Starting phenix.real_space_refine on Mon Mar 18 09:03:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt3_26109/03_2024/7tt3_26109.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt3_26109/03_2024/7tt3_26109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt3_26109/03_2024/7tt3_26109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt3_26109/03_2024/7tt3_26109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt3_26109/03_2024/7tt3_26109.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt3_26109/03_2024/7tt3_26109.pdb" } resolution = 4.3 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= 0.060 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 32 5.16 5 C 6600 2.51 5 N 1786 2.21 5 O 2046 1.98 5 H 10060 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 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 255": "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 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 493": "OD1" <-> "OD2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 95": "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 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 159": "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 "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 367": "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: 20524 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 9493 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 589} Chain breaks: 4 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: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 675 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "B" Number of atoms: 5199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5199 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain breaks: 2 Chain: "P" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 386 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain breaks: 1 Time building chain proxies: 9.06, per 1000 atoms: 0.44 Number of scatterers: 20524 At special positions: 0 Unit cell: (105.234, 124.563, 141.744, 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 32 16.00 O 2046 8.00 N 1786 7.00 C 6600 6.00 H 10060 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: 15.94 Conformation dependent library (CDL) restraints added in 2.2 seconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 24.1% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' 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: 3.777A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.558A pdb=" N ARG A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.947A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 removed outlier: 4.141A pdb=" N GLN A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.727A pdb=" N ASN A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.701A pdb=" N GLN A 753 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 83 removed outlier: 4.863A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 Processing helix chain 'D' and resid 104 through 118 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.705A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.284A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.822A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.813A 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 removed outlier: 3.757A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 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 179 through 183 removed outlier: 3.774A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.859A 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 276 removed outlier: 5.894A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.787A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 354 removed outlier: 7.852A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 354 removed outlier: 7.852A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.831A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL P1272 " --> pdb=" O ILE P1268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.184A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.906A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.579A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.999A