Starting phenix.real_space_refine on Fri Feb 16 05:05:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oxl_20220/02_2024/6oxl_20220_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oxl_20220/02_2024/6oxl_20220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oxl_20220/02_2024/6oxl_20220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oxl_20220/02_2024/6oxl_20220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oxl_20220/02_2024/6oxl_20220_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oxl_20220/02_2024/6oxl_20220_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.173 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 1 5.49 5 S 74 5.16 5 C 9236 2.51 5 N 2435 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 253": "NH1" <-> "NH2" Residue "M PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14413 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4629 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 4465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4465 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 539} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "M" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3118 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 372} Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1190 Classifications: {'peptide': 141} Link IDs: {'TRANS': 140} Chain: "N" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 975 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "n" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 7.60, per 1000 atoms: 0.53 Number of scatterers: 14413 At special positions: 0 Unit cell: (100.92, 107.88, 124.12, 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 74 16.00 P 1 15.00 O 2667 8.00 N 2435 7.00 C 9236 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 Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.4 seconds 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 12 sheets defined 50.6% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.643A pdb=" N PHE A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 44 Processing helix chain 'A' and resid 52 through 67 removed outlier: 3.791A pdb=" N LYS A 57 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 59 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 60 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 66 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.787A pdb=" N LEU A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.598A pdb=" N ILE A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.925A pdb=" N ARG A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.011A pdb=" N LEU A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 removed outlier: 4.173A pdb=" N ALA A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.872A pdb=" N GLN A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.977A pdb=" N HIS A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.669A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.966A pdb=" N SER A 227 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 234 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 237 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 removed outlier: 4.021A pdb=" N LEU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 274 through 290 removed outlier: 4.047A pdb=" N GLU A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 287 " --> pdb=" O CYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 305 through 320 removed outlier: 3.814A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 removed outlier: 4.177A pdb=" N GLN A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.702A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 379 removed outlier: 3.864A pdb=" N LYS A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 removed outlier: 3.830A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.695A pdb=" N ALA A 402 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN A 403 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 406 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 407 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A 411 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 412 " --> pdb=" O MET A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.737A pdb=" N ILE A 424 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 425 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 426 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 428 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 429 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 430 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 432 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.685A