Starting phenix.real_space_refine on Sun Mar 17 06:35:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezn_4161/03_2024/6ezn_4161_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezn_4161/03_2024/6ezn_4161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezn_4161/03_2024/6ezn_4161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezn_4161/03_2024/6ezn_4161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezn_4161/03_2024/6ezn_4161_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezn_4161/03_2024/6ezn_4161_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.005 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 P 5 5.49 5 S 52 5.16 5 C 11176 2.51 5 N 2670 2.21 5 O 3105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "F ARG 615": "NH1" <-> "NH2" Residue "F PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 190": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17008 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3534 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 106} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 973 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Chain: "D" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5186 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 625} Chain breaks: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3179 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 377} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1880 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 15, 'TRANS': 243} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 83 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'CPL': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.37, per 1000 atoms: 0.55 Number of scatterers: 17008 At special positions: 0 Unit cell: (123.54, 117.15, 159.75, 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 52 16.00 P 5 15.00 O 3105 8.00 N 2670 7.00 C 11176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG G 503 " - " ASN G 332 " " NAG I 1 " - " ASN A 336 " " NAG J 1 " - " ASN A 400 " " NAG K 1 " - " ASN F 539 " " NAG L 1 " - " ASN G 60 " Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 2.8 seconds 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 20 sheets defined 37.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 72 through 75 No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 443 through 446 No H-bonds generated for 'chain 'A' and resid 443 through 446' Processing helix chain 'A' and resid 448 through 466 Processing helix chain 'B' and resid 24 through 40 removed outlier: 3.624A pdb=" N LYS B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 67 removed outlier: 3.835A pdb=" N LEU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 removed outlier: 3.966A pdb=" N CYS B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 128 removed outlier: 3.809A pdb=" N GLU B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 232 Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'C' and resid 269 through 289 Processing helix chain 'C' and resid 291 through 297 removed outlier: 4.273A pdb=" N SER C 296 " --> pdb=" O GLN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 334 removed outlier: 4.177A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 31 Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 54 through 82 removed outlier: 3.830A pdb=" N PHE E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 30 Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 90 through 103 Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 119 through 137 removed outlier: 4.109A pdb=" N GLY F 124 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 removed outlier: 3.794A pdb=" N LEU F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 157 No H-bonds generated for 'chain 'F' and resid 154 through 157' Processing helix chain 'F' and resid 172 through 188 removed outlier: 4.180A pdb=" N VAL F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 205 removed outlier: 3.611A pdb=" N ALA F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE F 200 " --> pdb=" O CYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 218 through 227 Processing helix chain 'F' and resid 233 through 249 removed outlier: 4.865A pdb=" N THR F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 267 through 286 removed outlier: 4.122A pdb=" N GLN F 277 " --> pdb=" O PHE F 273 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE F 278 " --> pdb=" O GLY F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 294 No H-bonds generated for 'chain 'F' and resid 291 through 294' Processing helix chain 'F' and resid 356 through 362 Processing helix chain 'F' and resid 366 through 378 Proline residue: F 371 - end of helix removed outlier: 3.566A pdb=" N VAL F 374 " --> pdb=" O PHE F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 401 