pdb=" N THR B 50 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER B 389 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL B 52 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 387 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER B 54 " --> pdb=" O GLY B 385 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.843A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.114A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.773A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.951A pdb=" N ARG B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.932A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.725A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.517A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1305 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: 8.38 Time building geometry restraints manager: 16.68 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: 10060 1.03 - 1.22: 0 1.22 - 1.42: 4646 1.42 - 1.62: 5986 1.62 - 1.81: 60 Bond restraints: 20752 Sorted by residual: bond pdb=" CA TYR A 348 " pdb=" CB TYR A 348 " ideal model delta sigma weight residual 1.534 1.499 0.036 2.33e-02 1.84e+03 2.32e+00 bond pdb=" N HIS D 139 " pdb=" CA HIS D 139 " ideal model delta sigma weight residual 1.458 1.440 0.019 1.26e-02 6.30e+03 2.22e+00 bond pdb=" C LEU D 174 " pdb=" O LEU D 174 " ideal model delta sigma weight residual 1.236 1.254 -0.017 1.22e-02 6.72e+03 2.05e+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 2.01e+00 bond pdb=" CA VAL A 364 " pdb=" C VAL A 364 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.27e-02 6.20e+03 1.80e+00 ... (remaining 20747 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.46: 221 105.46 - 112.63: 23252 112.63 - 119.80: 5802 119.80 - 126.97: 7885 126.97 - 134.14: 127 Bond angle restraints: 37287 Sorted by residual: angle pdb=" C GLY B 265 " pdb=" N ASN B 266 " pdb=" CA ASN B 266 " ideal model delta sigma weight residual 122.47 115.74 6.73 1.50e+00 4.44e-01 2.01e+01 angle pdb=" N ASN A 579 " pdb=" CA ASN A 579 " pdb=" C ASN A 579 " ideal model delta sigma weight residual 107.61 114.99 -7.38 1.74e+00 3.30e-01 1.80e+01 angle pdb=" N ASP A 746 " pdb=" CA ASP A 746 " pdb=" C ASP A 746 " ideal model delta sigma weight residual 107.75 115.39 -7.64 1.86e+00 2.89e-01 1.69e+01 angle pdb=" N GLY B 196 " pdb=" CA GLY B 196 " pdb=" C GLY B 196 " ideal model delta sigma weight residual 113.18 103.88 9.30 2.37e+00 1.78e-01 1.54e+01 angle pdb=" N GLY B 214 " pdb=" CA GLY B 214 " pdb=" C GLY B 214 " ideal model delta sigma weight residual 114.76 108.31 6.45 1.70e+00 3.46e-01 1.44e+01 ... (remaining 37282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 9330 17.78 - 35.56: 306 35.56 - 53.33: 156 53.33 - 71.11: 54 71.11 - 88.89: 14 Dihedral angle restraints: 9860 sinusoidal: 5293 harmonic: 4567 Sorted by residual: dihedral pdb=" CA GLU B 197 " pdb=" C GLU B 197 " pdb=" N SER B 198 " pdb=" CA SER B 198 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CB GLU A 262 " pdb=" CG GLU A 262 " pdb=" CD GLU A 262 " pdb=" OE1 GLU A 262 " ideal model delta sinusoidal sigma weight residual 0.00 80.46 -80.46 1 3.00e+01 1.11e-03 8.90e+00 dihedral pdb=" CA PRO B 330 " pdb=" C PRO B 330 " pdb=" N VAL B 331 " pdb=" CA VAL B 331 " ideal model delta harmonic sigma weight residual 180.00 165.81 14.19 0 5.00e+00 4.00e-02 8.05e+00 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 891 0.036 - 0.072: 437 0.072 - 0.108: 165 0.108 - 0.144: 69 0.144 - 0.181: 13 Chirality restraints: 1575 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 2.33 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA ARG D 141 " pdb=" N ARG D 141 " pdb=" C ARG D 141 " pdb=" CB ARG D 141 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA TYR D 185 " pdb=" N TYR D 185 " pdb=" C TYR D 185 " pdb=" CB TYR D 185 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 1572 not shown) Planarity restraints: 3180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 158 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C