Starting phenix.real_space_refine on Mon Mar 18 02:08:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tsz_26105/03_2024/7tsz_26105.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tsz_26105/03_2024/7tsz_26105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tsz_26105/03_2024/7tsz_26105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tsz_26105/03_2024/7tsz_26105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tsz_26105/03_2024/7tsz_26105.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tsz_26105/03_2024/7tsz_26105.pdb" } resolution = 4.5 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= 0.006 sd= 0.051 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: 5 Type Number sf(0) Gaussians S 31 5.16 5 C 6345 2.51 5 N 1712 2.21 5 O 1964 1.98 5 H 9670 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19722 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9195 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 572} Chain breaks: 7 Chain: "B" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 4930 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 11, 'TRANS': 320} Chain breaks: 6 Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 676 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "E" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1371 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "P" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 160 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Time building chain proxies: 8.80, per 1000 atoms: 0.45 Number of scatterers: 19722 At special positions: 0 Unit cell: (112.751, 125.637, 139.597, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 O 1964 8.00 N 1712 7.00 C 6345 6.00 H 9670 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.16 Conformation dependent library (CDL) restraints added in 2.0 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 24.9% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.898A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.758A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.696A pdb=" N GLY A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.917A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.909A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 550 removed outlier: 4.999A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 4.190A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 722 through 727 Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'D' and resid 32 through 46 removed outlier: 4.148A pdb=" N ALA D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.776A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.590A pdb=" N ARG D 188 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.678A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.758A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 274 removed outlier: 5.667A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.087A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.660A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.638A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.886A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 802 through 806 removed outlier: 3.749A pdb=" N TRP A 776 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 785 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.395A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 51 Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.497A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.062A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.626A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.777A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 290 through 292 Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.045A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.764A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1287 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: 7.14 Time building geometry restraints manager: 15.