removed outlier: 3.595A pdb=" N CYS F 395 " --> pdb=" O TYR F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 428 removed outlier: 3.549A pdb=" N LEU F 407 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR F 408 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 410 " --> pdb=" O LEU F 407 " (cutoff:3.500A) Proline residue: F 411 - end of helix removed outlier: 3.775A pdb=" N SER F 416 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 417 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 420 " --> pdb=" O ALA F 417 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER F 422 " --> pdb=" O VAL F 419 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 424 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE F 425 " --> pdb=" O SER F 422 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR F 428 " --> pdb=" O PHE F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 473 removed outlier: 4.221A pdb=" N SER F 454 " --> pdb=" O ILE F 450 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 463 " --> pdb=" O LEU F 459 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE F 464 " --> pdb=" O TYR F 460 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR F 470 " --> pdb=" O SER F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 505 Processing helix chain 'F' and resid 517 through 526 removed outlier: 5.501A pdb=" N TYR F 521 " --> pdb=" O ASP F 518 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN F 522 " --> pdb=" O TYR F 519 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE F 523 " --> pdb=" O GLY F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 550 removed outlier: 3.914A pdb=" N VAL F 546 " --> pdb=" O HIS F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 563 removed outlier: 3.692A pdb=" N GLU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE F 560 " --> pdb=" O LYS F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 595 removed outlier: 3.872A pdb=" N ILE F 593 " --> pdb=" O TRP F 589 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER F 594 " --> pdb=" O MET F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 625 No H-bonds generated for 'chain 'F' and resid 622 through 625' Processing helix chain 'F' and resid 628 through 633 Processing helix chain 'F' and resid 692 through 698 Processing helix chain 'G' and resid 38 through 49 removed outlier: 6.436A pdb=" N VAL G 42 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU G 44 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS G 45 " --> pdb=" O VAL G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 96 through 105 removed outlier: 4.066A pdb=" N ASN G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 129 Processing helix chain 'G' and resid 155 through 157 No H-bonds generated for 'chain 'G' and resid 155 through 157' Processing helix chain 'G' and resid 248 through 257 Processing helix chain 'G' and resid 393 through 415 Processing helix chain 'H' and resid 122 through 128 Processing helix chain 'H' and resid 193 through 215 Processing helix chain 'H' and resid 231 through 252 removed outlier: 3.676A pdb=" N GLU H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 274 Proline residue: H 270 - end of helix removed outlier: 4.309A pdb=" N LEU H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 Processing sheet with id= A, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.502A pdb=" N PHE A 205 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A 54 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR A 36 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU A 52 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ARG A 38 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR A 50 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A 40 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 66 through 70 removed outlier: 3.569A pdb=" N ASN A 93 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 155 through 161 Processing sheet with id= D, first strand: chain 'A' and resid 372 through 374 removed outlier: 7.305A pdb=" N ASN A 231 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLU A 256 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A 236 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR A 254 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG A 238 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU A 252 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 240 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLN A 250 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU A 242 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR A 248 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 236 through 241 Processing sheet with id= F, first strand: chain 'A' and resid 291 through 294 Processing sheet with id= G, first strand: chain 'A' and resid 349 through 351 removed outlier: 