Starting phenix.real_space_refine on Sun Mar 17 11:39:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvq_20497/03_2024/6pvq_20497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvq_20497/03_2024/6pvq_20497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvq_20497/03_2024/6pvq_20497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvq_20497/03_2024/6pvq_20497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvq_20497/03_2024/6pvq_20497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvq_20497/03_2024/6pvq_20497.pdb" } resolution = 4.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 11348 2.51 5 N 2996 2.21 5 O 3196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 698": "NH1" <-> "NH2" Residue "C ARG 712": "NH1" <-> "NH2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 375": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 698": "NH1" <-> "NH2" Residue "D ARG 714": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4581 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 540} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 4239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4239 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4581 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 540} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 4239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4239 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 9.60, per 1000 atoms: 0.54 Number of scatterers: 17640 At special positions: 0 Unit cell: (138.86, 147.34, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3196 8.00 N 2996 7.00 C 11348 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: 8.22 Conformation dependent library (CDL) restraints added in 3.3 seconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4156 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 4 sheets defined 56.3% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 116 through 130 Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.789A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.575A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.911A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.725A pdb=" N GLU A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.972A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.714A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.789A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.569A pdb=" N ASN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.948A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.388A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.181A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 334 " --> pdb=" O TRP A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 334' Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.533A pdb=" N LYS A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.672A pdb=" N ARG A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.629A pdb=" N LEU A 370 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.543A pdb=" N ILE A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.135A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 457 removed outlier: 3.789A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 482 through 505 removed outlier: 3.970A pdb=" N GLY A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 536 removed outlier: 3.522A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.717A pdb=" N LEU A 541 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 561 removed outlier: 4.054A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.543A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.549A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 147 Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.763A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.705A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.662A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.840A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.735A pdb=" N LEU B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.786A pdb=" N ASN B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.913A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.898A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.513A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.662A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.964A pdb=" N ARG B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 4.282A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.790A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.687A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 455 " --> pdb=" O TYR B 451 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.684A pdb=" N LYS B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 474 through 479' Processing helix chain 'B' and resid 483 through 501 removed outlier: 3.506A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 4.107A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.617A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 removed outlier: 3.534A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 153 through 163 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.760A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.576A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.906A pdb=" N ASN C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 removed outlier: 3.725A pdb=" N GLU C 214 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.977A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.717A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.890A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.568A pdb=" N ASN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.946A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 4.390A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 4.186A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 334 " --> pdb=" O TRP C 