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9670 1.03 - 1.22: 1 1.22 - 1.42: 4459 1.42 - 1.62: 5749 1.62 - 1.81: 58 Bond restraints: 19937 Sorted by residual: bond pdb=" CG ARG A 366 " pdb=" CD ARG A 366 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.39e+00 bond pdb=" CG LEU A 377 " pdb=" CD1 LEU A 377 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.24e+00 bond pdb=" N ARG A 388 " pdb=" CA ARG A 388 " ideal model delta sigma weight residual 1.459 1.442 0.017 1.21e-02 6.83e+03 2.05e+00 bond pdb=" CB TRP A 745 " pdb=" CG TRP A 745 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB TRP A 376 " pdb=" CG TRP A 376 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 ... (remaining 19932 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.60: 235 105.60 - 112.70: 22471 112.70 - 119.80: 5354 119.80 - 126.90: 7601 126.90 - 134.00: 137 Bond angle restraints: 35798 Sorted by residual: angle pdb=" N GLY A 378 " pdb=" CA GLY A 378 " pdb=" C GLY A 378 " ideal model delta sigma weight residual 113.18 104.24 8.94 2.37e+00 1.78e-01 1.42e+01 angle pdb=" C ARG A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 120.68 114.45 6.23 1.70e+00 3.46e-01 1.34e+01 angle pdb=" N GLN D 70 " pdb=" CA GLN D 70 " pdb=" C GLN D 70 " ideal model delta sigma weight residual 112.45 107.40 5.05 1.39e+00 5.18e-01 1.32e+01 angle pdb=" CA TYR D 184 " pdb=" CB TYR D 184 " pdb=" CG TYR D 184 " ideal model delta sigma weight residual 113.90 107.59 6.31 1.80e+00 3.09e-01 1.23e+01 angle pdb=" N ASP A 222 " pdb=" CA ASP A 222 " pdb=" C ASP A 222 " ideal model delta sigma weight residual 112.90 108.49 4.41 1.31e+00 5.83e-01 1.13e+01 ... (remaining 35793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8967 17.82 - 35.65: 307 35.65 - 53.47: 136 53.47 - 71.29: 53 71.29 - 89.11: 17 Dihedral angle restraints: 9480 sinusoidal: 5090 harmonic: 4390 Sorted by residual: dihedral pdb=" CA ASP A 332 " pdb=" C ASP A 332 " pdb=" N LYS A 333 " pdb=" CA LYS A 333 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ALA A 679 " pdb=" C ALA A 679 " pdb=" N SER A 680 " pdb=" CA SER A 680 " ideal model delta harmonic sigma weight residual 180.00 163.92 16.08 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CB GLU B 107 " pdb=" CG GLU B 107 " pdb=" CD GLU B 107 " pdb=" OE1 GLU B 107 " ideal model delta sinusoidal sigma weight residual 0.00 85.38 -85.38 1 3.00e+01 1.11e-03 9.81e+00 ... (remaining 9477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1028 0.041 - 0.082: 315 0.082 - 0.123: 150 0.123 - 0.164: 23 0.164 - 0.205: 2 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CA TYR A 522 " pdb=" N TYR A 522 " pdb=" C TYR A 522 " pdb=" CB TYR A 522 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ARG A 366 " pdb=" N ARG A 366 " pdb=" C ARG A 366 " pdb=" CB ARG A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CA VAL A 629 " pdb=" N VAL A 629 " pdb=" C VAL A 629 " pdb=" CB VAL A 629 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 1515 not shown) Planarity restraints: 3042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 389 " 0.024 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" C LEU A 389 " -0.083 2.00e-02 2.50e+03 pdb=" O LEU A 389 " 0.031 2.00e-02 2.50e+03 pdb=" N ASN A 390 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 386 " 0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C LYS A 386 " -0.075 2.00e-02 2.50e+03 pdb=" O LYS A 386 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU A 387 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 325 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C MET A 325 " -0.063 2.00e-02 2.50e+03 pdb=" O MET A 325 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO A 326 " 0.021 2.00e-02 2.50e+03 ... (remaining 