SER B 158 " 0.071 2.00e-02 2.50e+03 pdb=" O SER B 158 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP B 159 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 73 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C LEU D 73 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU D 73 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP D 74 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 86 " -0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO D 86 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO D 86 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU D 87 " -0.021 2.00e-02 2.50e+03 ... (remaining 3177 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 384 2.07 - 2.71: 33662 2.71 - 3.34: 55532 3.34 - 3.97: 71843 3.97 - 4.60: 112152 Nonbonded interactions: 273573 Sorted by model distance: nonbonded pdb=" OD1 ASP B 271 " pdb=" H LEU B 272 " model vdw 1.442 1.850 nonbonded pdb=" H ILE A 352 " pdb=" OE2 GLU A 373 " model vdw 1.452 1.850 nonbonded pdb=" HG SER B 193 " pdb=" OD2 ASP B 242 " model vdw 1.508 1.850 nonbonded pdb=" HD1 HIS B 64 " pdb=" O PRO B 65 " model vdw 1.518 1.850 nonbonded pdb=" OD2 ASP A 569 " pdb="HD22 ASN A 606 " model vdw 1.527 1.850 ... (remaining 273568 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: 0.600 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: 0.320 Extract box with map and model: 3.950 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 65.990 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10692 Z= 0.362 Angle : 0.988 11.293 14524 Z= 0.606 Chirality : 0.052 0.181 1575 Planarity : 0.006 0.049 1911 Dihedral : 10.456 88.889 3854 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1312 helix: 0.33 (0.28), residues: 263 sheet: 1.20 (0.24), residues: 418 loop : 0.75 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 739 HIS 0.005 0.001 HIS A 533 PHE 0.017 0.002 PHE A 785 TYR 0.019 0.003 TYR D 205 ARG 0.029 0.003 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 1.734 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 178 GLN cc_start: 0.8791 (mt0) cc_final: 0.8543 (mp10) REVERT: A 240 ILE cc_start: 0.9170 (mt) cc_final: 0.8907 (mt) REVERT: A 254 ILE cc_start: 0.8570 (mt) cc_final: 0.8344 (tp) REVERT: A 446 GLN cc_start: 0.7139 (mt0) cc_final: 0.6878 (mt0) REVERT: A 648 PHE cc_start: 0.7885 (p90) cc_final: 0.7285 (p90) REVERT: A 673 VAL cc_start: 0.8468 (t) cc_final: 0.8228 (p) REVERT: A 711 MET cc_start: 0.8696 (ppp) cc_final: 0.8051 (ptt) REVERT: A 716 LEU cc_start: 0.8785 (tt) cc_final: 0.8460 (mp) REVERT: A 745 TRP cc_start: 0.8289 (p90) cc_final: 0.8021 (p90) REVERT: D 82 ASN cc_start: 0.7976 (t0) cc_final: 0.7520 (t0) REVERT: D 165 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8612 (mmmm) REVERT: C 42 LEU cc_start: 0.9042 (mt) cc_final: 0.8546 (tt) REVERT: C 82 ILE cc_start: 0.8965 (pt) cc_final: 0.8683 (mp) REVERT: B 95 VAL cc_start: 0.6903 (p) cc_final: 0.6657 (p) REVERT: B 154 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7604 (ttp80) REVERT: B 166 THR cc_start: 0.9057 (p) cc_final: 0.8798 (p) REVERT: B 327 LEU cc_start: 0.9067 (mt) cc_final: 0.8652 (mt) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.5382 time to fit residues: 303.4497 Evaluate side-chains 257 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10692 Z= 0.363 Angle : 0.668 7.796 14524 Z= 0.381 Chirality : 0.045 0.168 1575 Planarity : 0.005 0.046 1911 Dihedral : 5.171 60.382 1465 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: 1312 helix: 0.93 (0.29), residues: 276 sheet: 0.60 (0.23), residues: 421 loop : 0.33 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 48 HIS 0.006 0.001 HIS A 533 PHE 0.023 0.002 PHE P1274 TYR 0.020 0.002 TYR D 184 ARG 0.006 0.001 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.435 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: A 254 ILE cc_start: 0.8725 (mt) cc_final: 0.8288 (mm) REVERT: A 268 LEU cc_start: 0.8832 (tp) cc_final: 0.8476 (pp) REVERT: A 305 GLU cc_start: 0.8673 (tt0) cc_final: 0.8123 (tm-30) REVERT: A 369 MET cc_start: 0.9278 (mmp) cc_final: 0.8953 (mmm) REVERT: A 408 SER cc_start: 