pdb=" N ASP A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 476 through 486 removed outlier: 3.590A pdb=" N PHE A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 506 removed outlier: 3.689A pdb=" N LYS A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 519 through 528 removed outlier: 3.512A pdb=" N ASN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 551 removed outlier: 3.522A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.872A pdb=" N ASP A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 588 removed outlier: 3.579A pdb=" N GLU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.549A pdb=" N GLU B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.918A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 removed outlier: 3.636A pdb=" N PHE B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 4.501A pdb=" N VAL B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 78 removed outlier: 3.592A pdb=" N LEU B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 91 removed outlier: 3.568A pdb=" N ILE B 85 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N MET B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA B 87 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 3.546A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.805A pdb=" N THR B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU B 120 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 122 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS B 123 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU B 124 " --> pdb=" O TYR B 121 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.879A pdb=" N LYS B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 4.102A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 162 through 169 removed outlier: 3.764A pdb=" N ASP B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 189 removed outlier: 4.051A pdb=" N ASN B 179 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 218 through 228 removed outlier: 4.138A pdb=" N LEU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 248 removed outlier: 3.666A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.818A pdb=" N LEU B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 4.186A pdb=" N LEU B 281 " --> pdb=" O TYR B 277 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS B 282 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.695A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.583A pdb=" N TYR B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 344 removed outlier: 4.119A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.665A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 357 " --> pdb=" O GLN B 353 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 381 removed outlier: 4.116A pdb=" N LYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 401 removed outlier: 4.178A pdb=" N ALA B 388 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLU B 389 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 392 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 394 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B 396 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 399 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 420 removed outlier: 4.853A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 removed outlier: 4.116A pdb=" N ALA B 430 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU B 434 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 453 removed outlier: 3.638A pdb=" N TRP B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 4.056A pdb=" N GLU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 494 removed outlier: 3.600A pdb=" N VAL B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.889A pdb=" N GLN B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 530 removed outlier: 3.784A pdb=" N ARG B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 540 removed outlier: 3.752A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 566 removed outlier: 3.615A pdb=" N GLU B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 573 No H-bonds generated for 'chain 'B' and resid 570 through 573' Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'M' and resid 27 through 35 removed outlier: 3.520A pdb=" N PHE M 32 " --> pdb=" O ALA M 28 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 93 removed outlier: 3.766A pdb=" N CYS M 86 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA M 91 " --> pdb=" O ASP M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.540A pdb=" N LYS M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 98 through 102' Processing helix chain 'M' and resid 