6.698A pdb=" N ASP A 440 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE A 389 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 568 through 572 removed outlier: 6.006A pdb=" N GLN F 681 " --> pdb=" O GLU F 668 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLU F 668 " --> pdb=" O GLN F 681 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 28 through 31 removed outlier: 3.625A pdb=" N TYR G 30 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 78 through 81 removed outlier: 6.442A pdb=" N ASN G 108 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL G 81 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU G 110 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 131 through 133 Processing sheet with id= L, first strand: chain 'G' and resid 139 through 142 Processing sheet with id= M, first strand: chain 'G' and resid 151 through 154 Processing sheet with id= N, first strand: chain 'G' and resid 264 through 266 Processing sheet with id= O, first strand: chain 'G' and resid 270 through 273 Processing sheet with id= P, first strand: chain 'G' and resid 297 through 299 Processing sheet with id= Q, first strand: chain 'G' and resid 367 through 375 removed outlier: 4.592A pdb=" N ASP G 358 " --> pdb=" O GLN G 313 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN G 313 " --> pdb=" O ASP G 358 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 68 through 71 removed outlier: 6.287A pdb=" N TYR H 111 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS H 34 " --> pdb=" O TYR H 111 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE H 113 " --> pdb=" O LYS H 34 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 82 through 86 removed outlier: 6.646A pdb=" N LEU H 137 " --> pdb=" O GLU H 153 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU H 153 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 101 through 103 671 hydrogen bonds defined for protein. 1887 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: 5.21 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2626 1.31 - 1.43: 5025 1.43 - 1.56: 9695 1.56 - 1.69: 12 1.69 - 1.81: 87 Bond restraints: 17445 Sorted by residual: bond pdb=" C8 PTY F 810 " pdb=" O7 PTY F 810 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C30 PTY F 810 " pdb=" O4 PTY F 810 " ideal model delta sigma weight residual 1.331 1.449 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C11 CPL E 101 " pdb=" O3 CPL E 101 " ideal model delta sigma weight residual 1.327 1.421 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C31 CPL E 101 " pdb=" O2 CPL E 101 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C31 CPL F 809 " pdb=" O2 CPL F 809 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.00e+01 ... (remaining 17440 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.47: 247 104.47 - 112.18: 8404 112.18 - 119.89: 6948 119.89 - 127.61: 7887 127.61 - 135.32: 188 Bond angle restraints: 23674 Sorted by residual: angle pdb=" N PRO H 45 " pdb=" CA PRO H 45 " pdb=" CB PRO H 45 " ideal model delta sigma weight residual 103.25 111.56 -8.31 1.05e+00 9.07e-01 6.26e+01 angle pdb=" N PRO H 54 " pdb=" CA PRO H 54 " pdb=" CB PRO H 54 " ideal model delta sigma weight residual 103.25 111.14 -7.89 1.05e+00 9.07e-01 5.65e+01 angle pdb=" N PRO H 29 " pdb=" CA PRO H 29 " pdb=" CB PRO H 29 " ideal model delta sigma weight residual 103.25 110.87 -7.62 1.05e+00 9.07e-01 5.27e+01 angle pdb=" N PRO H 62 " pdb=" CA PRO H 62 " pdb=" CB PRO H 62 " ideal model delta sigma weight residual 103.25 110.70 -7.45 1.05e+00 9.07e-01 5.04e+01 angle pdb=" CA LEU A 310 " pdb=" CB LEU A 310 " pdb=" CG LEU A 310 " ideal model delta sigma weight residual 116.30 135.32 -19.02 3.50e+00 8.16e-02 2.95e+01 ... (remaining 23669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 10259 35.75 - 71.50: 131 71.50 - 107.25: 29 107.25 - 143.00: 4 143.00 - 178.75: 6 Dihedral angle restraints: 10429 sinusoidal: 4290 harmonic: 6139 Sorted by residual: dihedral pdb=" CA GLN A 280 " pdb=" C GLN A 280 " pdb=" N ASN A 281 " pdb=" CA ASN A 281 " ideal model delta harmonic sigma weight residual 180.00 136.48 43.52 0 5.00e+00 4.00e-02 7.58e+01 dihedral pdb=" CA ARG F 605 " pdb=" C ARG F 605 " pdb=" N ASP F 606 " pdb=" CA ASP F 606 " ideal model delta harmonic sigma weight residual 180.00 142.05 37.95 0 5.00e+00 4.00e-02 5.76e+01 dihedral pdb=" CA TYR A 144 " pdb=" C TYR A 144 " pdb=" N PRO A 145 " pdb=" CA PRO A 145 " ideal model delta harmonic sigma weight residual 180.00 148.47 31.53 0 5.00e+00 4.00e-02 3.98e+01 ... (remaining 10426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2283 0.086 - 0.172: 367 0.172 - 0.259: 36 0.259 - 0.345: 10 0.345 - 0.431: 2 Chirality restraints: 2698 Sorted by residual: chirality pdb=" CB ILE G 232 " pdb=" CA ILE G 232 " pdb=" CG1 ILE G 232 " pdb=" CG2 ILE G 232 