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 334' Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.524A pdb=" N LYS C 350 " --> pdb=" O GLN C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.515A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.615A pdb=" N LEU C 370 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.538A pdb=" N ILE C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.131A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 457 removed outlier: 3.789A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 482 through 505 removed outlier: 3.964A pdb=" N GLY C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 536 removed outlier: 3.524A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.724A pdb=" N LEU C 541 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 561 removed outlier: 4.057A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 556 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 706 removed outlier: 3.545A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.548A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 147 Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.762A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 163 " --> pdb=" O MET D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.705A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.662A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.841A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.735A pdb=" N LEU D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.786A pdb=" N ASN D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.909A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.899A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 336 Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.514A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.658A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.964A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 4.281A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.797A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.686A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS D 446 " --> pdb=" O PHE D 442 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 455 " --> pdb=" O TYR D 451 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 479 removed outlier: 3.686A pdb=" N LYS D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 474 through 479' Processing helix chain 'D' and resid 483 through 501 removed outlier: 3.501A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 4.113A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.615A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 556 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN D 561 " --> pdb=" O LEU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 688 through 706 removed outlier: 3.535A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA2, first strand: chain 'B' and resid 381 through 382 Processing sheet with id=AA3, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'D' and resid 381 through 382 removed outlier: 3.903A pdb=" N SER D 386 " --> pdb=" O ASN D 735 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 735 " --> pdb=" O SER D 386 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1899 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: 4.68 Time building geometry restraints manager: 8.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5002 1.33 - 1.45: 3739 1.45 - 1.57: 9123 1.57 - 1.70: 0 1.70 - 1.82: 164 Bond restraints: 18028 Sorted by residual: bond pdb=" C LEU D 469 " pdb=" N PRO D 470 " ideal model delta sigma weight residual 1.333 1.372 -0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" C LEU B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 1.333 1.372 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" N GLU D 257 " pdb=" CA GLU D 257 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.16e+00 bond pdb=" N GLU B 257 " pdb=" CA GLU B 257 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.97e+00 bond pdb=" C LEU A 707 " pdb=" N PRO A 708 " ideal model delta sigma weight residual 1.337 1.310 0.026 1.06e-02 8.90e+03 6.22e+00 ... (remaining 18023 not shown) Histogram of bond angle deviations from ideal: 98.95 - 106.34: 435 106.34 - 113.74: 10025 113.74 - 121.13: 9184 121.13 - 128.52: 4557 128.52 - 135.92: 195 Bond angle restraints: 24396 Sorted by residual: angle pdb=" N ASP C 166 " pdb=" CA ASP C 166 " pdb=" C ASP C 166 " ideal model delta sigma weight residual 114.62 106.96 7.66 1.14e+00 7.69e-01 4.52e+01 angle pdb=" N ASP A 166 " pdb=" CA ASP A 166 " pdb=" C ASP A 166 " ideal model delta sigma weight residual 114.62 107.01 7.61 1.14e+00 7.69e-01 4.46e+01 angle pdb=" N ARG D 416 " pdb=" CA ARG D 416 " pdb=" C ARG D 416 " ideal model delta sigma weight residual 112.59 104.88 7.71 1.22e+00 6.72e-01 3.99e+01 angle pdb=" N ARG B 416 " pdb=" CA ARG B 416 " pdb=" C ARG B 416 " ideal model delta sigma weight residual 112.59 104.89 7.70 1.22e+00 6.72e-01 3.98e+01 angle pdb=" N LEU B 730 " pdb=" CA LEU B 730 " pdb=" C LEU B 730 " ideal model delta sigma weight residual 110.91 117.98 -7.07 1.17e+00 7.31e-01 3.65e+01 ... (remaining 24391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 9814 16.14 - 32.27: 817 32.27 - 48.41: 178 48.41 - 64.54: 13 64.54 - 80.68: 24 Dihedral angle restraints: 10846 sinusoidal: 4466 harmonic: 6380 Sorted by residual: dihedral pdb=" CA ARG D 729 " pdb=" C ARG D 729 " pdb=" N LEU D 730 " pdb=" CA LEU D 730 " 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 B 729 " pdb=" C ARG B 729 " pdb=" N LEU B 730 " pdb=" CA LEU B 730 " ideal model delta harmonic sigma weight residual 180.00 136.54 43.46 0 5.00e+00 4.00e-02 7.56e+01 dihedral pdb=" CA PRO C 89 " pdb=" C PRO C 89 " pdb=" N GLN C 90 " pdb=" CA GLN C 90 " ideal model delta harmonic sigma weight residual -180.00 -140.64 -39.36 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 