105 through 111 removed outlier: 3.580A pdb=" N TYR M 109 " --> pdb=" O PHE M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 131 removed outlier: 4.007A pdb=" N LYS M 130 " --> pdb=" O THR M 126 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N THR M 131 " --> pdb=" O GLY M 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 126 through 131' Processing helix chain 'S' and resid 27 through 36 removed outlier: 3.513A pdb=" N HIS S 36 " --> pdb=" O ILE S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 95 removed outlier: 3.576A pdb=" N GLU S 82 " --> pdb=" O LEU S 78 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL S 90 " --> pdb=" O ASN S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 103 No H-bonds generated for 'chain 'S' and resid 101 through 103' Processing helix chain 'S' and resid 107 through 117 removed outlier: 3.526A pdb=" N TYR S 111 " --> pdb=" O PHE S 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR S 112 " --> pdb=" O TYR S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 139 removed outlier: 3.666A pdb=" N MET S 137 " --> pdb=" O LYS S 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 34 No H-bonds generated for 'chain 'N' and resid 32 through 34' Processing helix chain 'N' and resid 112 through 137 removed outlier: 3.745A pdb=" N PHE N 118 " --> pdb=" O ASP N 114 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS N 125 " --> pdb=" O ALA N 121 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE N 126 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS N 137 " --> pdb=" O CYS N 133 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'M' and resid 47 through 49 removed outlier: 3.567A pdb=" N PHE M 56 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'M' and resid 419 through 422 removed outlier: 7.094A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 178 through 181 removed outlier: 6.577A pdb=" N ILE M 425 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL M 181 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG M 427 " --> pdb=" O VAL M 181 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'M' and resid 183 through 185 Processing sheet with id= E, first strand: chain 'M' and resid 262 through 265 removed outlier: 3.828A pdb=" N LYS M 405 " --> pdb=" O LYS M 213 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR M 403 " --> pdb=" O GLY M 215 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'M' and resid 287 through 296 removed outlier: 3.879A pdb=" N VAL M 296 " --> pdb=" O LYS M 300 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M 300 " --> pdb=" O VAL M 296 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN M 334 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 316 through 318 Processing sheet with id= H, first strand: chain 'M' and resid 387 through 389 removed outlier: 3.574A pdb=" N ALA M 350 " --> pdb=" O LYS M 345 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 56 through 62 removed outlier: 6.154A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 42 through 44 Processing sheet with id= K, first strand: chain 'N' and resid 45 through 51 Processing sheet with id= L, first strand: chain 'N' and resid 81 through 83 555 hydrogen bonds defined for protein. 1497 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: 4.36 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4365 1.33 - 1.45: 2041 1.45 - 1.57: 8147 1.57 - 1.69: 3 1.69 - 1.81: 113 Bond restraints: 14669 Sorted by residual: bond pdb=" OG1 TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.717 1.629 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" O1P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O2P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.528 1.612 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C GLU B 544 " pdb=" N LYS B 545 " ideal model delta sigma weight residual 1.329 1.267 0.061 1.60e-02 3.91e+03 1.47e+01 bond pdb=" C THR S 14 " pdb=" N ARG S 15 " ideal model delta sigma weight residual 1.332 1.297 0.034 1.29e-02 6.01e+03 7.10e+00 ... (remaining 14664 not shown) Histogram of bond angle deviations from ideal: 95.97 - 103.68: 181 103.68 - 111.40: 6342 111.40 - 119.11: 5776 119.11 - 126.83: 7417 126.83 - 134.54: 148 Bond angle restraints: 19864 Sorted by residual: angle pdb=" N ALA B 254 " pdb=" CA ALA B 254 " pdb=" C ALA B 254 " ideal model delta sigma weight residual 111.28 119.34 -8.06 1.09e+00 8.42e-01 5.47e+01 angle pdb=" N LEU A 447 " pdb=" CA LEU A 447 " pdb=" C LEU A 447 " ideal model delta sigma weight residual 111.28 106.29 4.99 1.09e+00 8.42e-01 2.10e+01 angle pdb=" C PHE S 52 " pdb=" N ARG S 53 " pdb=" CA ARG S 53 