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 336 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CG LEU C 342 " pdb=" CB LEU C 342 " pdb=" CD1 LEU C 342 " pdb=" CD2 LEU C 342 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2695 not shown) Planarity restraints: 2929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 318 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C ARG A 318 " 0.054 2.00e-02 2.50e+03 pdb=" O ARG A 318 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 319 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 318 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C GLN G 318 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN G 318 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL G 319 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 153 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO F 154 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 154 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 154 " 0.039 5.00e-02 4.00e+02 ... (remaining 2926 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4869 2.81 - 3.33: 14940 3.33 - 3.86: 27394 3.86 - 4.38: 32083 4.38 - 4.90: 56061 Nonbonded interactions: 135347 Sorted by model distance: nonbonded pdb=" OH TYR F 630 " pdb=" OD2 ASP F 659 " model vdw 2.291 2.440 nonbonded pdb=" OG SER G 386 " pdb=" OH TYR H 252 " model vdw 2.295 2.440 nonbonded pdb=" OD2 ASP D 29 " pdb=" OG SER F 141 " model vdw 2.321 2.440 nonbonded pdb=" O GLU B 25 " pdb=" OG1 THR B 29 " model vdw 2.334 2.440 nonbonded pdb=" NH2 ARG G 385 " pdb=" O TYR H 252 " model vdw 2.339 2.520 ... (remaining 135342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.260 Check model and map are aligned: 0.190 Set scattering table: 0.150 Process input model: 46.250 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 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 : 0.008 0.126 17445 Z= 0.508 Angle : 1.208 19.020 23674 Z= 0.597 Chirality : 0.065 0.431 2698 Planarity : 0.007 0.072 2924 Dihedral : 14.620 178.745 6461 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.54 % Favored : 91.08 % Rotamer: Outliers : 0.51 % Allowed : 3.75 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.12 % Twisted General : 0.20 % 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: -4.93 (0.13), residues: 2062 helix: -3.24 (0.11), residues: 839 sheet: -2.43 (0.23), residues: 376 loop : -3.55 (0.16), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP F 208 HIS 0.018 0.003 HIS D 26 PHE 0.037 0.003 PHE B 50 TYR 0.046 0.003 TYR F 391 ARG 0.014 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 384 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PRO cc_start: 0.6948 (Cg_endo) cc_final: 0.6720 (Cg_exo) REVERT: A 185 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7461 (mt-10) REVERT: A 201 ASN cc_start: 0.7587 (m110) cc_final: 0.6652 (t0) REVERT: A 324 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7733 (mtt90) REVERT: A 378 GLU cc_start: 0.7430 (pt0) cc_final: 0.6884 (pm20) REVERT: A 462 MET cc_start: 0.7417 (mmm) cc_final: 0.7014 (mmt) REVERT: B 44 LEU cc_start: 0.7881 (mp) cc_final: 0.7660 (mt) REVERT: B 100 ASN cc_start: 0.7217 (m-40) cc_final: 0.6770 (p0) REVERT: C 264 HIS cc_start: 0.7896 (m-70) cc_final: 0.7671 (m-70) REVERT: C 338 TYR cc_start: 0.8445 (t80) cc_final: 0.8127 (t80) REVERT: E 5 GLN cc_start: 0.8393 (mt0) cc_final: 0.8110 (mm-40) REVERT: F 445 LEU cc_start: 0.8733 (tm) cc_final: 0.8493 (tp) REVERT: F 476 SER cc_start: 0.7996 (t) cc_final: 0.7758 (m) REVERT: F 510 ASP cc_start: 0.6959 (p0) cc_final: 0.6668 (m-30) REVERT: F 528 ASP cc_start: 0.7675 (t70) cc_final: 0.7426 (t0) REVERT: F 550 MET cc_start: 0.8371 (mmt) cc_final: 0.8125 (mmt) REVERT: F 609 THR cc_start: 0.8426 (p) cc_final: 0.7698 (p) REVERT: F 626 ASN cc_start: 0.8110 (m-40) cc_final: 0.7853 (m-40) REVERT: F 632 MET cc_start: 0.8882 (mtp) cc_final: 0.8624 (mtm) REVERT: G 32 GLN cc_start: 0.7141 (mm110) cc_final: 0.6908 (mm110) REVERT: G 161 LYS cc_start: 0.6562 (mtpt) cc_final: 0.6283 (ttpt) REVERT: G 234 SER cc_start: 0.7226 (t) cc_final: 0.6877 (t) REVERT: H 115 LEU cc_start: 0.6140 (mp) cc_final: 0.5842 (tt) REVERT: H 201 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6692 (mp) REVERT: H 225 ILE cc_start: 0.6639 (mp) cc_final: 0.6292 (pt) outliers start: 9 outliers final: 5 residues processed: 391 average time/residue: 0.2862 time to fit residues: 166.7847 Evaluate side-chains 224 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 218 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 716 LEU Chi-restraints excluded: chain H residue 201 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 105 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 95 GLN A 121 ASN A 201 ASN A 217 ASN A 334 ASN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS E 80 ASN F 68 ASN ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 