m) cc_final: 0.8141 (p) REVERT: B 717 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7322 (tt) REVERT: B 764 ASP cc_start: 0.8245 (p0) cc_final: 0.7905 (p0) REVERT: B 798 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7825 (p90) REVERT: E 43 ASN cc_start: 0.8030 (t0) cc_final: 0.7470 (m-40) REVERT: E 44 ASP cc_start: 0.8066 (t0) cc_final: 0.7755 (t0) REVERT: E 75 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7492 (mmm) REVERT: E 119 LEU cc_start: 0.8651 (mp) cc_final: 0.8254 (mp) REVERT: E 130 SER cc_start: 0.7530 (OUTLIER) cc_final: 0.7301 (p) REVERT: E 136 GLU cc_start: 0.7595 (tm-30) cc_final: 0.6976 (tm-30) REVERT: C 196 CYS cc_start: -0.0627 (OUTLIER) cc_final: -0.0882 (t) REVERT: C 493 ASP cc_start: 0.8499 (p0) cc_final: 0.8170 (p0) REVERT: C 614 LYS cc_start: 0.7788 (tttm) cc_final: 0.6668 (tttm) REVERT: C 745 SER cc_start: 0.7829 (p) cc_final: 0.7375 (t) REVERT: F 51 VAL cc_start: 0.8384 (m) cc_final: 0.7986 (t) REVERT: F 96 GLN cc_start: 0.8005 (tp40) cc_final: 0.7767 (tp40) REVERT: F 136 GLU cc_start: 0.6793 (pm20) cc_final: 0.6581 (pm20) outliers start: 148 outliers final: 106 residues processed: 510 average time/residue: 0.3243 time to fit residues: 259.1267 Evaluate side-chains 519 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 402 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 742 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 213 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 21 optimal weight: 0.0030 chunk 85 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN B 455 GLN B 742 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 ASN ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN F 109 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22466 Z= 0.226 Angle : 0.661 14.047 30601 Z= 0.324 Chirality : 0.047 0.381 3538 Planarity : 0.004 0.097 3790 Dihedral : 8.456 120.007 3391 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.42 % Favored : 95.40 % Rotamer: Outliers : 6.17 % Allowed : 33.64 % Favored : 60.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.25 (0.16), residues: 2672 helix: 1.46 (0.28), residues: 331 sheet: -0.16 (0.18), residues: 872 loop : -0.48 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 121 HIS 0.015 0.001 HIS E 109 PHE 0.017 0.001 PHE C 394 TYR 0.018 0.001 TYR A 411 ARG 0.010 0.000 ARG A 647 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 413 time to evaluate : 2.301 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: A 145 GLU cc_start: 0.3234 (OUTLIER) cc_final: 0.2796 (tm-30) REVERT: A 328 PHE cc_start: 0.7502 (t80) cc_final: 0.7176 (t80) REVERT: A 330 THR cc_start: 0.7235 (p) cc_final: 0.6395 (m) REVERT: A 348 VAL cc_start: 0.8399 (t) cc_final: 0.7940 (m) REVERT: A 364 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7885 (ptpp) REVERT: A 614 LYS cc_start: 0.7063 (tptt) cc_final: 0.6807 (tptt) REVERT: A 634 MET cc_start: 0.6598 (ppp) cc_final: 0.5809 (ppp) REVERT: A 667 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6187 (mm) REVERT: A 767 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.7022 (tt) REVERT: A 773 GLU cc_start: 0.7836 (pm20) cc_final: 0.7453 (pm20) REVERT: B 253 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5437 (tp) REVERT: B 271 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7854 (m) REVERT: B 400 LYS cc_start: 0.8776 (mptt) cc_final: 0.8403 (mptt) REVERT: B 410 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8080 (t) REVERT: B 448 ARG cc_start: 0.6604 (ptp-170) cc_final: 0.6190 (ptp-170) REVERT: B 506 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7912 (mp) REVERT: B 507 SER cc_start: 0.8510 (m) cc_final: 0.7985 (p) REVERT: B 584 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7808 (mtmm) REVERT: B 647 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7243 (tmt170) REVERT: B 668 MET cc_start: 0.7328 (mmm) cc_final: 0.7108 (tmm) REVERT: B 713 THR cc_start: 0.8487 (m) cc_final: 0.8195 (p) REVERT: B 717 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7378 (tt) REVERT: B 764 ASP cc_start: 0.8304 (p0) cc_final: 0.8104 (p0) REVERT: B 768 MET cc_start: 0.7599 (mpp) cc_final: 0.7318 (mpp) REVERT: B 786 LEU cc_start: 0.8522 (mm) cc_final: 0.8281 (mm) REVERT: B 798 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7861 (p90) REVERT: E 43 ASN cc_start: 0.8046 (t0) cc_final: 0.7471 (m-40) REVERT: E 44 ASP cc_start: 0.8072 (t0) cc_final: 0.7768 (t0) REVERT: E 119 LEU cc_start: 0.8631 (mp) cc_final: 0.8303 (mp) REVERT: E 130 SER cc_start: 0.7594 (OUTLIER) cc_final: 0.7353 (p) REVERT: C 196 CYS cc_start: -0.0759 (OUTLIER) cc_final: -0.1103 (t) REVERT: C 582 GLN cc_start: 0.7210 (mp10) cc_final: 0.6958 (mp10) REVERT: C 614 LYS cc_start: 0.7808 (tttm) cc_final: 0.6666 (tttm) REVERT: C 665 LYS cc_start: 0.8401 (mmtm) cc_final: 0.7934 (mmtm) REVERT: C 683 HIS cc_start: 0.6042 (OUTLIER) cc_final: 0.2211 (m-70) REVERT: C 745 SER cc_start: 0.7850 (p) cc_final: 0.7381 (t) REVERT: F 51 VAL cc_start: 0.8480 (m) cc_final: 0.8141 (t) REVERT: F 96 GLN cc_start: 0.8055 (tp40) cc_final: 0.7849 (tp40) outliers start: 155 outliers final: 117 residues processed: 524 average time/residue: 0.3268 time to fit residues: 266.7193 Evaluate side-chains 528 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 396 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 216 optimal weight: 0.6980 chunk 143 optimal weight: 0.3980 chunk 256 optimal weight: 0.0050 chunk 160 optimal weight: 0.9980 chunk 156 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN B 455 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 ASN ** C 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22466 Z= 0.200 Angle : 0.669 16.523 30601 Z= 0.325 Chirality : 0.047 0.381 3538 Planarity : 0.004 0.100 3790 Dihedral : 8.158 119.701 3391 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.45 % Favored : 95.40 % Rotamer: Outliers : 6.13 % Allowed : 34.32 % Favored : 59.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.27 (0.16), residues: 2672 helix: 1.48 (0.28), residues: 331 sheet: -0.18 (0.18), residues: 875 loop : -0.49 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 774 HIS 0.018 0.001 HIS E 109 PHE 0.016 0.001 PHE C 394 TYR 0.015 0.001 TYR A 411 ARG 0.011 0.001 ARG A 647 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 405 time to evaluate : 2.407 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: A 145 GLU cc_start: 0.3267 (OUTLIER) cc_final: 0.2823 (tm-30) REVERT: A 348 VAL cc_start: 0.8390 (t) cc_final: 0.7933 (m) REVERT: A 364 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7893 (ptpp) REVERT: A 614 LYS cc_start: 0.7213 (tptt) cc_final: 0.6993 (tptt) REVERT: A 615 ARG cc_start: 0.7604 (mmm160) cc_final: 0.6996 (mmm160) REVERT: A 634 MET cc_start: 0.6618 (ppp) cc_final: 0.5826 (ppp) REVERT: A 667 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6273 (mp) REVERT: A 675 SER cc_start: 0.2459 (OUTLIER) cc_final: 0.2159 (p) REVERT: A 773 GLU cc_start: 0.7956 (pm20) cc_final: 0.7162 (pm20) REVERT: B 355 LYS cc_start: 0.8016 (tppt) cc_final: 0.7319 (tptm) REVERT: B 400 LYS cc_start: 0.8779 (mptt) cc_final: 0.8404 (mptt) REVERT: B 410 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8077 (t) REVERT: B 448 ARG cc_start: 0.6621 (ptp-170) cc_final: 0.6110 (ptp-170) REVERT: B 468 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7939 (ttp80) REVERT: B 506 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7937 (mp) REVERT: B 507 SER cc_start: 0.8491 (m) cc_final: 0.7954 (p) REVERT: B 584 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7781 (mtmm) REVERT: B 647 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7158 (tmt170) REVERT: B 713 THR cc_start: 0.8479 (m) cc_final: 0.8238 (p) REVERT: B 717 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7445 (tt) REVERT: B 768 MET cc_start: 0.7660 (mpp) cc_final: 0.7375 (mpp) REVERT: B 786 LEU cc_start: 0.8497 (mm) cc_final: 0.8231 (mm) REVERT: B 798 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7861 (p90) REVERT: E 43 ASN cc_start: 0.8031 (t0) cc_final: 0.7454 (m-40) REVERT: E 44 ASP cc_start: 0.8066 (t0) cc_final: 0.7769 (t0) REVERT: E 109 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.7129 (t70) REVERT: E 119 LEU cc_start: 0.8638 (mp) cc_final: 0.8255 (mp) REVERT: E 130 SER cc_start: 0.7554 (OUTLIER) cc_final: 0.7318 (p) REVERT: E 136 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7039 (tm-30) REVERT: C 196 CYS cc_start: -0.0763 (OUTLIER) cc_final: -0.1087 (t) REVERT: C 493 ASP cc_start: 0.8463 (p0) cc_final: 0.8216 (p0) REVERT: C 582 GLN cc_start: 0.7221 (mp10) cc_final: 0.6963 (mp10) REVERT: C 614 LYS cc_start: 0.7789 (tttm) cc_final: 0.6641 (tttm) REVERT: C 683 HIS cc_start: 0.5906 (OUTLIER) cc_final: 0.2082 (m-70) REVERT: C 745 SER cc_start: 0.7850 (p) cc_final: 0.7384 (t) REVERT: F 51 VAL cc_start: 0.8475 (m) cc_final: 0.8121 (t) REVERT: F 96 GLN cc_start: 0.8050 (tp40) cc_final: 0.7702 (tp40) outliers start: 154 outliers final: 112 residues processed: 510 average time/residue: 0.3340 time to fit residues: 265.3054 Evaluate side-chains 522 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 396 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 0.1980 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 201 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN B 455 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 22466 Z= 0.216 Angle : 0.683 15.815 30601 Z= 0.332 Chirality : 0.047 0.378 3538 Planarity : 0.004 0.101 3790 Dihedral : 7.881 119.674 3390 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.53 % Favored : 95.28 % Rotamer: Outliers : 5.77 % Allowed : 34.91 % Favored : 59.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.28 (0.16), residues: 2672 helix: 1.45 (0.28), residues: 329 sheet: -0.21 (0.18), residues: 874 loop : -0.49 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 774 HIS 0.022 0.001 HIS E 109 PHE 0.016 0.001 PHE C 394 TYR 0.018 0.001 TYR A 411 ARG 0.011 0.001 ARG A 647 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 404 time to evaluate : 2.059 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: A 145 GLU cc_start: 0.3254 (OUTLIER) cc_final: 0.2808 (tm-30) REVERT: A 348 VAL cc_start: 0.8433 (t) cc_final: 0.7969 (m) REVERT: A 364 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7914 (ptpp) REVERT: A 614 LYS cc_start: 0.7291 (tptt) cc_final: 0.7066 (tptt) REVERT: A 615 ARG cc_start: 0.7782 (mmm160) cc_final: 0.7149 (mmm160) REVERT: A 634 MET cc_start: 0.6715 (ppp) cc_final: 0.5946 (ppp) REVERT: A 667 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6406 (mp) REVERT: A 794 LYS cc_start: 0.8147 (tptp) cc_final: 0.7810 (mmtt) REVERT: B 400 LYS cc_start: 0.8787 (mptt) cc_final: 0.8415 (mptt) REVERT: B 410 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8070 (t) REVERT: B 506 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7936 (mp) REVERT: B 507 SER cc_start: 0.8483 (m) cc_final: 0.7957 (p) REVERT: B 584 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7797 (mtmm) REVERT: B 647 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6957 (ptm-80) REVERT: B 658 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6986 (mmmt) REVERT: B 669 LYS cc_start: 0.8339 (tppp) cc_final: 0.8087 (tppp) REVERT: B 717 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7455 (tt) REVERT: B 768 MET cc_start: 0.7742 (mpp) cc_final: 0.7441 (mpp) REVERT: B 786 LEU cc_start: 0.8505 (mm) cc_final: 0.8220 (mm) REVERT: B 798 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7897 (p90) REVERT: E 43 ASN cc_start: 0.8041 (t0) cc_final: 0.7468 (m-40) REVERT: E 44 ASP cc_start: 0.8075 (t0) cc_final: 0.7787 (t0) REVERT: E 119 LEU cc_start: 0.8651 (mp) cc_final: 0.8326 (mp) REVERT: E 130 SER cc_start: 0.7583 (OUTLIER) cc_final: 0.7337 (p) REVERT: E 136 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6996 (tm-30) REVERT: C 196 CYS cc_start: -0.0753 (OUTLIER) cc_final: -0.1027 (t) REVERT: C 557 SER cc_start: 0.7669 (m) cc_final: 0.6917 (p) REVERT: C 582 GLN cc_start: 0.7223 (mp10) cc_final: 0.6953 (mp10) REVERT: C 587 GLU cc_start: 0.6231 (tm-30) cc_final: 0.5783 (tm-30) REVERT: C 614 LYS cc_start: 0.7819 (tttm) cc_final: 0.6613 (tttm) REVERT: C 688 ASN cc_start: 0.6815 (m-40) cc_final: 0.6394 (m-40) REVERT: C 745 SER cc_start: 0.7874 (p) cc_final: 0.7389 (t) REVERT: F 51 VAL cc_start: 0.8480 (m) cc_final: 0.8139 (t) REVERT: F 96 GLN cc_start: 0.8058 (tp40) cc_final: 0.7716 (tp40) outliers start: 145 outliers final: 113 residues processed: 502 average time/residue: 0.3132 time to fit residues: 244.3431 Evaluate side-chains 516 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 392 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.0980 chunk 245 optimal weight: 0.8980 chunk 224 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 225 optimal weight: 0.0470 chunk 156 optimal weight: 0.3980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 103 ASN F 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 22466 Z= 0.198 Angle : 0.690 16.604 30601 Z= 0.336 Chirality : 0.047 0.378 3538 Planarity : 0.004 0.102 3790 Dihedral : 7.658 119.378 3390 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.34 % Favored : 95.51 % Rotamer: Outliers : 5.49 % Allowed : 34.91 % Favored : 59.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.30 (0.16), residues: 2672 helix: 1.46 (0.28), residues: 331 sheet: -0.22 (0.18), residues: 874 loop : -0.51 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 664 HIS 0.019 0.001 HIS E 109 PHE 0.027 0.001 PHE B 701 TYR 0.018 0.001 TYR C 812 ARG 0.019 0.001 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 408 time to evaluate : 2.213 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: A 145 GLU cc_start: 0.3255 (OUTLIER) cc_final: 0.2811 (tm-30) REVERT: A 348 VAL cc_start: 0.8421 (t) cc_final: 0.7956 (m) REVERT: A 364 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7911 (ptpp) REVERT: A 615 ARG cc_start: 0.7805 (mmm160) cc_final: 0.7278 (mmm-85) REVERT: A 634 MET cc_start: 