10843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2096 0.070 - 0.140: 524 0.140 - 0.210: 93 0.210 - 0.279: 7 0.279 - 0.349: 8 Chirality restraints: 2728 Sorted by residual: chirality pdb=" CB THR A 94 " pdb=" CA THR A 94 " pdb=" OG1 THR A 94 " pdb=" CG2 THR A 94 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB THR C 94 " pdb=" CA THR C 94 " pdb=" OG1 THR C 94 " pdb=" CG2 THR C 94 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA THR C 94 " pdb=" N THR C 94 " pdb=" C THR C 94 " pdb=" CB THR C 94 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 2725 not shown) Planarity restraints: 3092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 112 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C GLN C 112 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN C 112 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG C 113 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 112 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.91e+00 pdb=" C GLN A 112 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN A 112 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 113 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 754 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO A 755 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 755 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 755 " -0.040 5.00e-02 4.00e+02 ... (remaining 3089 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4067 2.77 - 3.31: 17763 3.31 - 3.84: 28894 3.84 - 4.37: 32948 4.37 - 4.90: 51455 Nonbonded interactions: 135127 Sorted by model distance: nonbonded pdb=" OH TYR D 448 " pdb=" O GLY D 558 " model vdw 2.244 2.440 nonbonded pdb=" OH TYR B 448 " pdb=" O GLY B 558 " model vdw 2.245 2.440 nonbonded pdb=" OD2 ASP D 391 " pdb=" OG1 THR D 393 " model vdw 2.253 2.440 nonbonded pdb=" OD2 ASP B 391 " pdb=" OG1 THR B 393 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP D 379 " pdb=" OG SER D 387 " model vdw 2.257 2.440 ... (remaining 135122 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 'A' and (resid 115 through 508 or (resid 509 and (name N or name CA or na \ me C or name O or name CB )) or resid 510 through 745)) selection = (chain 'B' and ((resid 115 and (name N or name CA or name C or name O or name CB \ )) or resid 116 through 745)) selection = (chain 'C' and (resid 115 through 508 or (resid 509 and (name N or name CA or na \ me C or name O or name CB )) or resid 510 through 745)) selection = (chain 'D' and ((resid 115 and (name N or name CA or name C or name O or name CB \ )) or resid 116 through 745)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 3.400 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 50.050 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.070 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 0.099 18028 Z= 0.525 Angle : 1.315 11.566 24396 Z= 0.729 Chirality : 0.064 0.349 2728 Planarity : 0.008 0.073 3092 Dihedral : 13.013 80.677 6690 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.37 % Allowed : 14.41 % Favored : 85.21 % Rotamer: Outliers : 1.15 % Allowed : 9.35 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -5.23 (0.13), residues: 2144 helix: -3.14 (0.11), residues: 1018 sheet: -4.38 (0.49), residues: 60 loop : -3.82 (0.16), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 692 HIS 0.016 0.003 HIS B 301 PHE 0.043 0.004 PHE A 542 TYR 0.027 0.003 TYR A 359 ARG 0.032 0.001 ARG C 714 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 524 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8874 (p0) cc_final: 0.8509 (p0) REVERT: A 187 VAL cc_start: 0.9726 (t) cc_final: 0.9485 (p) REVERT: A 311 LYS cc_start: 0.8877 (mttt) cc_final: 0.8663 (tptt) REVERT: A 313 GLN cc_start: 0.8715 (mt0) cc_final: 0.8395 (pp30) REVERT: A 350 LYS cc_start: 0.9073 (ttmm) cc_final: 0.8835 (tppt) REVERT: A 353 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8606 (mmmm) REVERT: A 364 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8117 (mm-30) REVERT: A 370 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9268 (mm) REVERT: A 392 LEU cc_start: 0.9168 (tp) cc_final: 0.8906 (tp) REVERT: A 417 HIS cc_start: 0.8280 (p-80) cc_final: 0.7779 (p-80) REVERT: A 436 PHE cc_start: 0.8613 (p90) cc_final: 0.8310 (p90) REVERT: A 440 MET cc_start: 0.7415 (mmm) cc_final: 0.7140 (mmt) REVERT: A 730 LEU cc_start: 0.8176 (mp) cc_final: 0.7711 (mp) REVERT: B 118 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7927 (mmp80) REVERT: B 146 CYS cc_start: 0.9153 (t) cc_final: 0.8938 (p) REVERT: B 158 LEU cc_start: 0.9702 (tp) cc_final: 0.9344 (mt) REVERT: B 174 LYS cc_start: 0.9288 (tptt) cc_final: 0.8271 (mptt) REVERT: B 193 PHE cc_start: 0.8684 (t80) cc_final: 0.8139 (t80) REVERT: B 213 TYR cc_start: 0.8968 (p90) cc_final: 0.8196 (p90) REVERT: B 220 ASN cc_start: 0.8887 (t160) cc_final: 0.8604 (t0) REVERT: B 298 ASN cc_start: 0.9063 (p0) cc_final: 0.8298 (p0) REVERT: B 301 HIS cc_start: 0.8743 (m-70) cc_final: 0.8084 (m-70) REVERT: B 351 MET cc_start: 0.8874 (mmm) cc_final: 0.8215 (mmm) REVERT: B 416 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7586 (mmt180) REVERT: B 425 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8453 (tm) REVERT: B 440 MET cc_start: 0.8533 (mmt) cc_final: 0.7749 (mmt) REVERT: B 488 MET cc_start: -0.0001 (tpp) cc_final: -0.0281 (ppp) REVERT: B 698 ARG cc_start: 0.8956 (tpt90) cc_final: 0.8578 (tpt90) REVERT: B 701 LEU cc_start: 0.9427 (mt) cc_final: 0.9190 (mp) REVERT: B 703 PHE cc_start: 0.9072 (m-80) cc_final: 0.8830 (t80) REVERT: B 731 CYS cc_start: 0.8298 (p) cc_final: 0.6602 (p) REVERT: C 156 ASP cc_start: 0.8867 (p0) cc_final: 0.8502 (p0) REVERT: C 187 VAL cc_start: 0.9726 (t) cc_final: 0.9490 (p) REVERT: C 313 GLN cc_start: 0.8650 (mt0) cc_final: 0.8370 (pp30) REVERT: C 353 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8672 (mmmm) REVERT: C 364 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8193 (mm-30) REVERT: C 370 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9246 (mm) REVERT: C 392 LEU cc_start: 0.9151 (tp) cc_final: 0.8873 (tp) REVERT: C 417 HIS cc_start: 0.8288 (p-80) cc_final: 0.7798 (p-80) REVERT: C 436 PHE cc_start: 0.8599 (p90) cc_final: 0.8307 (p90) REVERT: C 440 MET cc_start: 0.7397 (mmm) cc_final: 0.7129 (mmt) REVERT: C 730 LEU cc_start: 0.8191 (mp) cc_final: 0.7772 (mp) REVERT: D 118 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7913 (mmp80) REVERT: D 146 CYS cc_start: 0.9144 (t) cc_final: 0.8926 (p) REVERT: D 158 LEU cc_start: 0.9695 (tp) cc_final: 0.9336 (mt) REVERT: D 174 LYS cc_start: 0.9285 (tptt) cc_final: 0.8273 (mptt) REVERT: D 193 PHE cc_start: 0.8702 (t80) cc_final: 0.8154 (t80) REVERT: D 213 TYR cc_start: 0.8970 (p90) cc_final: 0.8206 (p90) REVERT: D 220 ASN cc_start: 0.8886 (t160) cc_final: 0.8392 (m110) REVERT: D 351 MET cc_start: 0.8882 (mmm) cc_final: 0.8217 (mmm) REVERT: D 416 ARG cc_start: 0.7910 (mmt180) cc_final: 0.7593 (mmt180) REVERT: D 425 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8463 (tm) REVERT: D 440 MET cc_start: 0.8512 (mmt) cc_final: 0.7726 (mmt) REVERT: D 488 MET cc_start: 0.0150 (tpp) cc_final: -0.0160 (ppp) REVERT: D 703 PHE cc_start: 0.9064 (m-80) cc_final: 0.8830 (t80) REVERT: D 731 CYS cc_start: 0.8331 (p) cc_final: 0.6703 (p) outliers start: 22 outliers final: 2 residues processed: 538 average time/residue: 0.3365 time to fit residues: 256.3982 Evaluate side-chains 335 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 327 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 0.0770 chunk 86 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 50.0000 chunk 124 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 242 ASN A 274 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN C 242 ASN C 274 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS D 297 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18028 Z= 0.217 Angle : 0.800 14.207 24396 Z= 0.413 Chirality : 0.045 0.199 2728 Planarity : 0.006 0.066 3092 Dihedral : 7.066 41.080 2360 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.45 % Favored : 87.27 % Rotamer: Outliers : 0.21 % Allowed : 3.81 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.14 % 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: -3.99 (0.15), residues: 2144 helix: -1.68 (0.13), residues: 1140 sheet: -3.95 (0.52), residues: 60 loop : -3.85 (0.17), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 710 HIS 0.005 0.001 HIS A 745 PHE 0.023 0.002 PHE A 542 TYR 0.021 0.002 TYR A 359 ARG 0.008 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 413 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8775 (p0) cc_final: 0.8480 (p0) REVERT: A 159 MET cc_start: 0.9220 (mmt) cc_final: 0.8639 (mtt) REVERT: A 197 ASN cc_start: 0.7843 (m110) cc_final: 0.7498 (t0) REVERT: A 202 ARG cc_start: 0.8757 (ttt180) cc_final: 0.8438 (mtm-85) REVERT: A 309 ASP cc_start: 0.8295 (p0) cc_final: 0.7935 (m-30) REVERT: A 311 LYS cc_start: 0.8834 (mttt) cc_final: 0.8633 (tptt) REVERT: A 313 GLN cc_start: 0.8697 (mt0) cc_final: 0.8253 (pp30) REVERT: A 323 MET cc_start: 0.9461 (tpp) cc_final: 0.9256 (tpt) REVERT: A 364 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8071 (mm-30) REVERT: A 392 LEU cc_start: 0.9061 (tp) cc_final: 0.8853 (tp) REVERT: A 395 VAL cc_start: 0.6915 (t) cc_final: 0.6614 (m) REVERT: A 396 ASP cc_start: 0.8145 (t0) cc_final: 0.7942 (t0) REVERT: A 404 LEU cc_start: 0.9640 (mm) cc_final: 0.9201 (mt) REVERT: A 406 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7693 (pt) REVERT: A 417 HIS cc_start: 0.8508 (p-80) cc_final: 0.7974 (p-80) REVERT: A 419 MET cc_start: 0.8399 (mtm) cc_final: 0.7938 (mtt) REVERT: A 436 PHE cc_start: 0.8721 (p90) cc_final: 0.8412 (p90) REVERT: A 440 MET cc_start: 0.7540 (mmm) cc_final: 0.7220 (mmt) REVERT: A 488 MET cc_start: -0.0448 (ptt) cc_final: -0.1635 (mmt) REVERT: A 701 LEU cc_start: 0.9673 (mt) cc_final: 0.9433 (mt) REVERT: A 730 LEU cc_start: 0.8337 (mp) cc_final: 0.7939 (mp) REVERT: B 146 CYS cc_start: 0.9146 (t) cc_final: 0.8827 (p) REVERT: B 174 LYS cc_start: 0.9360 (tptt) cc_final: 0.8679 (tppt) REVERT: B 177 LEU cc_start: 0.9429 (mt) cc_final: 0.9223 (mp) REVERT: B 178 ASN cc_start: 0.9175 (t0) cc_final: 0.8688 (p0) REVERT: B 213 TYR cc_start: 0.8704 (p90) cc_final: 0.8123 (p90) REVERT: B 256 HIS cc_start: 0.8818 (m90) cc_final: 0.8480 (m90) REVERT: B 351 MET cc_start: 0.9091 (mmm) cc_final: 0.8708 (mmm) REVERT: B 408 VAL cc_start: 0.9114 (t) cc_final: 0.8867 (t) REVERT: B 440 MET cc_start: 0.8014 (mmt) cc_final: 0.7446 (mmt) REVERT: C 156 ASP cc_start: 0.8791 (p0) cc_final: 0.8549 (p0) REVERT: C 159 MET cc_start: 0.9198 (mmt) cc_final: 0.8633 (mtt) REVERT: C 197 ASN cc_start: 0.7844 (m110) cc_final: 0.7499 (t0) REVERT: C 202 ARG cc_start: 0.8748 (ttt180) cc_final: 0.8434 (mtm-85) REVERT: C 284 ASN cc_start: 0.8889 (t0) cc_final: 0.8684 (t0) REVERT: C 309 ASP cc_start: 0.8268 (p0) cc_final: 0.7953 (m-30) REVERT: C 313 GLN cc_start: 0.8782 (mt0) cc_final: 0.8264 (pp30) REVERT: C 323 MET cc_start: 0.9464 (tpp) cc_final: 0.9261 (tpt) REVERT: C 364 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8122 (mm-30) REVERT: C 392 LEU cc_start: 0.9075 (tp) cc_final: 0.8855 (tp) REVERT: C 395 VAL cc_start: 0.6940 (t) cc_final: 0.6665 (m) REVERT: C 396 ASP cc_start: 0.8130 (t0) cc_final: 0.7930 (t0) REVERT: C 404 LEU cc_start: 0.9641 (mm) cc_final: 0.9204 (mt) REVERT: C 406 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7740 (pt) REVERT: C 417 HIS cc_start: 0.8550 (p-80) cc_final: 0.7992 (p-80) REVERT: C 419 MET cc_start: 0.8430 (mtm) cc_final: 0.7962 (mtt) REVERT: C 436 PHE cc_start: 0.8731 (p90) cc_final: 0.8424 (p90) REVERT: C 440 MET cc_start: 0.7525 (mmm) cc_final: 0.7216 (mmt) REVERT: C 488 MET cc_start: -0.0505 (ptt) cc_final: -0.1629 (mmt) REVERT: C 694 LEU cc_start: 0.9516 (mt) cc_final: 0.9097 (pp) REVERT: C 717 MET cc_start: 0.8395 (mtp) cc_final: 0.8140 (mtp) REVERT: C 730 LEU cc_start: 0.8372 (mp) cc_final: 0.7990 (mp) REVERT: D 146 CYS cc_start: 0.9141 (t) cc_final: 0.8819 (p) REVERT: D 174 LYS cc_start: 0.9357 (tptt) cc_final: 0.8682 (tppt) REVERT: D 177 LEU cc_start: 0.9421 (mt) cc_final: 0.9215 (mp) REVERT: D 178 ASN cc_start: 0.9172 (t0) cc_final: 0.8685 (p0) REVERT: D 213 TYR cc_start: 0.8709 (p90) cc_final: 0.8107 (p90) REVERT: D 256 HIS cc_start: 0.8804 (m90) cc_final: 0.8470 (m90) REVERT: D 351 MET cc_start: 0.9099 (mmm) cc_final: 0.8703 (mmm) REVERT: D 440 MET cc_start: 0.7995 (mmt) cc_final: 0.7433 (mmt) outliers start: 4 outliers final: 0 residues processed: 415 average time/residue: 0.3106 time to fit residues: 188.6603 Evaluate side-chains 285 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 283 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 161 optimal weight: 0.0770 chunk 132 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 overall best weight: 3.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 HIS B 346 GLN C 242 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 18028 Z= 0.267 Angle : 0.773 14.101 24396 Z= 0.395 Chirality : 0.044 0.200 2728 Planarity : 0.006 0.064 3092 Dihedral : 6.636 38.928 2360 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.76 % Favored : 86.01 % Rotamer: Outliers : 0.21 % Allowed : 5.28 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.17 (0.17), residues: 2144 helix: -0.81 (0.14), residues: 1124 sheet: -3.86 (0.49), residues: 60 loop : -3.70 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 739 HIS 0.010 0.001 HIS D 417 PHE 0.028 0.002 PHE B 193 TYR 0.022 0.002 TYR A 359 ARG 0.015 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 338 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.9309 (mmt) cc_final: 0.8758 (mtp) REVERT: A 199 ILE cc_start: 0.7930 (tp) cc_final: 0.6721 (tp) REVERT: A 202 ARG cc_start: 0.8848 (ttt180) cc_final: 0.8542 (ttm110) REVERT: A 210 GLU cc_start: 0.8927 (tp30) cc_final: 0.8609 (tp30) REVERT: A 309 ASP cc_start: 0.8317 (p0) cc_final: 0.8038 (m-30) REVERT: A 311 LYS cc_start: 0.8879 (mttt) cc_final: 0.8629 (tptt) REVERT: A 323 MET cc_start: 0.9486 (tpp) cc_final: 0.9273 (tpt) REVERT: A 395 VAL cc_start: 0.7212 (t) cc_final: 0.6791 (m) REVERT: A 404 LEU cc_start: 0.9582 (mm) cc_final: 0.9117 (mt) REVERT: A 417 HIS cc_start: 0.8672 (p-80) cc_final: 0.8036 (p-80) REVERT: A 419 MET cc_start: 0.8353 (mtm) cc_final: 0.7953 (mtt) REVERT: A 436 PHE cc_start: 0.8627 (p90) cc_final: 0.8425 (p90) REVERT: A 440 MET cc_start: 0.7472 (mmm) cc_final: 0.7262 (mmp) REVERT: A 694 LEU cc_start: 0.9526 (mp) cc_final: 0.9155 (pp) REVERT: A 702 GLU cc_start: 0.9311 (mp0) cc_final: 0.9082 (mp0) REVERT: A 732 LEU cc_start: 0.8712 (mt) cc_final: 0.7876 (mt) REVERT: B 174 LYS cc_start: 0.9457 (tptt) cc_final: 0.8753 (mptt) REVERT: B 178 ASN cc_start: 0.9187 (t0) cc_final: 0.8755 (p0) REVERT: B 213 TYR cc_start: 0.8845 (p90) cc_final: 0.8299 (p90) REVERT: B 256 HIS cc_start: 0.8847 (m90) cc_final: 0.8519 (m90) REVERT: B 351 MET cc_start: 0.9291 (mmm) cc_final: 0.8985 (mmm) REVERT: B 440 MET cc_start: 0.8107 (mmt) cc_final: 0.7742 (mmt) REVERT: C 159 MET cc_start: 0.9286 (mmt) cc_final: 0.8763 (mtp) REVERT: C 199 ILE cc_start: 0.7932 (tp) cc_final: 0.6706 (tp) REVERT: C 202 ARG cc_start: 0.8812 (ttt180) cc_final: 0.8572 (ttm110) REVERT: C 210 GLU cc_start: 0.8886 (tp30) cc_final: 0.8583 (tp30) REVERT: C 309 ASP cc_start: 0.8327 (p0) cc_final: 0.8101 (m-30) REVERT: C 395 VAL cc_start: 0.7244 (t) cc_final: 0.6842 (m) REVERT: C 404 LEU cc_start: 0.9580 (mm) cc_final: 0.9129 (mt) REVERT: C 417 HIS cc_start: 0.8697 (p-80) cc_final: 0.8021 (p-80) REVERT: C 419 MET cc_start: 0.8348 (mtm) cc_final: 0.7952 (mtt) REVERT: C 436 PHE cc_start: 0.8629 (p90) cc_final: 0.8417 (p90) REVERT: C 440 MET cc_start: 0.7464 (mmm) cc_final: 0.7250 (mmp) REVERT: C 694 LEU cc_start: 0.9471 (mt) cc_final: 0.9190 (pp) REVERT: C 702 GLU cc_start: 0.9257 (mp0) cc_final: 0.8975 (mp0) REVERT: C 717 MET cc_start: 0.8388 (mtp) cc_final: 0.8069 (mtp) REVERT: C 732 LEU cc_start: 0.8740 (mt) cc_final: 0.7985 (mt) REVERT: D 170 THR cc_start: 0.8990 (p) cc_final: 0.8481 (p) REVERT: D 174 LYS cc_start: 0.9454 (tptt) cc_final: 0.8764 (mptt) REVERT: D 178 ASN cc_start: 0.9186 (t0) cc_final: 0.8736 (p0) REVERT: D 213 TYR cc_start: 0.8775 (p90) cc_final: 0.8279 (p90) REVERT: D 256 HIS cc_start: 0.8835 (m90) cc_final: 0.8509 (m90) REVERT: D 351 MET cc_start: 0.9306 (mmm) cc_final: 0.8977 (mmm) REVERT: D 440 MET cc_start: 0.8184 (mmt) cc_final: 0.7898 (mmt) outliers start: 4 outliers final: 0 residues processed: 340 average time/residue: 0.2987 time to fit residues: 152.4541 Evaluate side-chains 247 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 5.9990 chunk 146 optimal weight: 30.0000 chunk 101 optimal weight: 40.0000 chunk 21 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 chunk 130 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 206 optimal weight: 50.0000 chunk 102 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 55 optimal weight: 0.0270 overall best weight: 3.