ASN F 688 GLN ** G 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 GLN G 222 GLN G 243 GLN G 247 GLN G 271 HIS G 337 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17445 Z= 0.211 Angle : 0.665 9.853 23674 Z= 0.336 Chirality : 0.045 0.225 2698 Planarity : 0.005 0.061 2924 Dihedral : 14.481 176.231 2780 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.08 % Favored : 92.77 % Rotamer: Outliers : 2.50 % Allowed : 8.63 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.31 (0.16), residues: 2062 helix: -1.26 (0.16), residues: 833 sheet: -2.05 (0.24), residues: 389 loop : -3.18 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 208 HIS 0.005 0.001 HIS A 315 PHE 0.021 0.002 PHE G 409 TYR 0.018 0.001 TYR F 203 ARG 0.004 0.001 ARG F 592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 232 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.6859 (tt0) cc_final: 0.6521 (tt0) REVERT: A 201 ASN cc_start: 0.7715 (m-40) cc_final: 0.6860 (t0) REVERT: A 282 MET cc_start: 0.2643 (tpt) cc_final: 0.1994 (tpp) REVERT: A 324 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7590 (mtp85) REVERT: A 375 ASP cc_start: 0.8183 (m-30) cc_final: 0.7864 (m-30) REVERT: A 393 ASP cc_start: 0.7653 (m-30) cc_final: 0.7430 (m-30) REVERT: A 418 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7997 (ttpt) REVERT: B 100 ASN cc_start: 0.7128 (m-40) cc_final: 0.6570 (p0) REVERT: C 333 ILE cc_start: 0.7885 (tt) cc_final: 0.7645 (tt) REVERT: C 338 TYR cc_start: 0.8328 (t80) cc_final: 0.7888 (t80) REVERT: E 5 GLN cc_start: 0.8347 (mt0) cc_final: 0.8141 (mm110) REVERT: F 43 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7908 (mm) REVERT: F 510 ASP cc_start: 0.7173 (p0) cc_final: 0.6875 (m-30) REVERT: F 528 ASP cc_start: 0.7958 (t70) cc_final: 0.7618 (t0) REVERT: F 609 THR cc_start: 0.7707 (p) cc_final: 0.7453 (p) REVERT: F 632 MET cc_start: 0.8908 (mtp) cc_final: 0.8697 (mtm) REVERT: F 654 MET cc_start: 0.7878 (mtp) cc_final: 0.7598 (mtt) REVERT: H 80 GLN cc_start: 0.5232 (pt0) cc_final: 0.5000 (pt0) REVERT: H 201 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7170 (mt) REVERT: H 225 ILE cc_start: 0.6831 (mp) cc_final: 0.6549 (pt) outliers start: 44 outliers final: 27 residues processed: 256 average time/residue: 0.2880 time to fit residues: 112.4645 Evaluate side-chains 226 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 432 ASN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN B 97 GLN ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17445 Z= 0.302 Angle : 0.668 13.206 23674 Z= 0.339 Chirality : 0.046 0.231 2698 Planarity : 0.005 0.061 2924 Dihedral : 13.392 170.986 2772 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.05 % Favored : 91.80 % Rotamer: Outliers : 3.24 % Allowed : 10.39 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.17), residues: 2062 helix: -0.31 (0.17), residues: 838 sheet: -1.69 (0.25), residues: 389 loop : -2.98 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 241 HIS 0.007 0.001 HIS D 26 PHE 0.026 0.002 PHE A 321 TYR 0.025 0.002 TYR F 203 ARG 0.006 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 216 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.7123 (tt0) cc_final: 0.6870 (tt0) REVERT: A 201 ASN cc_start: 0.7720 (m-40) cc_final: 0.6798 (t0) REVERT: B 100 ASN cc_start: 0.7357 (m-40) cc_final: 0.6533 (p0) REVERT: C 333 ILE cc_start: 0.7864 (tt) cc_final: 0.7633 (tt) REVERT: E 5 GLN cc_start: 0.8398 (mt0) cc_final: 0.8111 (mm-40) REVERT: F 43 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7724 (mm) REVERT: F 510 ASP cc_start: 0.7379 (p0) cc_final: 0.7059 (m-30) REVERT: F 528 ASP cc_start: 0.8141 (t70) cc_final: 0.7851 (t0) REVERT: F 609 THR cc_start: 0.7878 (p) cc_final: 0.7594 (p) REVERT: F 632 MET cc_start: 0.8960 (mtp) cc_final: 0.8579 (mtm) REVERT: F 654 MET cc_start: 0.7835 (mtp) cc_final: 0.7560 (mtt) REVERT: G 32 GLN cc_start: 0.5965 (mm110) cc_final: 0.5762 (mm110) REVERT: H 225 ILE cc_start: 0.7295 (mp) cc_final: 0.6980 (pt) REVERT: H 250 ARG cc_start: 0.7383 (mtp85) cc_final: 0.7164 (mtm180) outliers start: 57 outliers final: 39 residues processed: 255 average time/residue: 0.2873 time to fit residues: 111.8829 Evaluate side-chains 235 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 178 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17445 Z= 0.231 Angle : 0.606 10.813 23674 Z= 0.307 Chirality : 0.044 0.199 2698 Planarity : 0.004 0.051 2924 Dihedral : 12.786 175.882 2770 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.03 % Favored : 92.82 % Rotamer: Outliers : 3.69 % Allowed : 11.58 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.96 (0.18), residues: 2062 helix: 0.26 (0.18), residues: 831 sheet: -1.52 (0.25), residues: 405 loop : -2.84 (0.18), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 299 HIS 0.006 0.001 HIS