0.8956 (t) cc_final: 0.8413 (m) REVERT: A 445 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 711 MET cc_start: 0.8618 (ppp) cc_final: 0.8018 (ptt) REVERT: A 716 LEU cc_start: 0.8820 (tt) cc_final: 0.8447 (mp) REVERT: D 82 ASN cc_start: 0.7691 (t0) cc_final: 0.7204 (t0) REVERT: D 107 TYR cc_start: 0.7988 (t80) cc_final: 0.7740 (t80) REVERT: D 165 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8665 (mmmm) REVERT: C 42 LEU cc_start: 0.8869 (mt) cc_final: 0.8382 (tt) REVERT: C 82 ILE cc_start: 0.8903 (pt) cc_final: 0.8593 (mp) REVERT: B 95 VAL cc_start: 0.6816 (p) cc_final: 0.5812 (p) REVERT: B 154 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7659 (ttp80) REVERT: B 192 LEU cc_start: 0.7622 (tp) cc_final: 0.7406 (tp) REVERT: B 327 LEU cc_start: 0.8992 (mt) cc_final: 0.8777 (mt) REVERT: B 388 TYR cc_start: 0.7475 (m-80) cc_final: 0.6881 (m-80) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.4964 time to fit residues: 196.1113 Evaluate side-chains 239 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 0.0970 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10692 Z= 0.185 Angle : 0.541 5.354 14524 Z= 0.303 Chirality : 0.043 0.173 1575 Planarity : 0.004 0.044 1911 Dihedral : 4.903 56.791 1465 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1312 helix: 1.24 (0.30), residues: 276 sheet: 0.49 (0.23), residues: 417 loop : 0.12 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 739 HIS 0.004 0.001 HIS C 51 PHE 0.023 0.002 PHE A 738 TYR 0.022 0.001 TYR A 550 ARG 0.003 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.780 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: A 254 ILE cc_start: 0.8743 (mt) cc_final: 0.8256 (tp) REVERT: A 268 LEU cc_start: 0.8889 (tp) cc_final: 0.8516 (pp) REVERT: A 325 MET cc_start: 0.8773 (pmm) cc_final: 0.8283 (pmm) REVERT: A 408 SER cc_start: 0.8910 (t) cc_final: 0.8366 (m) REVERT: A 445 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 446 GLN cc_start: 0.7245 (mt0) cc_final: 0.6897 (mt0) REVERT: A 651 ASN cc_start: 0.8364 (m-40) cc_final: 0.8010 (m-40) REVERT: A 711 MET cc_start: 0.8554 (ppp) cc_final: 0.8017 (ptt) REVERT: A 716 LEU cc_start: 0.8671 (tt) cc_final: 0.8355 (mp) REVERT: D 82 ASN cc_start: 0.7684 (t0) cc_final: 0.7254 (t0) REVERT: D 165 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8586 (mmmm) REVERT: C 42 LEU cc_start: 0.8874 (mt) cc_final: 0.8292 (tt) REVERT: C 82 ILE cc_start: 0.8908 (pt) cc_final: 0.8664 (mp) REVERT: B 154 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7649 (ttp80) REVERT: B 192 LEU cc_start: 0.7717 (tp) cc_final: 0.7498 (tp) REVERT: B 388 TYR cc_start: 0.7423 (m-80) cc_final: 0.6816 (m-80) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.5377 time to fit residues: 219.8630 Evaluate side-chains 236 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10692 Z= 0.394 Angle : 0.616 5.607 14524 Z= 0.348 Chirality : 0.044 0.156 1575 Planarity : 0.005 0.051 1911 Dihedral : 5.082 55.409 1465 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.09 % Allowed : 1.08 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1312 helix: 0.71 (0.29), residues: 276 sheet: 0.12 (0.24), residues: 409 loop : -0.25 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 576 HIS 0.005 0.001 HIS B 64 PHE 0.016 0.002 PHE A 785 TYR 0.020 0.002 TYR D 184 ARG 0.007 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 1.834 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: A 254 ILE cc_start: 0.8740 (mt) cc_final: 0.8291 (mm) REVERT: A 268 LEU cc_start: 0.8991 (tp) cc_final: 0.8659 (pp) REVERT: A 305 GLU cc_start: 0.8670 (tt0) cc_final: 0.8074 (tm-30) REVERT: A 338 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.8010 (mtm110) REVERT: A 408 SER cc_start: 0.8957 (t) cc_final: 0.8442 (m) REVERT: A 445 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 651 ASN cc_start: 0.8403 (m-40) cc_final: 0.8030 (m-40) REVERT: A 716 LEU cc_start: 0.8672 (tt) cc_final: 0.8367 (mp) REVERT: D 82 ASN cc_start: 0.7851 (t0) cc_final: 0.7364 (t0) REVERT: D 165 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8728 (mmmm) REVERT: C 42 LEU cc_start: 0.8920 (mt) cc_final: 0.8447 (tt) REVERT: C 82 ILE cc_start: 0.8968 (pt) cc_final: 0.8741 (mp) REVERT: B 154 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7725 (ttp80) REVERT: B 388 TYR cc_start: 0.7478 (m-80) cc_final: 0.6837 (m-80) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.5612 time to fit residues: 202.8176 Evaluate side-chains 221 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 113 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10692 Z= 0.200 Angle : 0.528 5.431 14524 Z= 0.293 Chirality : 0.043 0.153 1575 Planarity : 0.004 0.045 1911 Dihedral : 4.804 49.932 1465 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1312 helix: 0.90 (0.30), residues: 276 sheet: 0.16 (0.24), residues: 414 loop : -0.34 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 576 HIS 0.006 0.001 HIS B 64 PHE 0.008 0.001 PHE A 570 TYR 0.026 0.001 TYR A 550 ARG 0.004 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.740 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: A 254 ILE cc_start: 0.8693 (mt) cc_final: 0.8226 (mm) REVERT: A 268 LEU cc_start: 0.8937 (tp) cc_final: 0.8626 (pp) REVERT: A 305 GLU cc_start: 0.8622 (tt0) cc_final: 0.8100 (tm-30) REVERT: A 338 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.8149 (mtp-110) REVERT: A 364 VAL cc_start: 0.9359 (t) cc_final: 0.9150 (t) REVERT: A 408 SER cc_start: 0.8962 (t) cc_final: 0.8509 (m) REVERT: A 458 ILE cc_start: 0.9093 (mp) cc_final: 0.8893 (mt) REVERT: A 648 PHE cc_start: 0.8021 (p90) cc_final: 0.6789 (p90) REVERT: A 651 ASN cc_start: 0.8262 (m-40) cc_final: 0.7922 (m-40) REVERT: A 711 MET cc_start: 0.8438 (ppp) cc_final: 0.8206 (tmm) REVERT: A 716 LEU cc_start: 0.8645 (tt) cc_final: 0.8360 (mp) REVERT: D 49 ARG cc_start: 0.8853 (mtp180) cc_final: 0.8640 (mmm-85) REVERT: D 82 ASN cc_start: 0.7978 (t0) cc_final: 0.7450 (t0) REVERT: D 165 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8697 (mmmm) REVERT: C 42 LEU cc_start: 0.8886 (mt) cc_final: 0.8405 (tt) REVERT: B 154 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7679 (ttp80) REVERT: B 324 HIS cc_start: 0.7700 (m-70) cc_final: 0.7432 (m-70) REVERT: B 388 TYR cc_start: 0.7551 (m-80) cc_final: 0.6953 (m-80) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.5128 time to fit residues: 182.4618 Evaluate side-chains 216 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.0030 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10692 Z= 0.326 Angle : 0.568 5.096 14524 Z= 0.318 Chirality : 0.043 0.149 1575 Planarity : 0.005 0.063 1911 Dihedral : 4.859 44.658 1465 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -0.28 (0.22), residues: 1312 helix: 0.61 (0.29), residues: 275 sheet: -0.10 (0.24), residues: 414 loop : -0.50 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 317 HIS 0.006 0.001 HIS B 64 PHE 0.032 0.002 PHE A 738 TYR 0.018 0.002 TYR D 184 ARG 0.007 0.001 ARG P1269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.264 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: A 254 ILE cc_start: 0.8698 (mt) cc_final: 0.8242 (mm) REVERT: A 268 LEU cc_start: 0.8962 (tp) cc_final: 0.8658 (pp) REVERT: A 305 GLU cc_start: 0.8631 (tt0) cc_final: 0.8092 (tm-30) REVERT: A 338 ARG cc_start: 0.8537 (mtp-110) cc_final: 0.8146 (mtm110) REVERT: A 408 SER cc_start: 0.8943 (t) cc_final: 0.8464 (m) REVERT: A 445 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 539 MET cc_start: 0.8499 (mmm) cc_final: 0.8250 (tpp) REVERT: A 651 ASN cc_start: 0.8391 (m-40) cc_final: 0.8035 (m-40) REVERT: A 711 MET cc_start: 0.8401 (ppp) cc_final: 0.8107 (tmm) REVERT: A 716 LEU cc_start: 0.8661 (tt) cc_final: 0.8349 (mp) REVERT: D 49 ARG cc_start: 0.8881 (mtp180) cc_final: 0.8640 (mmm-85) REVERT: D 82 ASN cc_start: 0.7995 (t0) cc_final: 0.7464 (t0) REVERT: D 165 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8678 (mmmm) REVERT: C 42 LEU cc_start: 0.8895 (mt) cc_final: 0.8463 (tt) REVERT: B 127 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7058 (tm-30) REVERT: B 154 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7730 (ttp80) REVERT: B 388 TYR cc_start: 0.7614 (m-80) cc_final: 0.7020 (m-80) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.5241 time to fit residues: 179.9422 Evaluate side-chains 209 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10692 Z= 0.359 Angle : 0.599 5.480 14524 Z= 0.337 Chirality : 0.043 0.162 1575 Planarity : 0.005 0.061 1911 Dihedral : 5.037 39.305 1465 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.60 (0.22), residues: 1312 helix: 0.27 (0.29), residues: 274 sheet: -0.24 (0.25), residues: 399 loop : -0.70 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 576 HIS 0.006 0.001 HIS B 64 PHE 0.018 0.002 PHE A 804 TYR 0.035 0.002 TYR B 345 ARG 0.005 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.467 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: A 254 ILE cc_start: 0.8731 (mt) cc_final: 0.8280 (mm) REVERT: A 268 LEU cc_start: 0.8997 (tp) cc_final: 0.8702 (pp) REVERT: A 305 GLU cc_start: 0.8646 (tt0) cc_final: 0.8106 (tm-30) REVERT: A 338 ARG cc_start: 0.8619 (mtp-110) cc_final: 0.8284 (mtp-110) REVERT: A 372 MET cc_start: 0.8553 (mmt) cc_final: 0.8131 (mmt) REVERT: A 408 SER cc_start: 0.8977 (t) cc_final: 0.8552 (m) REVERT: A 651 ASN cc_start: 0.8428 (m-40) cc_final: 0.8060 (m-40) REVERT: A 711 MET cc_start: 0.8382 (ppp) cc_final: 0.8065 (tmm) REVERT: A 716 LEU cc_start: 0.8692 (tt) cc_final: 0.8365 (mp) REVERT: D 38 THR cc_start: 0.9271 (t) cc_final: 0.8928 (t) REVERT: D 82 ASN cc_start: 0.8063 (t0) cc_final: 0.7555 (t0) REVERT: D 165 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8720 (mmmm) REVERT: C 42 LEU cc_start: 0.8889 (mt) cc_final: 0.8488 (tt) REVERT: B 154 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7726 (ttp80) REVERT: B 377 LYS cc_start: 0.8769 (mttp) cc_final: 0.8516 (mttt) REVERT: B 388 TYR cc_start: 0.7700 (m-80) cc_final: 0.7197 (m-80) REVERT: P 1298 TYR cc_start: 0.8109 (t80) cc_final: 0.7837 (t80) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.5116 time to fit residues: 171.8319 Evaluate side-chains 205 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10692 Z= 0.238 Angle : 0.537 6.194 14524 Z= 0.297 Chirality : 0.043 0.145 1575 Planarity : 0.004 0.047 1911 Dihedral : 4.892 41.009 1465 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1312 helix: 0.68 (0.30), residues: 275 sheet: -0.14 (0.25), residues: 393 loop : -0.68 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 576 HIS 0.005 0.001 HIS B 64 PHE 0.010 0.001 PHE A 738 TYR 0.020 0.001 TYR D 205 ARG 0.004 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.690 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: A 254 ILE cc_start: 0.8790 (mt) cc_final: 0.8327 (mm) REVERT: A 268 LEU cc_start: 0.8970 (tp) cc_final: 0.8679 (pp) REVERT: A 305 GLU cc_start: 0.8628 (tt0) cc_final: 0.8043 (tm-30) REVERT: A 338 ARG cc_start: 0.8624 (mtp-110) cc_final: 0.8315 (mtp-110) REVERT: A 408 SER cc_start: 0.8950 (t) cc_final: 0.8507 (m) REVERT: A 539 MET cc_start: 0.8351 (mmm) cc_final: 0.8151 (tpp) REVERT: A 651 ASN cc_start: 0.8455 (m-40) cc_final: 0.8090 (m-40) REVERT: A 711 MET cc_start: 0.8391 (ppp) cc_final: 0.8063 (tmm) REVERT: A 716 LEU cc_start: 0.8676 (tt) cc_final: 0.8353 (mp) REVERT: D 82 ASN cc_start: 0.8053 (t0) cc_final: 0.7557 (t0) REVERT: D 165 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8734 (mmmm) REVERT: C 42 LEU cc_start: 0.8877 (mt) cc_final: 0.8450 (tt) REVERT: B 154 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7748 (ttp80) REVERT: B 388 TYR cc_start: 0.7571 (m-80) cc_final: 0.7070 (m-80) REVERT: P 1298 TYR cc_start: 0.8035 (t80) cc_final: 0.7762 (t80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.5470 time to fit residues: 184.0318 Evaluate side-chains 206 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10692 Z= 0.415 Angle : 0.634 6.134 14524 Z= 0.356 Chirality : 0.043 0.180 1575 Planarity : 0.005 0.065 1911 Dihedral : 5.221 44.557 1465 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -0.95 (0.22), residues: 1312 helix: 0.08 (0.29), residues: 275 sheet: -0.41 (0.25), residues: 393 loop : -1.02 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 576 HIS 0.006 0.001 HIS B 64 PHE 0.017 0.002 PHE A 347 TYR 0.023 0.002 TYR A 574 ARG 0.006 