3039 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 406 2.07 - 2.70: 32904 2.70 - 3.34: 54958 3.34 - 3.97: 70752 3.97 - 4.60: 109433 Nonbonded interactions: 268453 Sorted by model distance: nonbonded pdb=" OD2 ASP A 410 " pdb=" H THR E 61 " model vdw 1.438 1.850 nonbonded pdb=" OH TYR D 77 " pdb=" H ARG C 83 " model vdw 1.461 1.850 nonbonded pdb=" H VAL D 192 " pdb=" OE1 GLN E 34 " model vdw 1.468 1.850 nonbonded pdb=" O GLY A 424 " pdb=" H PHE P1300 " model vdw 1.492 1.850 nonbonded pdb=" H ILE A 352 " pdb=" OE2 GLU A 373 " model vdw 1.510 1.850 ... (remaining 268448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.660 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: 0.280 Extract box with map and model: 3.790 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 61.470 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.005 0.055 10267 Z= 0.353 Angle : 0.886 8.944 13944 Z= 0.540 Chirality : 0.048 0.205 1518 Planarity : 0.005 0.048 1829 Dihedral : 11.128 89.114 3684 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1248 helix: 0.09 (0.29), residues: 247 sheet: 0.84 (0.24), residues: 389 loop : 0.58 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 73 HIS 0.009 0.003 HIS D 139 PHE 0.013 0.002 PHE A 570 TYR 0.015 0.002 TYR D 184 ARG 0.011 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8425 (mm) cc_final: 0.7996 (tp) REVERT: A 303 LYS cc_start: 0.9390 (tttm) cc_final: 0.8941 (ttpp) REVERT: A 304 MET cc_start: 0.8980 (mtm) cc_final: 0.8404 (ttm) REVERT: A 307 ASP cc_start: 0.8940 (m-30) cc_final: 0.8634 (m-30) REVERT: A 372 MET cc_start: 0.8224 (mtp) cc_final: 0.7911 (mtm) REVERT: A 441 GLN cc_start: 0.9052 (tt0) cc_final: 0.8822 (tp40) REVERT: A 449 TRP cc_start: 0.8513 (t60) cc_final: 0.7989 (t60) REVERT: A 450 LEU cc_start: 0.9366 (mt) cc_final: 0.8810 (tt) REVERT: A 461 THR cc_start: 0.7913 (t) cc_final: 0.7044 (t) REVERT: A 540 GLN cc_start: 0.8476 (tp40) cc_final: 0.8058 (tp40) REVERT: B 112 SER cc_start: 0.8165 (p) cc_final: 0.7682 (p) REVERT: B 150 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 369 THR cc_start: 0.7827 (p) cc_final: 0.7622 (p) REVERT: D 116 ASN cc_start: 0.9394 (m-40) cc_final: 0.8749 (m110) REVERT: D 172 ASP cc_start: 0.8765 (m-30) cc_final: 0.8422 (t0) REVERT: D 183 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8226 (pt0) REVERT: E 28 TYR cc_start: 0.8302 (t80) cc_final: 0.7999 (t80) REVERT: E 92 THR cc_start: 0.8936 (m) cc_final: 0.8678 (p) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.5243 time to fit residues: 237.2591 Evaluate side-chains 222 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS E 36 ASN E 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10267 Z= 0.398 Angle : 0.689 8.145 13944 Z= 0.392 Chirality : 0.044 0.155 1518 Planarity : 0.005 0.071 1829 Dihedral : 5.633 83.806 1399 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1248 helix: 0.95 (0.31), residues: 242 sheet: 0.11 (0.24), residues: 373 loop : -0.18 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 73 HIS 0.022 0.002 HIS B 324 PHE 0.022 0.002 PHE D 147 TYR 0.025 0.002 TYR A 578 ARG 0.006 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8387 (mm) cc_final: 0.7894 (tp) REVERT: A 307 ASP cc_start: 0.8853 (m-30) cc_final: 0.8571 (m-30) REVERT: A 383 ASP cc_start: 0.8674 (m-30) cc_final: 0.8378 (m-30) REVERT: A 423 THR cc_start: 0.9439 (p) cc_final: 0.9178 (m) REVERT: A 449 TRP cc_start: 0.8484 (t60) cc_final: 0.8214 (t60) REVERT: A 450 LEU cc_start: 0.9328 (mt) cc_final: 0.8895 (tt) REVERT: A 586 PHE cc_start: 0.6569 (m-80) cc_final: 0.6351 (m-10) REVERT: B 42 PHE cc_start: 0.6011 (t80) cc_final: 0.5789 (t80) REVERT: B 67 LEU cc_start: 0.9106 (mt) cc_final: 0.8760 (tt) REVERT: B 150 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7420 (mt-10) REVERT: B 388 TYR cc_start: 0.6252 (m-80) cc_final: 0.5857 (m-80) REVERT: D 50 GLN cc_start: 0.9311 (tm-30) cc_final: 0.9104 (tm-30) REVERT: D 172 ASP cc_start: 0.8814 (m-30) cc_final: 0.8457 (t0) REVERT: E 42 ASP cc_start: 0.8444 (m-30) cc_final: 0.8221 (m-30) REVERT: P 1293 ASN cc_start: 0.8549 (p0) cc_final: 0.8338 (p0) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.4981 time to fit residues: 172.3539 Evaluate side-chains 187 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10267 Z= 0.209 Angle : 0.539 6.309 13944 Z= 0.302 Chirality : 0.042 0.160 1518 Planarity : 0.004 0.035 1829 Dihedral : 5.139 73.644 1399 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1248 helix: 1.36 (0.32), residues: 245 sheet: 0.14 (0.25), residues: 362 loop : -0.26 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 739 HIS 0.007 0.001 HIS B 324 PHE 0.013 0.001 PHE D 147 TYR 0.023 0.001 TYR D 184 ARG 0.003 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.8927 (tt0) cc_final: 0.8702 (tt0) REVERT: A 306 ASP cc_start: 0.9011 (m-30) cc_final: 0.8795 (m-30) REVERT: A 307 ASP cc_start: 0.8884 (m-30) cc_final: 0.8547 (m-30) REVERT: A 449 TRP cc_start: 0.8480 (t60) cc_final: 0.8158 (t60) REVERT: A 450 LEU cc_start: 0.9339 (mt) cc_final: 0.8841 (tt) REVERT: A 470 GLU cc_start: 0.7865 (tt0) cc_final: 0.7654 (tt0) REVERT: A 533 HIS cc_start: 0.7526 (t-90) cc_final: 0.7302 (t-90) REVERT: A 586 PHE cc_start: 0.6730 (m-80) cc_final: 0.6468 (m-10) REVERT: B 42 PHE cc_start: 0.6013 (t80) cc_final: 0.5801 (t80) REVERT: B 67 LEU cc_start: 0.8969 (mt) cc_final: 0.8746 (tt) REVERT: B 111 LEU cc_start: 0.8694 (mt) cc_final: 0.8435 (mp) REVERT: B 150 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 388 TYR cc_start: 0.6311 (m-80) cc_final: 0.6023 (m-80) REVERT: D 50 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9093 (tm-30) REVERT: D 172 ASP cc_start: 0.8777 (m-30) cc_final: 0.8422 (t0) REVERT: E 36 ASN cc_start: 0.8230 (m-40) cc_final: 0.7942 (m-40) REVERT: E 42 ASP cc_start: 0.8390 (m-30) cc_final: 0.8156 (m-30) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.4840 time to fit residues: 161.0219 Evaluate side-chains 196 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 86 optimal weight: 0.0000 chunk 59 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 0.2980 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10267 Z= 0.128 Angle : 0.467 4.936 13944 Z= 0.256 Chirality : 0.041 0.148 1518 Planarity : 0.003 0.037 1829 Dihedral : 4.720 65.822 1399 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1248 helix: 1.74 (0.32), residues: 245 sheet: 0.12 (0.25), residues: 354 loop : -0.21 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 739 HIS 0.005 0.001 HIS B 324 PHE 0.012 0.001 PHE D 147 TYR 0.024 0.001 TYR D 184 ARG 0.008 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8380 (m-30) cc_final: 0.7989 (m-30) REVERT: A 305 GLU cc_start: 0.8918 (tt0) cc_final: 0.8689 (tt0) REVERT: A 306 ASP cc_start: 0.9030 (m-30) cc_final: 0.8821 (m-30) REVERT: A 307 ASP cc_start: 0.8861 (m-30) cc_final: 0.8527 (m-30) REVERT: A 449 TRP cc_start: 0.8399 (t60) cc_final: 0.8109 (t60) REVERT: A 450 LEU cc_start: 0.9298 (mt) cc_final: 0.8756 (tt) REVERT: A 533 HIS cc_start: 0.7518 (t-90) cc_final: 0.7250 (t-90) REVERT: A 741 MET cc_start: 0.6420 (pmm) cc_final: 0.6211 (pmm) REVERT: B 111 LEU cc_start: 0.8687 (mt) cc_final: 0.8453 (mp) REVERT: B 388 TYR cc_start: 0.6168 (m-80) cc_final: 0.5942 (m-80) REVERT: D 50 GLN cc_start: 0.9295 (tm-30) cc_final: 0.9032 (tm-30) REVERT: D 172 ASP cc_start: 0.8735 (m-30) cc_final: 0.8373 (t0) REVERT: D 219 GLU cc_start: 0.8838 (tt0) cc_final: 0.8495 (tp30) REVERT: E 36 ASN cc_start: 0.8106 (m-40) cc_final: 0.7899 (m-40) REVERT: E 42 ASP cc_start: 0.8281 (m-30) cc_final: 0.8078 (m-30) REVERT: E 89 GLN cc_start: 0.7987 (tt0) cc_final: 0.7377 (tt0) REVERT: E 90 THR cc_start: 0.8633 (p) cc_final: 0.8294 (m) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.4984 time to fit residues: 170.7052 Evaluate side-chains 206 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN E 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10267 Z= 0.409 Angle : 0.653 7.883 13944 Z= 0.371 Chirality : 0.043 0.166 1518 Planarity : 0.006 0.095 1829 Dihedral : 5.207 43.521 1399 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.23), residues: 1248 helix: 0.91 (0.31), residues: 245 sheet: -0.40 (0.25), residues: 369 loop : -0.77 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 745 HIS 0.006 0.002 HIS B 324 PHE 0.014 0.002 PHE A 426 TYR 0.022 0.002 TYR E 75 ARG 0.006 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7610 (m-30) cc_final: 0.7379 (m-30) REVERT: A 306 ASP cc_start: 0.9048 (m-30) cc_final: 0.8834 (m-30) REVERT: A 307 ASP cc_start: 0.8830 (m-30) cc_final: 0.8516 (m-30) REVERT: A 368 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8847 (mm-30) REVERT: A 383 ASP cc_start: 0.8447 (m-30) cc_final: 0.8102 (m-30) REVERT: A 586 PHE cc_start: 0.6765 (m-80) cc_final: 0.6408 (m-10) REVERT: A 618 TYR cc_start: 0.7526 (m-80) cc_final: 0.7277 (m-80) REVERT: A 735 THR cc_start: 0.9011 (m) cc_final: 0.8782 (p) REVERT: A 767 ARG cc_start: 0.8361 (ptp-110) cc_final: 0.8152 (ptp-110) REVERT: A 774 LEU cc_start: 0.8658 (tp) cc_final: 0.8419 (tp) REVERT: B 388 TYR cc_start: 0.6276 (m-80) cc_final: 0.5960 (m-80) REVERT: D 50 GLN cc_start: 0.9361 (tm-30) cc_final: 0.9126 (tm-30) REVERT: D 172 ASP cc_start: 0.8941 (m-30) cc_final: 0.8469 (t0) REVERT: E 36 ASN cc_start: 0.8180 (m110) cc_final: 0.7971 (m-40) REVERT: E 42 ASP cc_start: 0.8456 (m-30) cc_final: 0.8175 (m-30) REVERT: E 101 LEU cc_start: 0.8725 (tp) cc_final: 0.8423 (tp) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.5136 time to fit residues: 152.2098 Evaluate side-chains 182 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 56 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN E 36 ASN E 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10267 Z= 0.177 Angle : 0.498 4.986 13944 Z= 0.278 Chirality : 0.041 0.152 1518 Planarity : 0.004 0.050 1829 Dihedral : 4.739 36.760 1399 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1248 helix: 1.39 (0.32), residues: 245 sheet: -0.39 (0.25), residues: 373 loop : -0.59 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 739 HIS 0.007 0.001 HIS A 280 PHE 0.011 0.001 PHE D 147 TYR 0.021 0.001 TYR D 184 ARG 0.003 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 222 ASP cc_start: 0.8401 (m-30) cc_final: 0.7997 (m-30) REVERT: A 232 ASP cc_start: 0.7604 (m-30) cc_final: 0.7398 (m-30) REVERT: A 284 ILE cc_start: 0.8460 (mm) cc_final: 0.7985 (tp) REVERT: A 337 LEU cc_start: 0.8601 (tp) cc_final: 0.8400 (pp) REVERT: A 533 HIS cc_start: 0.7390 (t-90) cc_final: 0.7141 (t-90) REVERT: A 586 PHE cc_start: 0.6758 (m-80) cc_final: 0.6476 (m-10) REVERT: A 735 THR cc_start: 0.9020 (m) cc_final: 0.8779 (p) REVERT: A 774 LEU cc_start: 0.8625 (tp) cc_final: 0.8415 (tp) REVERT: B 111 LEU cc_start: 0.8744 (mt) cc_final: 0.8438 (mp) REVERT: B 388 TYR cc_start: 0.6234 (m-80) cc_final: 0.5795 (m-80) REVERT: D 50 GLN cc_start: 0.9326 (tm-30) cc_final: 0.9092 (tm-30) REVERT: D 172 ASP cc_start: 0.8860 (m-30) cc_final: 0.8442 (t0) REVERT: D 219 GLU cc_start: 0.8945 (tt0) cc_final: 0.8465 (tp30) REVERT: E 42 ASP cc_start: 0.8363 (m-30) cc_final: 0.8103 (m-30) REVERT: E 101 LEU cc_start: 0.8609 (tp) cc_final: 0.8340 (tp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.5165 time to fit residues: 162.2989 Evaluate side-chains 191 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN E 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10267 Z= 0.190 Angle : 0.489 5.818 13944 Z= 0.273 Chirality : 0.041 0.147 1518 Planarity : 0.004 0.041 1829 Dihedral : 4.589 33.890 1399 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.23), residues: 