C 297 PHE 0.018 0.001 PHE H 70 TYR 0.017 0.001 TYR F 203 ARG 0.004 0.000 ARG F 651 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 208 time to evaluate : 1.895 Fit side-chains revert: symmetry clash REVERT: A 55 ILE cc_start: 0.5706 (OUTLIER) cc_final: 0.5490 (mt) REVERT: A 146 GLU cc_start: 0.7167 (tt0) cc_final: 0.6944 (tt0) REVERT: A 201 ASN cc_start: 0.7638 (m-40) cc_final: 0.6790 (t0) REVERT: A 411 ASP cc_start: 0.7954 (m-30) cc_final: 0.7562 (m-30) REVERT: B 100 ASN cc_start: 0.7343 (m-40) cc_final: 0.6488 (p0) REVERT: C 333 ILE cc_start: 0.7923 (tt) cc_final: 0.7687 (tt) REVERT: E 5 GLN cc_start: 0.8415 (mt0) cc_final: 0.8107 (mm-40) REVERT: F 43 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7549 (mm) REVERT: F 159 ARG cc_start: 0.8014 (mmm160) cc_final: 0.7435 (mtp85) REVERT: F 168 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.4394 (mp0) REVERT: F 528 ASP cc_start: 0.8206 (t70) cc_final: 0.7910 (t0) REVERT: F 609 THR cc_start: 0.7855 (p) cc_final: 0.7611 (p) REVERT: F 654 MET cc_start: 0.7890 (mtp) cc_final: 0.7614 (mtt) REVERT: H 225 ILE cc_start: 0.7473 (mp) cc_final: 0.7130 (pt) outliers start: 65 outliers final: 50 residues processed: 247 average time/residue: 0.2584 time to fit residues: 99.9162 Evaluate side-chains 250 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 197 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 chunk 169 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17445 Z= 0.261 Angle : 0.606 8.040 23674 Z= 0.307 Chirality : 0.045 0.193 2698 Planarity : 0.004 0.049 2924 Dihedral : 12.406 173.130 2770 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.90 % Favored : 91.95 % Rotamer: Outliers : 3.63 % Allowed : 13.12 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.73 (0.18), residues: 2062 helix: 0.53 (0.18), residues: 828 sheet: -1.42 (0.25), residues: 405 loop : -2.80 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 299 HIS 0.006 0.001 HIS C 297 PHE 0.025 0.002 PHE C 307 TYR 0.017 0.001 TYR F 243 ARG 0.004 0.000 ARG F 693 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 199 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 55 ILE cc_start: 0.5627 (OUTLIER) cc_final: 0.5416 (mt) REVERT: A 201 ASN cc_start: 0.7559 (m-40) cc_final: 0.6732 (t0) REVERT: A 282 MET cc_start: 0.2699 (tpt) cc_final: 0.1991 (tpp) REVERT: A 411 ASP cc_start: 0.8078 (m-30) cc_final: 0.7689 (m-30) REVERT: B 100 ASN cc_start: 0.7379 (m-40) cc_final: 0.6534 (p0) REVERT: C 333 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7737 (tt) REVERT: E 5 GLN cc_start: 0.8360 (mt0) cc_final: 0.8018 (mm-40) REVERT: F 43 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7365 (mm) REVERT: F 159 ARG cc_start: 0.8074 (mmm160) cc_final: 0.7597 (mtp85) REVERT: F 528 ASP cc_start: 0.8218 (t70) cc_final: 0.7907 (t0) REVERT: F 609 THR cc_start: 0.7809 (p) cc_final: 0.7518 (p) REVERT: F 654 MET cc_start: 0.7886 (mtp) cc_final: 0.7605 (mtt) REVERT: G 186 GLU cc_start: 0.6463 (tt0) cc_final: 0.6126 (tt0) REVERT: H 225 ILE cc_start: 0.7587 (mp) cc_final: 0.7238 (pt) outliers start: 64 outliers final: 52 residues processed: 243 average time/residue: 0.2640 time to fit residues: 100.4133 Evaluate side-chains 246 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 191 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 0.0570 chunk 179 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 116 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17445 Z= 0.180 Angle : 0.565 7.748 23674 Z= 0.286 Chirality : 0.043 0.192 2698 Planarity : 0.003 0.042 2924 Dihedral : 11.926 163.382 2770 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 3.29 % Allowed : 14.08 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.48 (0.18), residues: 2062 helix: 0.81 (0.18), residues: 832 sheet: -1.27 (0.25), residues: 405 loop : -2.76 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 538 HIS 0.004 0.001 HIS D 26 PHE 0.019 0.001 PHE H 70 TYR 0.015 0.001 TYR F 243 ARG 0.004 0.000 ARG F 693 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 193 time to evaluate : 1.747 Fit side-chains revert: symmetry clash REVERT: A 55 ILE cc_start: 0.5614 (OUTLIER) cc_final: 0.5411 (mt) REVERT: A 201 ASN cc_start: 0.7397 (m-40) cc_final: 0.6639 (t0) REVERT: A 282 MET cc_start: 0.2472 (tpt) cc_final: 0.1899 (tpp) REVERT: A 411 ASP cc_start: 0.8047 (m-30) cc_final: 0.7653 (m-30) REVERT: B 100 ASN cc_start: 0.7231 (m-40) cc_final: 0.6380 (p0) REVERT: F 159 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7315 (mtp85) REVERT: F 168 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.4270 (mp0) REVERT: F 451 VAL cc_start: 0.7645 (p) cc_final: 0.7387 (p) REVERT: F 528 ASP cc_start: 0.8244 (t70) cc_final: 0.7932 (t0) REVERT: F 609 THR cc_start: 0.7791 (p) cc_final: 0.7523 (p) REVERT: F 654 MET cc_start: 0.7897 (mtp) cc_final: 0.7630 (mtt) REVERT: G 167 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.7750 (mtm-85) REVERT: G 186 GLU cc_start: 0.6460 (tt0) cc_final: 0.6098 (tt0) REVERT: H 191 VAL cc_start: 0.8072 (p) cc_final: 0.7862 (p) REVERT: H 225 ILE cc_start: 0.7557 (mp) cc_final: 0.7269 (pt) outliers start: 58 outliers final: 40 residues processed: 230 average time/residue: 0.2837 time to fit residues: 101.1674 Evaluate side-chains 227 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 185 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN G 242 ASN ** G 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 17445 Z= 0.399 Angle : 0.669 9.408 23674 Z= 0.339 Chirality : 0.047 0.190 2698 Planarity : 0.004 0.045 2924 Dihedral : 12.025 159.138 2768 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.39 % Favored : 91.46 % Rotamer: Outliers : 3.58 % Allowed : 14.03 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.62 (0.18), residues: 2062 helix: 0.55 (0.18), residues: 843 sheet: -1.22 (0.26), residues: 402 loop : -2.78 (0.19), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 299 HIS 0.008 0.002 HIS F 44 PHE 0.024 0.002 PHE B 128 TYR 0.020 0.002 TYR F 203 ARG 0.005 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 191 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7458 (m-40) cc_final: 0.6601 (t0) REVERT: A 411 ASP cc_start: 0.8154 (m-30) cc_final: 0.7772 (m-30) REVERT: B 100 ASN cc_start: 0.7295 (m-40) cc_final: 0.6546 (p0) REVERT: B 130 ASN cc_start: 0.8099 (t0) cc_final: 0.7335 (t0) REVERT: C 333 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7736 (tt) REVERT: E 25 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: F 168 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.4671 (mp0) REVERT: F 609 THR cc_start: 0.7903 (p) cc_final: 0.7617 (p) REVERT: F 654 MET cc_start: 0.7837 (mtp) cc_final: 0.7536 (mtt) REVERT: G 186 GLU cc_start: 0.6443 (tt0) cc_final: 0.6086 (tt0) REVERT: H 225 ILE cc_start: 0.7954 (mp) cc_final: 0.7607 (pt) outliers start: 63 outliers final: 49 residues processed: 234 average time/residue: 0.2705 time to fit residues: 98.6029 Evaluate side-chains 236 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 184 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 25 GLN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 593 ILE Chi-restraints excluded: chain F residue 594 SER Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS F 216 ASN ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17445 Z= 0.176 Angle : 0.575 8.951 23674 Z= 0.290 Chirality : 0.043 0.209 2698 Planarity : 0.004 0.041 2924 Dihedral : 11.420 151.782 2768 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.64 % Favored : 93.21 % Rotamer: Outliers : 3.07 % Allowed : 14.54 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.25 (0.18), residues: 2062 helix: 0.98 (0.18), residues: 828 sheet: -1.09 (0.26), residues: 404 loop : -2.64 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 31 HIS 0.004 0.001 HIS D 26 PHE 0.027 0.001 PHE A 214 TYR 0.013 0.001 TYR F 165 ARG 0.013 0.000 ARG F 605 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 194 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7402 (m-40) cc_final: 0.6650 (t0) REVERT: A 282 MET cc_start: 0.2427 (tpt) cc_final: 0.1775 (tpp) REVERT: A 411 ASP cc_start: 0.8096 (m-30) cc_final: 0.7699 (m-30) REVERT: B 93 SER cc_start: 0.8801 (t) cc_final: 0.7953 (m) REVERT: B 100 ASN cc_start: 0.7088 (m-40) cc_final: 0.6318 (p0) REVERT: C 338 TYR cc_start: 0.8284 (t80) cc_final: 0.7650 (t80) REVERT: F 159 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7354 (mtp85) REVERT: F 168 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.4518 (mp0) REVERT: F 451 VAL cc_start: 0.7612 (p) cc_final: 0.7357 (p) REVERT: F 528 ASP cc_start: 0.8173 (t70) cc_final: 0.7853 (t0) REVERT: F 654 MET cc_start: 0.7839 (mtp) cc_final: 0.7556 (mtt) REVERT: G 156 ASN cc_start: 0.7680 (m-40) cc_final: 0.7476 (m110) REVERT: G 167 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.7744 (mtm-85) REVERT: G 186 GLU cc_start: 0.6541 (tt0) cc_final: 0.6154 (tt0) REVERT: H 109 TYR cc_start: 0.2034 (m-80) cc_final: 0.1236 (m-10) REVERT: H 225 ILE cc_start: 0.7882 (mp) cc_final: 0.7541 (pt) outliers start: 54 outliers final: 46 residues processed: 229 average time/residue: 0.2759 time to fit residues: 98.7004 Evaluate side-chains 228 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 185 optimal weight: 20.0000 chunk 111 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 145 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 184 optimal weight: 40.