0.6714 (ppp) cc_final: 0.5925 (ppp) REVERT: A 667 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6371 (mp) REVERT: A 794 LYS cc_start: 0.8117 (tptp) cc_final: 0.7835 (mmtt) REVERT: B 355 LYS cc_start: 0.8110 (tppt) cc_final: 0.7472 (tptm) REVERT: B 400 LYS cc_start: 0.8786 (mptt) cc_final: 0.8416 (mptt) REVERT: B 410 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8044 (t) REVERT: B 506 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7932 (mp) REVERT: B 507 SER cc_start: 0.8468 (m) cc_final: 0.7940 (p) REVERT: B 584 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7781 (mtmm) REVERT: B 647 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6971 (ptm-80) REVERT: B 669 LYS cc_start: 0.8279 (tppp) cc_final: 0.7994 (tppp) REVERT: B 768 MET cc_start: 0.7792 (mpp) cc_final: 0.7495 (mpp) REVERT: B 786 LEU cc_start: 0.8531 (mm) cc_final: 0.8234 (mm) REVERT: B 798 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7872 (p90) REVERT: E 43 ASN cc_start: 0.8026 (t0) cc_final: 0.7454 (m-40) REVERT: E 44 ASP cc_start: 0.8079 (t0) cc_final: 0.7790 (t0) REVERT: E 109 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7213 (t70) REVERT: E 119 LEU cc_start: 0.8656 (mp) cc_final: 0.8297 (mp) REVERT: E 130 SER cc_start: 0.7541 (OUTLIER) cc_final: 0.7287 (p) REVERT: E 136 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7036 (tm-30) REVERT: C 196 CYS cc_start: -0.0749 (OUTLIER) cc_final: -0.1020 (t) REVERT: C 557 SER cc_start: 0.7646 (m) cc_final: 0.6893 (p) REVERT: C 582 GLN cc_start: 0.7244 (mp10) cc_final: 0.6981 (mp10) REVERT: C 587 GLU cc_start: 0.6212 (tm-30) cc_final: 0.5771 (tm-30) REVERT: C 614 LYS cc_start: 0.7732 (tttm) cc_final: 0.6583 (tttm) REVERT: C 688 ASN cc_start: 0.6854 (m-40) cc_final: 0.6441 (m-40) REVERT: C 745 SER cc_start: 0.7874 (p) cc_final: 0.7430 (t) REVERT: F 51 VAL cc_start: 0.8469 (m) cc_final: 0.8113 (t) REVERT: F 96 GLN cc_start: 0.8037 (tp40) cc_final: 0.7706 (tp40) outliers start: 138 outliers final: 107 residues processed: 499 average time/residue: 0.3263 time to fit residues: 253.3612 Evaluate side-chains 516 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 398 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 175 optimal weight: 0.2980 chunk 265 optimal weight: 0.8980 chunk 243 optimal weight: 0.4980 chunk 211 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 163 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 167 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN B 455 GLN B 778 ASN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 103 ASN F 109 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 22466 Z= 0.208 Angle : 0.717 16.606 30601 Z= 0.347 Chirality : 0.047 0.376 3538 Planarity : 0.004 0.101 3790 Dihedral : 7.549 119.313 3388 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 5.18 % Allowed : 35.23 % Favored : 59.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.32 (0.16), residues: 2672 helix: 1.45 (0.28), residues: 331 sheet: -0.22 (0.18), residues: 875 loop : -0.53 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 664 HIS 0.023 0.001 HIS E 109 PHE 0.016 0.001 PHE C 394 TYR 0.016 0.001 TYR A 411 ARG 0.018 0.001 ARG A 678 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 405 time to evaluate : 2.339 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: A 145 GLU cc_start: 0.3267 (OUTLIER) cc_final: 0.2830 (tm-30) REVERT: A 348 VAL cc_start: 0.8420 (t) cc_final: 0.7948 (m) REVERT: A 585 MET cc_start: 0.6700 (tpt) cc_final: 0.6356 (tpt) REVERT: A 647 ARG cc_start: 0.6166 (mtm110) cc_final: 0.5676 (ptm-80) REVERT: A 667 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6363 (mp) REVERT: A 794 LYS cc_start: 0.8044 (tptp) cc_final: 0.7524 (tptp) REVERT: B 355 LYS cc_start: 0.8116 (tppt) cc_final: 0.7506 (tptp) REVERT: B 400 LYS cc_start: 0.8787 (mptt) cc_final: 0.8416 (mptt) REVERT: B 410 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8046 (t) REVERT: B 448 ARG cc_start: 0.7184 (ptp-170) cc_final: 0.6709 (ptp-170) REVERT: B 506 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7894 (mp) REVERT: B 507 SER cc_start: 0.8434 (m) cc_final: 0.7935 (p) REVERT: B 584 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7790 (mtmm) REVERT: B 647 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6974 (ptm-80) REVERT: B 669 LYS cc_start: 0.8284 (tppp) cc_final: 0.8023 (tppp) REVERT: B 768 MET cc_start: 0.7790 (mpp) cc_final: 0.7501 (mpp) REVERT: B 798 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7898 (p90) REVERT: B 823 LYS cc_start: 0.7806 (tptp) cc_final: 0.7520 (tptp) REVERT: E 43 ASN cc_start: 0.8033 (t0) cc_final: 0.7461 (m-40) REVERT: E 44 ASP cc_start: 0.8084 (t0) cc_final: 0.7795 (t0) REVERT: E 119 LEU cc_start: 0.8650 (mp) cc_final: 0.8340 (mp) REVERT: E 130 SER cc_start: 0.7550 (OUTLIER) cc_final: 0.7298 (p) REVERT: E 136 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7068 (tm-30) REVERT: C 196 CYS cc_start: -0.0861 (OUTLIER) cc_final: -0.1143 (t) REVERT: C 557 SER cc_start: 0.7624 (m) cc_final: 0.6876 (p) REVERT: C 582 GLN cc_start: 0.7254 (mp10) cc_final: 0.6989 (mp10) REVERT: C 587 GLU cc_start: 0.6199 (tm-30) cc_final: 0.5743 (tm-30) REVERT: C 614 LYS cc_start: 0.7770 (tttm) cc_final: 0.6616 (tttm) REVERT: C 688 ASN cc_start: 0.6875 (m-40) cc_final: 0.6459 (m-40) REVERT: C 745 SER cc_start: 0.7889 (p) cc_final: 0.7432 (t) REVERT: C 787 ARG cc_start: 0.6970 (tmt170) cc_final: 0.6728 (tmm160) REVERT: F 51 VAL cc_start: 0.8477 (m) cc_final: 0.8121 (t) REVERT: F 96 GLN cc_start: 0.8055 (tp40) cc_final: 0.7727 (tp40) outliers start: 130 outliers final: 111 residues processed: 490 average time/residue: 0.3344 time to fit residues: 255.2570 Evaluate side-chains 518 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 398 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 217 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS E 160 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.244978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.224840 restraints weight = 80897.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.223269 restraints weight = 76090.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.221251 restraints weight = 64970.267| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 22466 Z= 0.264 Angle : 0.730 17.157 30601 Z= 0.357 Chirality : 0.048 0.373 3538 Planarity : 0.005 0.103 3790 Dihedral : 7.564 119.682 3388 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.75 % Favored : 95.02 % Rotamer: Outliers : 5.06 % Allowed : 35.43 % Favored : 59.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.37 (0.16), residues: 2672 helix: 1.38 (0.28), residues: 331 sheet: -0.24 (0.18), residues: 881 loop : -0.57 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 664 HIS 0.018 0.001 HIS E 109 PHE 0.032 0.002 PHE B 701 TYR 0.024 0.001 TYR A 411 ARG 0.016 0.001 ARG A 678 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5956.69 seconds wall clock time: 107 minutes 36.13 seconds (6456.13 seconds total)