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN B 417 HIS C 242 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18028 Z= 0.238 Angle : 0.728 11.187 24396 Z= 0.373 Chirality : 0.044 0.185 2728 Planarity : 0.005 0.057 3092 Dihedral : 6.323 37.899 2360 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.27 % Favored : 85.54 % Rotamer: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.04 (0.17), residues: 2144 helix: -0.55 (0.14), residues: 1154 sheet: -3.87 (0.48), residues: 62 loop : -3.94 (0.17), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 742 HIS 0.012 0.001 HIS B 417 PHE 0.019 0.002 PHE D 193 TYR 0.021 0.001 TYR A 359 ARG 0.011 0.001 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 336 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.9333 (mmt) cc_final: 0.8758 (mtp) REVERT: A 210 GLU cc_start: 0.8970 (tp30) cc_final: 0.8627 (tp30) REVERT: A 309 ASP cc_start: 0.8586 (p0) cc_final: 0.8069 (m-30) REVERT: A 311 LYS cc_start: 0.8964 (mttt) cc_final: 0.8715 (tptp) REVERT: A 395 VAL cc_start: 0.7276 (t) cc_final: 0.7000 (m) REVERT: A 401 ASN cc_start: 0.8560 (t0) cc_final: 0.8251 (t0) REVERT: A 404 LEU cc_start: 0.9572 (mm) cc_final: 0.9206 (mt) REVERT: A 417 HIS cc_start: 0.8789 (p-80) cc_final: 0.8212 (p-80) REVERT: A 419 MET cc_start: 0.8511 (mtm) cc_final: 0.8126 (mtt) REVERT: A 694 LEU cc_start: 0.9569 (mp) cc_final: 0.9237 (pp) REVERT: A 732 LEU cc_start: 0.8918 (mt) cc_final: 0.8698 (mt) REVERT: B 177 LEU cc_start: 0.9591 (mt) cc_final: 0.9350 (mp) REVERT: B 178 ASN cc_start: 0.9206 (t0) cc_final: 0.8721 (p0) REVERT: B 213 TYR cc_start: 0.8846 (p90) cc_final: 0.8369 (p90) REVERT: B 256 HIS cc_start: 0.8725 (m90) cc_final: 0.8440 (m90) REVERT: B 268 LEU cc_start: 0.9679 (pt) cc_final: 0.9392 (pt) REVERT: B 351 MET cc_start: 0.9407 (mmm) cc_final: 0.9165 (mmm) REVERT: B 408 VAL cc_start: 0.9141 (t) cc_final: 0.8898 (t) REVERT: B 416 ARG cc_start: 0.7858 (mmt180) cc_final: 0.7632 (mmt180) REVERT: B 419 MET cc_start: 0.8890 (mtt) cc_final: 0.8456 (ttt) REVERT: B 440 MET cc_start: 0.8112 (mmt) cc_final: 0.7722 (mmt) REVERT: C 159 MET cc_start: 0.9237 (mmt) cc_final: 0.8728 (mtp) REVERT: C 176 LEU cc_start: 0.9444 (mm) cc_final: 0.8276 (tt) REVERT: C 210 GLU cc_start: 0.8856 (tp30) cc_final: 0.8600 (tp30) REVERT: C 221 ILE cc_start: 0.9620 (mp) cc_final: 0.9191 (mp) REVERT: C 263 GLU cc_start: 0.7743 (pt0) cc_final: 0.7308 (mp0) REVERT: C 293 ASP cc_start: 0.8256 (t0) cc_final: 0.7475 (t0) REVERT: C 309 ASP cc_start: 0.8491 (p0) cc_final: 0.8028 (m-30) REVERT: C 395 VAL cc_start: 0.7299 (t) cc_final: 0.7062 (m) REVERT: C 404 LEU cc_start: 0.9539 (mm) cc_final: 0.9180 (mt) REVERT: C 417 HIS cc_start: 0.8700 (p-80) cc_final: 0.8077 (p-80) REVERT: C 419 MET cc_start: 0.8518 (mtm) cc_final: 0.8140 (mtt) REVERT: C 694 LEU cc_start: 0.9525 (mt) cc_final: 0.9259 (pp) REVERT: C 719 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8579 (tm-30) REVERT: C 732 LEU cc_start: 0.8939 (mt) cc_final: 0.8725 (mt) REVERT: D 174 LYS cc_start: 0.9495 (tptt) cc_final: 0.9294 (tppt) REVERT: D 177 LEU cc_start: 0.9600 (mt) cc_final: 0.9359 (mp) REVERT: D 178 ASN cc_start: 0.9215 (t0) cc_final: 0.8714 (p0) REVERT: D 213 TYR cc_start: 0.8972 (p90) cc_final: 0.8375 (p90) REVERT: D 256 HIS cc_start: 0.8698 (m90) cc_final: 0.8411 (m90) REVERT: D 268 LEU cc_start: 0.9674 (pt) cc_final: 0.9394 (pt) REVERT: D 351 MET cc_start: 0.9364 (mmm) cc_final: 0.9116 (mmm) REVERT: D 408 VAL cc_start: 0.9130 (t) cc_final: 0.8892 (t) REVERT: D 416 ARG cc_start: 0.7861 (mmt180) cc_final: 0.7622 (mmt180) REVERT: D 419 MET cc_start: 0.8889 (mtt) cc_final: 0.8463 (ttt) outliers start: 2 outliers final: 0 residues processed: 336 average time/residue: 0.2815 time to fit residues: 144.8673 Evaluate side-chains 240 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 154 optimal weight: 30.0000 chunk 85 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 185 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 overall best weight: 5.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 452 ASN B 523 HIS ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN D 523 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18028 Z= 0.348 Angle : 0.828 11.560 24396 Z= 0.427 Chirality : 0.047 0.220 2728 Planarity : 0.007 0.100 3092 Dihedral : 6.643 39.644 2360 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.93 % Favored : 84.79 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.03 (0.17), residues: 2144 helix: -0.57 (0.14), residues: 1140 sheet: -3.74 (0.51), residues: 62 loop : -3.85 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 742 HIS 0.009 0.002 HIS B 244 PHE 0.042 0.002 PHE D 193 TYR 0.034 0.002 TYR C 382 ARG 0.012 0.001 ARG B 733 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.9417 (mmt) cc_final: 0.8837 (mmm) REVERT: A 176 LEU cc_start: 0.9536 (mm) cc_final: 0.8446 (tt) REVERT: A 199 ILE cc_start: 0.8101 (tp) cc_final: 0.7805 (tp) REVERT: A 221 ILE cc_start: 0.9670 (mp) cc_final: 0.9250 (mp) REVERT: A 309 ASP cc_start: 0.8660 (p0) cc_final: 0.8171 (m-30) REVERT: A 311 LYS cc_start: 0.8944 (mttt) cc_final: 0.8684 (tptp) REVERT: A 339 ASN cc_start: 0.9310 (t0) cc_final: 0.8956 (m110) REVERT: A 401 ASN cc_start: 0.8690 (t0) cc_final: 0.8369 (t0) REVERT: A 419 MET cc_start: 0.8745 (mtm) cc_final: 0.8208 (mtt) REVERT: A 716 ARG cc_start: 0.8790 (pmt170) cc_final: 0.8430 (pmt170) REVERT: B 178 ASN cc_start: 0.9101 (t0) cc_final: 0.8462 (p0) REVERT: B 213 TYR cc_start: 0.9029 (p90) cc_final: 0.8580 (p90) REVERT: B 419 MET cc_start: 0.8817 (mtt) cc_final: 0.8610 (ttt) REVERT: B 420 LEU cc_start: 0.9398 (mt) cc_final: 0.9138 (mt) REVERT: B 695 GLN cc_start: 0.8920 (mt0) cc_final: 0.8686 (mm110) REVERT: C 176 LEU cc_start: 0.9532 (mm) cc_final: 0.8458 (tt) REVERT: C 221 ILE cc_start: 0.9672 (mp) cc_final: 0.9265 (mp) REVERT: C 309 ASP cc_start: 0.8566 (p0) cc_final: 0.8020 (m-30) REVERT: C 323 MET cc_start: 0.9254 (tpt) cc_final: 0.8966 (tpt) REVERT: C 339 ASN cc_start: 0.9303 (t0) cc_final: 0.8924 (m110) REVERT: C 419 MET cc_start: 0.8699 (mtm) cc_final: 0.8272 (mtt) REVERT: C 694 LEU cc_start: 0.9541 (mt) cc_final: 0.9279 (pp) REVERT: C 702 GLU cc_start: 0.9416 (mp0) cc_final: 0.8968 (mp0) REVERT: C 716 ARG cc_start: 0.8797 (pmt170) cc_final: 0.8431 (pmt170) REVERT: C 717 MET cc_start: 0.8208 (mtp) cc_final: 0.7556 (mtt) REVERT: D 174 LYS cc_start: 0.9575 (tptt) cc_final: 0.8989 (tttm) REVERT: D 177 LEU cc_start: 0.9682 (mt) cc_final: 0.9473 (mt) REVERT: D 178 ASN cc_start: 0.9124 (t0) cc_final: 0.8462 (p0) REVERT: D 213 TYR cc_start: 0.8962 (p90) cc_final: 0.8596 (p90) REVERT: D 320 MET cc_start: 0.9401 (mmm) cc_final: 0.9200 (mmm) REVERT: D 351 MET cc_start: 0.9477 (mmm) cc_final: 0.9262 (mmm) REVERT: D 408 