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.598 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: A 254 ILE cc_start: 0.8760 (mt) cc_final: 0.8325 (mm) REVERT: A 268 LEU cc_start: 0.9012 (tp) cc_final: 0.8713 (pp) REVERT: A 305 GLU cc_start: 0.8620 (tt0) cc_final: 0.7703 (tm-30) REVERT: A 338 ARG cc_start: 0.8834 (mtp-110) cc_final: 0.8470 (mtp-110) REVERT: A 408 SER cc_start: 0.8971 (t) cc_final: 0.8582 (m) REVERT: A 711 MET cc_start: 0.8254 (ppp) cc_final: 0.8022 (tmm) REVERT: A 716 LEU cc_start: 0.8746 (tt) cc_final: 0.8360 (mp) REVERT: A 783 LEU cc_start: 0.7572 (mm) cc_final: 0.7223 (mt) REVERT: D 82 ASN cc_start: 0.8140 (t0) cc_final: 0.7625 (t0) REVERT: D 165 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8771 (mmmm) REVERT: C 42 LEU cc_start: 0.8889 (mt) cc_final: 0.8516 (tt) REVERT: B 154 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7812 (ttp80) REVERT: B 388 TYR cc_start: 0.7622 (m-80) cc_final: 0.7141 (m-80) REVERT: P 1298 TYR cc_start: 0.8314 (t80) cc_final: 0.7950 (t80) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.5423 time to fit residues: 174.7114 Evaluate side-chains 202 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 86 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10692 Z= 0.148 Angle : 0.514 7.469 14524 Z= 0.282 Chirality : 0.043 0.150 1575 Planarity : 0.004 0.040 1911 Dihedral : 4.788 48.753 1465 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.36 (0.22), residues: 1312 helix: 0.90 (0.30), residues: 275 sheet: -0.10 (0.25), residues: 377 loop : -0.75 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 576 HIS 0.003 0.001 HIS B 64 PHE 0.010 0.001 PHE A 785 TYR 0.056 0.001 TYR B 345 ARG 0.003 0.000 ARG A 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.495 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: A 254 ILE cc_start: 0.8802 (mt) cc_final: 0.8340 (mm) REVERT: A 268 LEU cc_start: 0.8924 (tp) cc_final: 0.8623 (pp) REVERT: A 305 GLU cc_start: 0.8586 (tt0) cc_final: 0.7729 (tm-30) REVERT: A 338 ARG cc_start: 0.8683 (mtp-110) cc_final: 0.8345 (mtp-110) REVERT: A 408 SER cc_start: 0.8873 (t) cc_final: 0.8483 (m) REVERT: A 609 TYR cc_start: 0.7913 (p90) cc_final: 0.7458 (p90) REVERT: A 641 LEU cc_start: 0.7522 (mm) cc_final: 0.7158 (mm) REVERT: A 648 PHE cc_start: 0.8306 (p90) cc_final: 0.7923 (p90) REVERT: A 711 MET cc_start: 0.8324 (ppp) cc_final: 0.8021 (tmm) REVERT: A 716 LEU cc_start: 0.8676 (tt) cc_final: 0.8342 (mp) REVERT: A 774 LEU cc_start: 0.8444 (tp) cc_final: 0.8239 (tt) REVERT: A 783 LEU cc_start: 0.7428 (mm) cc_final: 0.7202 (mt) REVERT: D 82 ASN cc_start: 0.8109 (t0) cc_final: 0.7594 (t0) REVERT: D 165 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8601 (mmmm) REVERT: C 42 LEU cc_start: 0.8843 (mt) cc_final: 0.8371 (tt) REVERT: B 154 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7714 (ttp80) REVERT: B 327 LEU cc_start: 0.9169 (mt) cc_final: 0.8953 (mt) REVERT: B 377 LYS cc_start: 0.8734 (mttt) cc_final: 0.8433 (mttt) REVERT: B 388 TYR cc_start: 0.7590 (m-80) cc_final: 0.7114 (m-80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.5200 time to fit residues: 173.0339 Evaluate side-chains 207 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.149625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101835 restraints weight = 65384.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104195 restraints weight = 36255.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105489 restraints weight = 24513.459| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10692 Z= 0.157 Angle : 0.493 5.778 14524 Z= 0.270 Chirality : 0.042 0.145 1575 Planarity : 0.004 0.039 1911 Dihedral : 4.657 48.486 1465 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -0.28 (0.23), residues: 1312 helix: 0.88 (0.31), residues: 281 sheet: -0.01 (0.25), residues: 395 loop : -0.72 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 576 HIS 0.004 0.001 HIS B 64 PHE 0.013 0.001 PHE A 428 TYR 0.025 0.001 TYR E 28 ARG 0.003 0.000 ARG A 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4885.06 seconds wall clock time: 87 minutes 33.27 seconds (5253.27 seconds total)