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17445 Z= 0.187 Angle : 0.572 9.313 23674 Z= 0.288 Chirality : 0.043 0.188 2698 Planarity : 0.004 0.038 2924 Dihedral : 10.949 149.314 2768 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.37 % Favored : 92.48 % Rotamer: Outliers : 3.18 % Allowed : 14.42 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.15 (0.18), residues: 2062 helix: 1.05 (0.18), residues: 840 sheet: -1.05 (0.26), residues: 402 loop : -2.60 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 31 HIS 0.004 0.001 HIS D 26 PHE 0.024 0.001 PHE A 214 TYR 0.011 0.001 TYR F 391 ARG 0.008 0.000 ARG F 605 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 191 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7423 (m-40) cc_final: 0.6663 (t0) REVERT: A 205 PHE cc_start: 0.3840 (p90) cc_final: 0.3630 (p90) REVERT: A 282 MET cc_start: 0.2777 (tpt) cc_final: 0.2480 (tpt) REVERT: A 411 ASP cc_start: 0.8083 (m-30) cc_final: 0.7718 (m-30) REVERT: B 93 SER cc_start: 0.8794 (t) cc_final: 0.7942 (m) REVERT: B 100 ASN cc_start: 0.7160 (m-40) cc_final: 0.6302 (p0) REVERT: C 333 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7732 (tt) REVERT: C 338 TYR cc_start: 0.8222 (t80) cc_final: 0.7594 (t80) REVERT: F 159 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7365 (mtp85) REVERT: F 168 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.4604 (mp0) REVERT: F 528 ASP cc_start: 0.8174 (t70) cc_final: 0.7854 (t0) REVERT: F 654 MET cc_start: 0.7864 (mtp) cc_final: 0.7584 (mtt) REVERT: G 167 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.7757 (mtm-85) REVERT: G 186 GLU cc_start: 0.6534 (tt0) cc_final: 0.6175 (tt0) REVERT: H 225 ILE cc_start: 0.7848 (mp) cc_final: 0.7515 (pt) outliers start: 56 outliers final: 46 residues processed: 231 average time/residue: 0.2717 time to fit residues: 97.7962 Evaluate side-chains 233 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 185 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 136 optimal weight: 0.0770 chunk 205 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 17445 Z= 0.377 Angle : 0.664 9.422 23674 Z= 0.335 Chirality : 0.047 0.189 2698 Planarity : 0.004 0.042 2924 Dihedral : 11.027 149.795 2768 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.15 % Favored : 91.71 % Rotamer: Outliers : 2.95 % Allowed : 14.93 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.36 (0.18), residues: 2062 helix: 0.76 (0.18), residues: 843 sheet: -1.08 (0.26), residues: 399 loop : -2.63 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 299 HIS 0.006 0.001 HIS D 26 PHE 0.028 0.002 PHE C 307 TYR 0.018 0.002 TYR F 203 ARG 0.008 0.001 ARG F 605 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 179 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7399 (m-40) cc_final: 0.6619 (t0) REVERT: A 282 MET cc_start: 0.2603 (tpt) cc_final: 0.2318 (tpt) REVERT: B 93 SER cc_start: 0.8887 (t) cc_final: 0.8100 (m) REVERT: B 100 ASN cc_start: 0.7270 (m-40) cc_final: 0.6462 (p0) REVERT: C 333 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7770 (tt) REVERT: E 25 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: F 168 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.4804 (mp0) REVERT: F 267 MET cc_start: 0.8897 (mmp) cc_final: 0.8531 (mmp) REVERT: F 654 MET cc_start: 0.7826 (mtp) cc_final: 0.7524 (mtt) REVERT: G 167 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.7709 (mtm-85) REVERT: G 186 GLU cc_start: 0.6476 (tt0) cc_final: 0.6094 (tt0) REVERT: H 225 ILE cc_start: 0.8131 (mp) cc_final: 0.7796 (pt) outliers start: 52 outliers final: 45 residues processed: 219 average time/residue: 0.2805 time to fit residues: 95.9246 Evaluate side-chains 225 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 177 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 25 GLN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain F residue 594 SER Chi-restraints excluded: chain F residue 611 GLU Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 714 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 163 optimal weight: 0.0070 chunk 68 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 377 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.159104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125952 restraints weight = 21245.809| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.83 r_work: 0.3169 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17445 Z= 0.184 Angle : 0.575 9.561 23674 Z= 0.289 Chirality : 0.043 0.188 2698 Planarity : 0.004 0.038 2924 Dihedral : 10.512 144.352 2768 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.32 % Favored : 92.53 % Rotamer: Outliers : 2.78 % Allowed : 15.11 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2062 helix: 1.07 (0.18), residues: 835 sheet: -0.99 (0.26), residues: 402 loop : -2.55 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 31 HIS 0.004 0.001 HIS D 26 PHE 0.028 0.001 PHE C 307 TYR 0.012 0.001 TYR F 203 ARG 0.010 0.000 ARG F 605 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3380.13 seconds wall clock time: 62 minutes 7.02 seconds (3727.02 seconds total)