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C THR B 8 " pdb=" N THR B 9 " pdb=" CA THR B 9 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CA LEU A 532 " pdb=" CB LEU A 532 " pdb=" CG LEU A 532 " ideal model delta sigma weight residual 116.30 130.49 -14.19 3.50e+00 8.16e-02 1.64e+01 ... (remaining 19859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.34: 8538 15.34 - 30.69: 336 30.69 - 46.03: 78 46.03 - 61.37: 3 61.37 - 76.72: 2 Dihedral angle restraints: 8957 sinusoidal: 3592 harmonic: 5365 Sorted by residual: dihedral pdb=" CA GLN B 154 " pdb=" C GLN B 154 " pdb=" N MET B 155 " pdb=" CA MET B 155 " ideal model delta harmonic sigma weight residual 180.00 150.87 29.13 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA CYS S 70 " pdb=" C CYS S 70 " pdb=" N VAL S 71 " pdb=" CA VAL S 71 " ideal model delta harmonic sigma weight residual 180.00 -153.22 -26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA TRP M 421 " pdb=" C TRP M 421 " pdb=" N VAL M 422 " pdb=" CA VAL M 422 " ideal model delta harmonic sigma weight residual 180.00 156.12 23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 8954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1667 0.059 - 0.117: 530 0.117 - 0.176: 104 0.176 - 0.234: 11 0.234 - 0.293: 2 Chirality restraints: 2314 Sorted by residual: chirality pdb=" CB ILE M 355 " pdb=" CA ILE M 355 " pdb=" CG1 ILE M 355 " pdb=" CG2 ILE M 355 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ALA B 254 " pdb=" N ALA B 254 " pdb=" C ALA B 254 " pdb=" CB ALA B 254 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASP M 282 " pdb=" N ASP M 282 " pdb=" C ASP M 282 " pdb=" CB ASP M 282 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2311 not shown) Planarity restraints: 2522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO N 22 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO N 23 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO N 23 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO N 23 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 245 " -0.049 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO B 246 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 246 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 246 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 421 " -0.023 2.00e-02 2.50e+03 1.64e-02 6.72e+00 pdb=" CG TRP M 421 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP M 421 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP M 421 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 421 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP M 421 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP M 421 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 421 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 421 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP M 421 " -0.001 2.00e-02 2.50e+03 ... (remaining 2519 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3336 2.77 - 3.30: 12964 3.30 - 3.83: 23113 3.83 - 4.37: 28610 4.37 - 4.90: 47805 Nonbonded interactions: 115828 Sorted by model distance: nonbonded pdb=" OE2 GLU M 179 " pdb=" OH TYR M 277 " model vdw 2.236 2.440 nonbonded pdb=" OE2 GLU A 494 " pdb=" OG1 THR A 537 " model vdw 2.240 2.440 nonbonded pdb=" O PHE M 287 " pdb=" OH TYR M 431 " model vdw 2.255 2.440 nonbonded pdb=" NE2 GLN B 348 " pdb=" OE1 GLN B 386 " model vdw 2.271 2.520 nonbonded pdb=" OH TYR B 328 " pdb=" OD1 ASP N 117 " model vdw 2.273 2.440 ... (remaining 115823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 6.520 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 38.940 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.010 0.094 14669 Z= 0.650 Angle : 1.086 14.188 19864 Z= 0.611 Chirality : 0.058 0.293 2314 Planarity : 0.007 0.073 2522 Dihedral : 9.339 76.719 5457 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.06 % Allowed : 0.95 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.46 (0.14), residues: 1772 helix: -4.63 (0.06), residues: 965 sheet: -1.75 (0.36), residues: 193 loop : -1.99 (0.21), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP M 421 HIS 0.014 0.002 HIS A 320 PHE 0.040 0.004 PHE S 67 TYR 0.036 0.004 TYR B 455 ARG 0.009 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8388 (mmmt) REVERT: A 77 MET cc_start: 0.8564 (tpp) cc_final: 0.8305 (tpp) REVERT: A 114 ASN cc_start: 0.8569 (t0) cc_final: 0.8247 (t0) REVERT: A 128 MET cc_start: 0.8408 (mtm) cc_final: 0.8159 (mtp) REVERT: B 205 ASN cc_start: 0.8699 (t0) cc_final: 0.8464 (m-40) REVERT: B 340 ASP cc_start: 0.9121 (t0) cc_final: 0.8690 (t0) REVERT: B 344 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8303 (mtt-85) REVERT: B 384 VAL cc_start: 0.8929 (t) cc_final: 0.8621 (m) REVERT: B 408 GLN cc_start: 0.8502 (mt0) cc_final: 0.8214 (mt0) REVERT: B 565 CYS cc_start: 0.9052 (m) cc_final: 0.8632 (t) REVERT: M 218 ASP cc_start: 0.8217 (m-30) cc_final: 0.7808 (p0) REVERT: M 282 ASP cc_start: 0.8870 (p0) cc_final: 0.8626 (p0) REVERT: M 298 ARG cc_start: 0.8095 (ptp90) cc_final: 0.7587 (mtt180) REVERT: S 1 MET cc_start: 0.8369 (ptm) cc_final: 0.8065 (ptt) REVERT: S 21 MET cc_start: 0.8304 (mtp) cc_final: 0.8079 (mtp) REVERT: N 53 LYS cc_start: 0.8746 (mttt) cc_final: 0.8432 (mmtt) REVERT: N 61 ASP cc_start: 0.8215 (t0) cc_final: 0.7824 (m-30) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.3257 time to fit residues: 120.1702 Evaluate side-chains 156 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 76 HIS A 81 ASN A 92 GLN A 200 HIS A 216 GLN A 266 GLN ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 550 ASN A 568 GLN B 56 ASN B 75 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN B 203 ASN B 250 HIS B 386 GLN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 GLN M 412 ASN S 8 GLN S 36 HIS N 39 GLN N 125 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14669 Z= 0.216 Angle : 0.622 12.731 19864 Z= 0.324 Chirality : 0.043 0.181 2314 Planarity : 0.005 0.065 2522 Dihedral : 5.529 27.478 1956 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.45 % Allowed : 5.30 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.17), residues: 1772 helix: -3.14 (0.12), residues: 972 sheet: -1.67 (0.33), residues: 217 loop : -1.40 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 421 HIS 0.005 0.001 HIS B 250 PHE 0.021 0.002 PHE S 4 TYR 0.011 0.001 TYR A 412 ARG 0.003 0.000 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8371 (mmmt) REVERT: A 118 ASN cc_start: 0.8103 (m-40) cc_final: 0.7630 (t0) REVERT: A 128 MET cc_start: 0.8443 (mtm) cc_final: 0.8161 (mtp) REVERT: B 29 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8255 (mppt) REVERT: B 205 ASN cc_start: 0.8479 (t0) cc_final: 0.8237 (m-40) REVERT: B 340 ASP cc_start: 0.8949 (t0) cc_final: 0.8742 (t0) REVERT: B 565 CYS cc_start: 0.9182 (m) cc_final: 0.8687 (t) REVERT: S 13 LYS cc_start: 0.8334 (mttt) cc_final: 0.7996 (tppt) REVERT: S 27 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7822 (mt-10) REVERT: N 53 LYS cc_start: 0.8707 (mttt) cc_final: 0.8378 (mmtt) REVERT: N 54 VAL cc_start: 0.8869 (t) cc_final: 0.8643 (p) REVERT: N 61 ASP cc_start: 0.8227 (t0) cc_final: 0.7709 (m-30) REVERT: N 76 PHE cc_start: 0.7543 (t80) cc_final: 0.7320 (t80) outliers start: 23 outliers final: 10 residues processed: 186 average time/residue: 0.2943 time to fit residues: 78.2438 Evaluate side-chains 155 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 161 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 369 HIS B 75 ASN B 179 ASN B 408 GLN M 122 GLN S 36 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14669 Z= 0.196 Angle : 0.552 11.151 19864 Z= 0.283 Chirality : 0.042 0.209 2314 Planarity : 0.004 0.062 2522 Dihedral : 5.008 25.828 1956 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 1.45 % Allowed : 7.00 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.18), residues: 1772 helix: -2.23 (0.14), residues: 984 sheet: -1.42 (0.32), residues: 226 loop : -1.05 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 421 HIS 0.012 0.001 HIS S 36 PHE 0.021 0.001 PHE S 4 TYR 0.014 0.001 TYR N 56 ARG 0.003 0.000 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 1.672 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8382 (mmmt) REVERT: A 118 ASN cc_start: 0.8079 (m-40) cc_final: 0.7621 (t0) REVERT: A 128 MET cc_start: 0.8468 (mtm) cc_final: 0.8209 (mtp) REVERT: B 29 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8471 (mppt) REVERT: B 205 ASN cc_start: 0.8551 (t0) cc_final: 0.8300 (m-40) REVERT: B 253 SER cc_start: 0.8798 (m) cc_final: 0.8582 (t) REVERT: B 264 MET cc_start: 0.8421 (mmm) cc_final: 0.8172 (mmm) REVERT: B 340 ASP cc_start: 0.8977 (t0) cc_final: 0.8696 (t0) REVERT: B 448 MET cc_start: 0.8603 (tpp) cc_final: 0.8162 (tpt) REVERT: B 565 CYS cc_start: 0.9168 (m) cc_final: 0.8696 (t) REVERT: S 13 LYS cc_start: 0.8354 (mttt) cc_final: 0.8008 (tppt) REVERT: N 53 LYS cc_start: 0.8767 (mttt) cc_final: 0.8344 (mmtt) REVERT: N 61 ASP cc_start: 0.8148 (t0) cc_final: 0.7666 (m-30) REVERT: N 70 GLN cc_start: 0.8314 (tt0) cc_final: 0.7954 (tt0) REVERT: N 76 PHE cc_start: 0.7552 (t80) cc_final: 0.7306 (t80) REVERT: N 134 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8439 (tm-30) outliers start: 23 outliers final: 11 residues processed: 158 average time/residue: 0.3081 time to fit residues: 69.7895 Evaluate side-chains 148 