VAL cc_start: 0.8951 (t) cc_final: 0.8529 (t) REVERT: D 420 LEU cc_start: 0.9396 (mt) cc_final: 0.9155 (mt) REVERT: D 440 MET cc_start: 0.7976 (mmp) cc_final: 0.7725 (mmm) REVERT: D 695 GLN cc_start: 0.8969 (mt0) cc_final: 0.8698 (mm110) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2722 time to fit residues: 130.0143 Evaluate side-chains 227 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 207 optimal weight: 40.0000 chunk 171 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 108 optimal weight: 0.2980 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 242 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 242 ASN B 452 ASN C 242 ASN C 452 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN D 242 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18028 Z= 0.243 Angle : 0.742 10.179 24396 Z= 0.377 Chirality : 0.044 0.197 2728 Planarity : 0.005 0.074 3092 Dihedral : 6.214 37.807 2360 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.09 % Favored : 85.73 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.86 (0.17), residues: 2144 helix: -0.44 (0.15), residues: 1150 sheet: -3.70 (0.52), residues: 62 loop : -3.79 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 742 HIS 0.005 0.001 HIS D 244 PHE 0.038 0.002 PHE B 193 TYR 0.019 0.001 TYR A 359 ARG 0.005 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.9539 (mm) cc_final: 0.8365 (tt) REVERT: A 221 ILE cc_start: 0.9624 (mp) cc_final: 0.9215 (mp) REVERT: A 309 ASP cc_start: 0.8596 (p0) cc_final: 0.8091 (m-30) REVERT: A 311 LYS cc_start: 0.9012 (mttt) cc_final: 0.8723 (tptp) REVERT: A 339 ASN cc_start: 0.9307 (t0) cc_final: 0.8956 (m110) REVERT: A 401 ASN cc_start: 0.8698 (t0) cc_final: 0.8386 (t0) REVERT: A 404 LEU cc_start: 0.9471 (mm) cc_final: 0.9129 (mt) REVERT: A 417 HIS cc_start: 0.9225 (p-80) cc_final: 0.8676 (p-80) REVERT: A 419 MET cc_start: 0.8776 (mtm) cc_final: 0.8262 (mtt) REVERT: A 716 ARG cc_start: 0.8661 (pmt170) cc_final: 0.8342 (pmt170) REVERT: B 178 ASN cc_start: 0.9136 (t0) cc_final: 0.8582 (p0) REVERT: B 210 GLU cc_start: 0.7891 (tt0) cc_final: 0.7622 (mt-10) REVERT: B 213 TYR cc_start: 0.8874 (p90) cc_final: 0.8483 (p90) REVERT: B 268 LEU cc_start: 0.9734 (pt) cc_final: 0.9498 (pt) REVERT: B 351 MET cc_start: 0.9597 (mmm) cc_final: 0.9361 (mmm) REVERT: B 407 ILE cc_start: 0.8821 (tp) cc_final: 0.7756 (tp) REVERT: B 408 VAL cc_start: 0.8832 (t) cc_final: 0.8588 (t) REVERT: B 440 MET cc_start: 0.8173 (mmp) cc_final: 0.7929 (mmp) REVERT: B 695 GLN cc_start: 0.8927 (mt0) cc_final: 0.8594 (mm110) REVERT: C 159 MET cc_start: 0.9441 (mmt) cc_final: 0.8956 (mtp) REVERT: C 176 LEU cc_start: 0.9530 (mm) cc_final: 0.8394 (tt) REVERT: C 221 ILE cc_start: 0.9633 (mp) cc_final: 0.9206 (mp) REVERT: C 263 GLU cc_start: 0.7563 (pt0) cc_final: 0.7106 (mt-10) REVERT: C 282 MET cc_start: 0.9215 (ttp) cc_final: 0.9010 (ttt) REVERT: C 309 ASP cc_start: 0.8668 (p0) cc_final: 0.8177 (m-30) REVERT: C 339 ASN cc_start: 0.9292 (t0) cc_final: 0.8974 (m110) REVERT: C 404 LEU cc_start: 0.9485 (mm) cc_final: 0.9146 (mt) REVERT: C 417 HIS cc_start: 0.9200 (p-80) cc_final: 0.8556 (p-80) REVERT: C 419 MET cc_start: 0.8696 (mtm) cc_final: 0.8276 (mtt) REVERT: C 694 LEU cc_start: 0.9552 (mt) cc_final: 0.9282 (pp) REVERT: C 716 ARG cc_start: 0.8684 (pmt170) cc_final: 0.8377 (pmt170) REVERT: C 719 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8490 (tm-30) REVERT: D 174 LYS cc_start: 0.9537 (tptt) cc_final: 0.9004 (mptt) REVERT: D 178 ASN cc_start: 0.9143 (t0) cc_final: 0.8597 (p0) REVERT: D 213 TYR cc_start: 0.8832 (p90) cc_final: 0.8535 (p90) REVERT: D 268 LEU cc_start: 0.9744 (pt) cc_final: 0.9535 (pt) REVERT: D 407 ILE cc_start: 0.8110 (tp) cc_final: 0.7781 (tt) REVERT: D 408 VAL cc_start: 0.8910 (t) cc_final: 0.8592 (t) REVERT: D 440 MET cc_start: 0.8196 (mmp) cc_final: 0.7692 (mmm) REVERT: D 695 GLN cc_start: 0.8931 (mt0) cc_final: 0.8610 (mm110) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2780 time to fit residues: 135.7121 Evaluate side-chains 233 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.0070 chunk 23 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 151 optimal weight: 40.0000 chunk 174 optimal weight: 8.9990 chunk 115 optimal weight: 0.0870 chunk 206 optimal weight: 40.0000 chunk 129 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18028 Z= 0.191 Angle : 0.702 9.369 24396 Z= 0.355 Chirality : 0.043 0.185 2728 Planarity : 0.005 0.065 3092 Dihedral : 5.925 37.644 2360 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.85 % Favored : 85.96 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.68 (0.17), residues: 2144 helix: -0.25 (0.15), residues: 1156 sheet: -3.70 (0.52), residues: 62 loop : -3.77 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 742 HIS 0.003 0.001 HIS B 244 PHE 0.021 0.001 PHE B 124 TYR 0.017 0.001 TYR A 359 ARG 0.010 0.000 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.9509 (mmt) cc_final: 0.9072 (mtp) REVERT: A 293 ASP cc_start: 0.8140 (t70) cc_final: 0.7488 (t70) REVERT: A 309 ASP cc_start: 0.8605 (p0) cc_final: 0.8099 (m-30) REVERT: A 339 ASN cc_start: 0.9242 (t0) cc_final: 0.8941 (m110) REVERT: A 392 LEU cc_start: 0.8578 (tp) cc_final: 0.8030 (tp) REVERT: A 401 ASN cc_start: 0.8662 (t0) cc_final: 0.8325 (t0) REVERT: A 404 LEU cc_start: 0.9466 (mm) cc_final: 0.9117 (mt) REVERT: A 417 HIS cc_start: 0.9199 (p-80) cc_final: 0.8521 (p-80) REVERT: A 419 MET cc_start: 0.8701 (mtm) cc_final: 0.8141 (mtt) REVERT: A 716 ARG cc_start: 0.8611 (pmt170) cc_final: 0.8072 (pmt170) REVERT: B 178 ASN cc_start: 0.9115 (t0) cc_final: 0.8561 (p0) REVERT: B 183 THR cc_start: 0.9448 (m) cc_final: 0.9243 (p) REVERT: B 210 GLU cc_start: 0.7814 (tt0) cc_final: 0.7573 (tt0) REVERT: B 351 MET cc_start: 0.9586 (mmm) cc_final: 0.9385 (mmm) REVERT: B 407 ILE cc_start: 0.8387 (tp) cc_final: 0.7617 (tp) REVERT: B 408 VAL cc_start: 0.8875 (t) cc_final: 0.8665 (t) REVERT: B 695 GLN