1248 helix: 1.42 (0.32), residues: 245 sheet: -0.40 (0.25), residues: 373 loop : -0.61 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 739 HIS 0.004 0.001 HIS B 324 PHE 0.012 0.001 PHE A 791 TYR 0.022 0.001 TYR D 159 ARG 0.003 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 222 ASP cc_start: 0.8420 (m-30) cc_final: 0.8027 (m-30) REVERT: A 284 ILE cc_start: 0.8456 (mm) cc_final: 0.7843 (tp) REVERT: A 368 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8619 (mm-30) REVERT: A 533 HIS cc_start: 0.7324 (t-90) cc_final: 0.7080 (t-90) REVERT: A 586 PHE cc_start: 0.6990 (m-80) cc_final: 0.6673 (m-10) REVERT: A 735 THR cc_start: 0.9006 (m) cc_final: 0.8788 (p) REVERT: B 388 TYR cc_start: 0.6279 (m-80) cc_final: 0.5833 (m-80) REVERT: D 50 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9097 (tm-30) REVERT: D 172 ASP cc_start: 0.8890 (m-30) cc_final: 0.8449 (t0) REVERT: D 219 GLU cc_start: 0.8933 (tt0) cc_final: 0.8470 (tp30) REVERT: E 42 ASP cc_start: 0.8366 (m-30) cc_final: 0.8083 (m-30) REVERT: E 101 LEU cc_start: 0.8539 (tp) cc_final: 0.8268 (tp) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.5279 time to fit residues: 161.4676 Evaluate side-chains 189 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10267 Z= 0.215 Angle : 0.503 5.630 13944 Z= 0.280 Chirality : 0.041 0.143 1518 Planarity : 0.004 0.048 1829 Dihedral : 4.605 35.497 1399 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1248 helix: 1.38 (0.33), residues: 245 sheet: -0.32 (0.25), residues: 365 loop : -0.72 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 739 HIS 0.004 0.001 HIS B 324 PHE 0.012 0.001 PHE D 95 TYR 0.024 0.002 TYR D 159 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 222 ASP cc_start: 0.8522 (m-30) cc_final: 0.8166 (m-30) REVERT: A 284 ILE cc_start: 0.8453 (mm) cc_final: 0.7829 (tp) REVERT: A 304 MET cc_start: 0.8627 (mtp) cc_final: 0.8280 (ttm) REVERT: A 306 ASP cc_start: 0.9056 (m-30) cc_final: 0.8809 (m-30) REVERT: A 307 ASP cc_start: 0.8834 (m-30) cc_final: 0.8553 (m-30) REVERT: A 368 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8677 (mm-30) REVERT: A 533 HIS cc_start: 0.7325 (t-90) cc_final: 0.7076 (t-90) REVERT: A 561 GLN cc_start: 0.8542 (tt0) cc_final: 0.8226 (pm20) REVERT: A 586 PHE cc_start: 0.7009 (m-80) cc_final: 0.6663 (m-10) REVERT: A 735 THR cc_start: 0.8991 (m) cc_final: 0.8781 (p) REVERT: B 111 LEU cc_start: 0.8717 (mt) cc_final: 0.8409 (mp) REVERT: B 388 TYR cc_start: 0.6251 (m-80) cc_final: 0.5826 (m-80) REVERT: D 50 GLN cc_start: 0.9336 (tm-30) cc_final: 0.9105 (tm-30) REVERT: D 116 ASN cc_start: 0.9594 (m-40) cc_final: 0.8966 (m110) REVERT: D 165 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8307 (mmmt) REVERT: D 172 ASP cc_start: 0.8910 (m-30) cc_final: 0.8438 (t0) REVERT: D 219 GLU cc_start: 0.8884 (tt0) cc_final: 0.8442 (tp30) REVERT: E 42 ASP cc_start: 0.8356 (m-30) cc_final: 0.8075 (m-30) REVERT: E 101 LEU cc_start: 0.8588 (tp) cc_final: 0.8329 (tp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.5186 time to fit residues: 155.9208 Evaluate side-chains 191 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10267 Z= 0.148 Angle : 0.464 5.093 13944 Z= 0.256 Chirality : 0.041 0.143 1518 Planarity : 0.004 0.059 1829 Dihedral : 4.417 32.609 1399 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1248 helix: 1.46 (0.32), residues: 255 sheet: -0.33 (0.25), residues: 363 loop : -0.71 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 739 HIS 0.004 0.001 HIS B 165 PHE 0.008 0.001 PHE D 147 TYR 0.026 0.001 TYR B 345 ARG 0.002 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 222 ASP cc_start: 0.8485 (m-30) cc_final: 0.8146 (m-30) REVERT: A 284 ILE cc_start: 0.8403 (mm) cc_final: 0.7895 (tp) REVERT: A 306 ASP cc_start: 0.9032 (m-30) cc_final: 0.8797 (m-30) REVERT: A 307 ASP cc_start: 0.8791 (m-30) cc_final: 0.8510 (m-30) REVERT: A 368 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8650 (mm-30) REVERT: A 533 HIS cc_start: 0.7446 (t-90) cc_final: 0.7123 (t-90) REVERT: A 561 GLN cc_start: 0.8466 (tt0) cc_final: 0.8161 (pm20) REVERT: A 586 PHE cc_start: 0.6929 (m-80) cc_final: 0.6611 (m-10) REVERT: A 735 THR cc_start: 0.8974 (m) cc_final: 0.8763 (p) REVERT: B 111 LEU cc_start: 0.8705 (mt) cc_final: 0.8395 (mp) REVERT: D 50 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9093 (tm-30) REVERT: D 116 ASN cc_start: 0.9570 (m-40) cc_final: 0.8911 (m110) REVERT: D 165 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8271 (mmmt) REVERT: D 172 ASP cc_start: 0.8867 (m-30) cc_final: 0.8400 (t0) REVERT: E 42 ASP cc_start: 0.8319 (m-30) cc_final: 0.8054 (m-30) REVERT: E 101 LEU cc_start: 0.8534 (tp) cc_final: 0.8266 (tp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.5125 time to fit residues: 157.1013 Evaluate side-chains 186 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0060 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10267 Z= 0.176 Angle : 0.473 5.035 13944 Z= 0.263 Chirality : 0.041 0.147 1518 Planarity : 0.004 0.047 1829 Dihedral : 4.419 35.818 1399 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1248 helix: 1.44 (0.32), residues: 255 sheet: -0.34 (0.26), residues: 357 loop : -0.77 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 739 HIS 0.004 0.001 HIS B 165 PHE 0.009 0.001 PHE A 791 TYR 0.024 0.001 TYR D 159 ARG 0.002 0.000 ARG A 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8455 (m-30) cc_final: 0.8117 (m-30) REVERT: A 223 LEU cc_start: 0.9533 (mt) cc_final: 0.8999 (tt) REVERT: A 284 ILE cc_start: 0.8417 (mm) cc_final: 0.7869 (tp) REVERT: A 304 MET cc_start: 0.8660 (mtp) cc_final: 0.8290 (ttm) REVERT: A 306 ASP cc_start: 0.9059 (m-30) cc_final: 0.8810 (m-30) REVERT: A 307 ASP cc_start: 0.8794 (m-30) cc_final: 0.8517 (m-30) REVERT: A 368 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8617 (mm-30) REVERT: A 533 HIS cc_start: 0.7439 (t-90) cc_final: 0.7123 (t-90) REVERT: A 561 GLN cc_start: 0.8439 (tt0) cc_final: 0.8180 (pm20) REVERT: A 586 PHE cc_start: 0.6936 (m-80) cc_final: 0.6595 (m-10) REVERT: A 735 THR cc_start: 0.8959 (m) cc_final: 0.8754 (p) REVERT: D 50 GLN cc_start: 0.9337 (tm-30) cc_final: 0.9098 (tm-30) REVERT: D 116 ASN cc_start: 0.9585 (m-40) cc_final: 0.8940 (m110) REVERT: D 165 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8290 (mmmt) REVERT: D 172 ASP cc_start: 0.8918 (m-30) cc_final: 0.8430 (t0) REVERT: E 42 ASP cc_start: 0.8319 (m-30) cc_final: 0.8071 (m-30) REVERT: E 101 LEU cc_start: 0.8554 (tp) cc_final: 0.8279 (tp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.5223 time to fit residues: 160.7877 Evaluate side-chains 186 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.0070 chunk 100 optimal weight: 6.9990 chunk 41 optimal weight: 0.1980 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.121370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088091 restraints weight = 84675.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.091206 restraints weight = 50038.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092399 restraints weight = 33979.190| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10267 Z= 0.124 Angle : 0.445 4.738 13944 Z= 0.244 Chirality : 0.041 0.148 1518 Planarity : 0.003 0.041 1829 Dihedral : 4.198 32.691 1399 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.23), residues: 1248 helix: 1.72 (0.32), residues: 255 sheet: -0.27 (0.25), residues: 370 loop : -0.70 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 739 HIS 0.004 0.001 HIS B 165 PHE 0.008 0.001 PHE D 147 TYR 0.022 0.001 TYR D 159 ARG 0.002 0.000 ARG A 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4656.56 seconds wall clock time: 82 minutes 51.64 seconds (4971.64 seconds total)