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 84 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 163 optimal weight: 0.0570 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 0.0570 chunk 154 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14669 Z= 0.143 Angle : 0.502 11.575 19864 Z= 0.255 Chirality : 0.041 0.163 2314 Planarity : 0.004 0.053 2522 Dihedral : 4.587 25.127 1956 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 1.51 % Allowed : 6.94 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.19), residues: 1772 helix: -1.51 (0.15), residues: 987 sheet: -1.17 (0.32), residues: 229 loop : -0.81 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 421 HIS 0.005 0.001 HIS B 250 PHE 0.020 0.001 PHE S 4 TYR 0.008 0.001 TYR B 405 ARG 0.003 0.000 ARG S 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8377 (mmmt) REVERT: A 128 MET cc_start: 0.8439 (mtm) cc_final: 0.8182 (mtp) REVERT: B 29 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8379 (mppt) REVERT: B 205 ASN cc_start: 0.8541 (t0) cc_final: 0.8284 (m-40) REVERT: B 264 MET cc_start: 0.8362 (mmm) cc_final: 0.8122 (mmm) REVERT: B 340 ASP cc_start: 0.8932 (t0) cc_final: 0.8675 (t0) REVERT: B 448 MET cc_start: 0.8611 (tpp) cc_final: 0.8163 (tpt) REVERT: B 565 CYS cc_start: 0.9174 (m) cc_final: 0.8675 (t) REVERT: M 1 MET cc_start: 0.7809 (tpp) cc_final: 0.7526 (tpp) REVERT: M 357 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.8511 (mtm-85) REVERT: S 13 LYS cc_start: 0.8350 (mttt) cc_final: 0.8040 (tppt) REVERT: N 53 LYS cc_start: 0.8793 (mttt) cc_final: 0.8354 (mmtt) REVERT: N 61 ASP cc_start: 0.8103 (t0) cc_final: 0.7524 (m-30) REVERT: N 134 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8386 (tm-30) outliers start: 24 outliers final: 13 residues processed: 166 average time/residue: 0.2896 time to fit residues: 69.9244 Evaluate side-chains 149 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 130 LYS Chi-restraints excluded: chain S residue 140 SER Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 74 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 155 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14669 Z= 0.179 Angle : 0.508 10.591 19864 Z= 0.256 Chirality : 0.042 0.168 2314 Planarity : 0.003 0.052 2522 Dihedral : 4.403 23.173 1956 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 1.51 % Allowed : 7.76 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.19), residues: 1772 helix: -1.06 (0.15), residues: 989 sheet: -1.06 (0.32), residues: 239 loop : -0.63 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 64 HIS 0.005 0.001 HIS S 36 PHE 0.019 0.001 PHE S 4 TYR 0.012 0.001 TYR A 247 ARG 0.003 0.000 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8389 (mmmt) REVERT: A 128 MET cc_start: 0.8495 (mtm) cc_final: 0.8239 (mtp) REVERT: B 205 ASN cc_start: 0.8506 (t0) cc_final: 0.8235 (m-40) REVERT: B 340 ASP cc_start: 0.8951 (t0) cc_final: 0.8663 (t0) REVERT: B 448 MET cc_start: 0.8636 (tpp) cc_final: 0.8176 (tpt) REVERT: B 565 CYS cc_start: 0.9155 (m) cc_final: 0.8674 (t) REVERT: S 13 LYS cc_start: 0.8358 (mttt) cc_final: 0.8001 (tppt) REVERT: N 53 LYS cc_start: 0.8751 (mttt) cc_final: 0.8340 (mmtt) REVERT: N 61 ASP cc_start: 0.8121 (t0) cc_final: 0.7564 (m-30) REVERT: N 134 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8346 (tm-30) outliers start: 24 outliers final: 18 residues processed: 157 average time/residue: 0.3032 time to fit residues: 69.2619 Evaluate side-chains 144 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 130 LYS Chi-restraints excluded: chain S residue 140 SER Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 143 optimal weight: 0.0670 chunk 80 optimal weight: 0.0670 chunk 14 optimal weight: 0.0270 chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14669 Z= 0.126 Angle : 0.484 10.273 19864 Z= 0.244 Chirality : 0.041 0.186 2314 Planarity : 0.003 0.051 2522 Dihedral : 4.173 22.811 1956 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 1.20 % Allowed : 8.39 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1772 helix: -0.55 (0.16), residues: 996 sheet: -0.84 (0.32), residues: 239 loop : -0.52 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 421 HIS 0.003 0.001 HIS B 250 PHE 0.018 0.001 PHE S 4 TYR 0.008 0.001 TYR A 247 ARG 0.003 0.000 ARG S 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8322 (mmmt) REVERT: A 77 MET cc_start: 0.7863 (tpp) cc_final: 0.7636 (tpp) REVERT: A 128 MET cc_start: 0.8445 (mtm) cc_final: 0.8175 (mtp) REVERT: B 71 LEU cc_start: 0.8871 (mm) cc_final: 0.8547 (mt) REVERT: B 205 ASN cc_start: 0.8514 (t0) cc_final: 0.8232 (m-40) REVERT: B 340 ASP cc_start: 0.8916 (t0) cc_final: 0.8688 (t0) REVERT: B 448 MET cc_start: 0.8611 (tpp) cc_final: 0.8127 (tpt) REVERT: B 565 CYS cc_start: 0.9128 (m) cc_final: 0.8670 (t) REVERT: M 410 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6278 (ptmt) REVERT: S 13 LYS cc_start: 0.8315 (mttt) cc_final: 0.7949 (tppt) REVERT: S 49 PHE cc_start: 0.8680 (m-10) cc_final: 0.8440 (m-10) REVERT: S 77 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8525 (p0) REVERT: N 53 LYS cc_start: 0.8663 (mttt) cc_final: 0.8297 (mmtt) REVERT: N 61 ASP cc_start: 0.7977 (t0) cc_final: 0.7278 (m-30) REVERT: N 134 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8325 (tm-30) outliers start: 19 outliers final: 9 residues processed: 167 average time/residue: 0.2910 time to fit residues: 70.6641 Evaluate side-chains 144 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 130 LYS Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 74 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14669 Z= 0.224 Angle : 0.520 9.517 19864 Z= 0.260 Chirality : 0.042 0.163 2314 Planarity : 0.004 0.051 2522 Dihedral : 4.211 20.908 1956 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 1.51 % Allowed : 8.83 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1772 helix: -0.44 (0.16), residues: 988 sheet: -0.79 (0.33), residues: 239 loop : -0.38 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 462 HIS 0.005 0.001 HIS M 10 PHE 0.018 0.001 PHE S 4 TYR 0.010 0.001 TYR A 247 ARG 0.004 0.000 ARG M 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8388 (mmmt) REVERT: A 128 MET cc_start: 0.8541 (mtm) cc_final: 0.8279 (mtp) REVERT: A 601 GLU cc_start: 0.7651 (tt0) cc_final: 0.7445 (mp0) REVERT: B 71 LEU cc_start: 0.8940 (mm) cc_final: 0.8556 (mt) REVERT: B 205 ASN cc_start: 0.8499 (t0) cc_final: 0.8210 (m-40) REVERT: B 340 ASP cc_start: 0.9000 (t0) cc_final: 0.8713 (t0) REVERT: B 448 MET cc_start: 0.8673 (tpp) cc_final: 0.8186 (tpt) REVERT: B 565 CYS cc_start: 0.9104 (m) cc_final: 0.8683 (t) REVERT: S 49 PHE cc_start: 0.8749 (m-10) cc_final: 0.8529 (m-10) REVERT: S 77 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8511 (p0) REVERT: N 53 LYS cc_start: 0.8678 (mttt) cc_final: 0.8306 (mmtt) REVERT: N 61 ASP cc_start: 0.8011 (t0) cc_final: 0.7288 (m-30) REVERT: N 134 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8318 (tm-30) outliers start: 24 outliers final: 15 residues processed: 156 average time/residue: 0.2686 time to fit residues: 62.7857 Evaluate side-chains 149 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 130 LYS Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 103 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 HIS M 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14669 Z= 0.167 Angle : 0.498 9.483 19864 Z= 0.249 Chirality : 0.041 0.175 2314 Planarity : 0.003 0.052 2522 Dihedral : 4.142 21.558 1956 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 1.32 % Allowed : 9.08 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1772 helix: -0.23 (0.16), residues: 992 sheet: -0.72 (0.33), residues: 239 loop : -0.38 (0.29), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 421 HIS 0.005 0.001 HIS M 10 PHE 0.019 0.001 PHE S 4 TYR 0.011 0.001 TYR A 247 ARG 0.002 0.000 ARG N 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8382 (mmmt) REVERT: A 128 MET cc_start: 0.8506 (mtm) cc_final: 0.8241 (mtp) REVERT: A 601 GLU cc_start: 0.7635 (tt0) cc_final: 0.7421 (mp0) REVERT: B 71 LEU cc_start: 0.8876 (mm) cc_final: 0.8523 (mt) REVERT: B 205 ASN cc_start: 0.8490 (t0) cc_final: 0.8201 (m-40) REVERT: B 340 ASP cc_start: 0.8949 (t0) cc_final: 0.8664 (t0) REVERT: B 448 MET cc_start: 0.8670 (tpp) cc_final: 0.8223 (tpt) REVERT: B 504 GLN cc_start: 0.7250 (mm-40) cc_final: 0.6980 (mp10) REVERT: B 565 CYS cc_start: 0.9131 (m) cc_final: 0.8664 (t) REVERT: M 217 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8554 (p0) REVERT: M 410 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6340 (ptmt) REVERT: S 49 PHE cc_start: 0.8718 (m-10) cc_final: 0.8486 (m-10) REVERT: S 77 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8493 (p0) REVERT: N 53 LYS cc_start: 0.8700 (mttt) cc_final: 0.8322 (mmtt) REVERT: N 61 ASP cc_start: 0.7973 (t0) cc_final: 0.7274 (m-30) REVERT: N 134 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8319 (tm-30) outliers start: 21 outliers final: 14 residues processed: 149 average time/residue: 0.2751 time to fit residues: 60.1708 Evaluate side-chains 148 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 126 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14669 Z= 0.159 Angle : 0.493 9.015 19864 Z= 0.246 Chirality : 0.041 0.158 2314 Planarity : 0.003 0.047 2522 Dihedral : 4.067 18.950 1956 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 1.39 % Allowed : 9.21 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1772 helix: -0.06 (0.16), residues: 993 sheet: -0.63 (0.33), residues: 239 loop : -0.35 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 462 HIS 0.005 0.001 HIS M 10 PHE 0.018 0.001 PHE S 4 TYR 0.011 0.001 TYR A 247 ARG 0.004 0.000 ARG N 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.629 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8392 (mmmt) REVERT: A 128 MET cc_start: 0.8505 (mtm) cc_final: 0.8239 (mtp) REVERT: A 601 GLU cc_start: 0.7627 (tt0) cc_final: 0.7413 (mp0) REVERT: B 71 LEU cc_start: 0.8865 (mm) cc_final: 0.8570 (mt) REVERT: B 205 ASN cc_start: 0.8490 (t0) cc_final: 0.8196 (m-40) REVERT: B 340 ASP cc_start: 0.8955 (t0) cc_final: 0.8682 (t0) REVERT: B 448 MET cc_start: 0.8673 (tpp) cc_final: 0.8223 (tpt) REVERT: B 504 GLN cc_start: 0.7268 (mm-40) cc_final: 0.6978 (mp10) REVERT: B 565 CYS cc_start: 0.9102 (m) cc_final: 0.8661 (t) REVERT: M 217 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8633 (p0) REVERT: M 298 ARG cc_start: 0.8199 (ptp90) cc_final: 0.7534 (mtt180) REVERT: M 410 LYS cc_start: 0.7118 (mmtt) cc_final: 0.6335 (ptmt) REVERT: S 49 PHE cc_start: 0.8723 (m-10) cc_final: 0.8500 (m-10) REVERT: S 77 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8564 (p0) REVERT: N 53 LYS cc_start: 0.8694 (mttt) cc_final: 0.8316 (mmtt) REVERT: N 61 ASP cc_start: 0.7952 (t0) cc_final: 0.7258 (m-30) REVERT: N 134 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8319 (tm-30) outliers start: 22 outliers final: 16 residues processed: 152 average time/residue: 0.2741 time to fit residues: 61.4768 Evaluate side-chains 152 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 86 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 0.0060 chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14669 Z= 0.144 Angle : 0.491 9.112 19864 Z= 0.245 Chirality : 0.041 0.152 2314 Planarity : 0.003 0.046 2522 Dihedral : 4.011 21.937 1956 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.13 % Allowed : 9.71 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1772 helix: 0.07 (0.16), residues: 994 sheet: -0.53 (0.33), residues: 239 loop : -0.35 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.004 0.001 HIS M 10 PHE 0.019 0.001 PHE S 4 TYR 0.011 0.001 TYR A 247 ARG 0.005 0.000 ARG N 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8416 (mmmt) REVERT: A 128 MET cc_start: 0.8475 (mtm) cc_final: 0.8199 (mtp) REVERT: B 71 LEU cc_start: 0.8816 (mm) cc_final: 0.8349 (mm) REVERT: B 155 MET cc_start: 0.5028 (tpp) cc_final: 0.4693 (tpp) REVERT: B 205 ASN cc_start: 0.8508 (t0) cc_final: 0.8226 (m-40) REVERT: B 340 ASP cc_start: 0.8965 (t0) cc_final: 0.8681 (t0) REVERT: B 448 MET cc_start: 0.8660 (tpp) cc_final: 0.8206 (tpt) REVERT: B 504 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6915 (mp10) REVERT: B 565 CYS cc_start: 0.9093 (m) cc_final: 0.8660 (t) REVERT: M 217 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8612 (p0) REVERT: M 298 ARG cc_start: 0.8187 (ptp90) cc_final: 0.7524 (mtt180) REVERT: M 410 LYS cc_start: 0.7024 (mmtt) cc_final: 0.6281 (ptmt) REVERT: S 49 PHE cc_start: 0.8743 (m-10) cc_final: 0.8529 (m-10) REVERT: S 77 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8556 (p0) REVERT: N 53 LYS cc_start: 0.8666 (mttt) cc_final: 0.8272 (mmtt) REVERT: N 61 ASP cc_start: 0.7898 (t0) cc_final: 0.7196 (m-30) outliers start: 18 outliers final: 14 residues processed: 151 average time/residue: 0.2722 time to fit residues: 60.6606 Evaluate side-chains 149 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 217 ASN Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 86 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.114401 restraints weight = 23208.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117988 restraints weight = 12496.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120379 restraints weight = 7920.746| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14669 Z= 0.180 Angle : 0.505 9.043 19864 Z= 0.250 Chirality : 0.041 0.150 2314 Planarity : 0.003 0.047 2522 Dihedral : 4.002 19.183 1956 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 1.20 % Allowed : 9.90 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1772 helix: 0.14 (0.17), residues: 985 sheet: -0.44 (0.33), residues: 240 loop : -0.29 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.004 0.001 HIS M 10 PHE 0.020 0.001 PHE S 4 TYR 0.011 0.001 TYR A 247 ARG 0.004 0.000 ARG N 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2618.23 seconds wall clock time: 48 minutes 57.99 seconds (2937.99 seconds total)