cc_start: 0.8923 (mt0) cc_final: 0.8604 (mm110) REVERT: B 729 ARG cc_start: 0.7749 (mpt180) cc_final: 0.7496 (mmt180) REVERT: C 159 MET cc_start: 0.9433 (mmt) cc_final: 0.8963 (mtp) REVERT: C 169 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8548 (mtpp) REVERT: C 176 LEU cc_start: 0.9537 (mm) cc_final: 0.8467 (tt) REVERT: C 221 ILE cc_start: 0.9614 (mp) cc_final: 0.9213 (mp) REVERT: C 268 LEU cc_start: 0.9389 (tp) cc_final: 0.9151 (tp) REVERT: C 309 ASP cc_start: 0.8725 (p0) cc_final: 0.8243 (m-30) REVERT: C 339 ASN cc_start: 0.9244 (t0) cc_final: 0.8956 (m110) REVERT: C 367 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7843 (tm-30) REVERT: C 404 LEU cc_start: 0.9477 (mm) cc_final: 0.9122 (mt) REVERT: C 417 HIS cc_start: 0.9170 (p-80) cc_final: 0.8436 (p-80) REVERT: C 419 MET cc_start: 0.8634 (mtm) cc_final: 0.8225 (mtt) REVERT: C 694 LEU cc_start: 0.9553 (mt) cc_final: 0.9281 (pp) REVERT: C 702 GLU cc_start: 0.9459 (mp0) cc_final: 0.9071 (mp0) REVERT: C 732 LEU cc_start: 0.8863 (mt) cc_final: 0.8638 (mt) REVERT: C 733 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7484 (mmp-170) REVERT: D 174 LYS cc_start: 0.9560 (tptt) cc_final: 0.9022 (mptt) REVERT: D 178 ASN cc_start: 0.9070 (t0) cc_final: 0.8571 (p0) REVERT: D 351 MET cc_start: 0.9604 (mmm) cc_final: 0.9380 (mmm) REVERT: D 408 VAL cc_start: 0.8835 (t) cc_final: 0.8627 (t) REVERT: D 695 GLN cc_start: 0.8923 (mt0) cc_final: 0.8590 (mm110) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2845 time to fit residues: 142.9658 Evaluate side-chains 237 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 101 optimal weight: 40.0000 chunk 19 optimal weight: 6.9990 chunk 162 optimal weight: 0.3980 chunk 187 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 244 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 220 ASN C 242 ASN C 452 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18028 Z= 0.223 Angle : 0.720 9.107 24396 Z= 0.365 Chirality : 0.044 0.193 2728 Planarity : 0.005 0.089 3092 Dihedral : 5.881 38.108 2360 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.41 % Favored : 85.40 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.61 (0.17), residues: 2144 helix: -0.22 (0.15), residues: 1154 sheet: -3.77 (0.52), residues: 62 loop : -3.69 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 742 HIS 0.008 0.001 HIS B 417 PHE 0.030 0.002 PHE D 193 TYR 0.017 0.001 TYR A 359 ARG 0.006 0.000 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.9541 (mmt) cc_final: 0.9080 (mtp) REVERT: A 268 LEU cc_start: 0.9450 (tp) cc_final: 0.9239 (tp) REVERT: A 351 MET cc_start: 0.8701 (mpp) cc_final: 0.8428 (mpp) REVERT: A 392 LEU cc_start: 0.8718 (tp) cc_final: 0.8186 (tp) REVERT: A 401 ASN cc_start: 0.8738 (t0) cc_final: 0.8375 (t0) REVERT: A 404 LEU cc_start: 0.9483 (mm) cc_final: 0.9168 (mt) REVERT: A 419 MET cc_start: 0.8746 (mtm) cc_final: 0.8313 (mtt) REVERT: A 702 GLU cc_start: 0.9487 (mp0) cc_final: 0.9114 (mp0) REVERT: A 716 ARG cc_start: 0.8650 (pmt170) cc_final: 0.8201 (pmt170) REVERT: B 178 ASN cc_start: 0.9115 (t0) cc_final: 0.8548 (p0) REVERT: B 210 GLU cc_start: 0.7724 (tt0) cc_final: 0.7464 (mt-10) REVERT: B 407 ILE cc_start: 0.8384 (tp) cc_final: 0.7780 (tp) REVERT: B 695 GLN cc_start: 0.8920 (mt0) cc_final: 0.8605 (mm110) REVERT: B 729 ARG cc_start: 0.7805 (mpt180) cc_final: 0.7471 (mmt180) REVERT: C 159 MET cc_start: 0.9433 (mmt) cc_final: 0.8956 (mtp) REVERT: C 169 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8356 (mtpp) REVERT: C 176 LEU cc_start: 0.9588 (mm) cc_final: 0.8588 (tt) REVERT: C 221 ILE cc_start: 0.9624 (mp) cc_final: 0.9265 (mp) REVERT: C 309 ASP cc_start: 0.8723 (p0) cc_final: 0.8186 (m-30) REVERT: C 404 LEU cc_start: 0.9453 (mm) cc_final: 0.9078 (mt) REVERT: C 419 MET cc_start: 0.8668 (mtm) cc_final: 0.8295 (mtt) REVERT: C 694 LEU cc_start: 0.9557 (mt) cc_final: 0.9283 (pp) REVERT: C 732 LEU cc_start: 0.8906 (mt) cc_final: 0.8670 (mt) REVERT: C 733 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7729 (mmp-170) REVERT: D 174 LYS cc_start: 0.9514 (tptt) cc_final: 0.9251 (tppt) REVERT: D 177 LEU cc_start: 0.9634 (mt) cc_final: 0.9418 (mp) REVERT: D 178 ASN cc_start: 0.9069 (t0) cc_final: 0.8582 (p0) REVERT: D 220 ASN cc_start: 0.9447 (m110) cc_final: 0.9130 (m-40) REVERT: D 407 ILE cc_start: 0.8135 (tp) cc_final: 0.6335 (tp) REVERT: D 408 VAL cc_start: 0.8756 (t) cc_final: 0.8513 (t) REVERT: D 415 ASN cc_start: 0.7774 (p0) cc_final: 0.7327 (p0) REVERT: D 695 GLN cc_start: 0.8919 (mt0) cc_final: 0.8612 (mm110) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2673 time to fit residues: 123.5239 Evaluate side-chains 240 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 20.0000 chunk 180 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 452 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 242 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18028 Z= 0.177 Angle : 0.697 8.638 24396 Z= 0.348 Chirality : 0.043 0.174 2728 Planarity : 0.004 0.070 3092 Dihedral : 5.602 37.267 2360 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.03 % Favored : 87.78 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.39 (0.18), residues: 2144 helix: -0.04 (0.15), residues: 1152 sheet: -3.77 (0.52), residues: 62 loop : -3.58 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 742 HIS 0.004 0.001 HIS B 417 PHE 0.023 0.001 PHE D 124 TYR 0.016 0.001 TYR D 213 ARG 0.007 0.000 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.9470 (mmt) cc_final: 0.8972 (mtp) REVERT: A 293 ASP cc_start: 0.8017 (t70) cc_final: 0.7061 (t70) REVERT: A 309 ASP cc_start: 0.8274 (p0) cc_final: 0.7830 (m-30) REVERT: A 351 MET cc_start: 0.8553 (mpp) cc_final: 0.8345 (mpp) REVERT: A 401 ASN cc_start: 0.8649 (t0) cc_final: 0.8273 (t0) REVERT: A 404 LEU cc_start: 0.9481 (mm) cc_final: 0.9166 (mt) REVERT: A 417 HIS cc_start: 0.9210 (p-80) cc_final: 0.8516 (p-80) REVERT: A 419 MET cc_start: 0.8749 (mtm) cc_final: 0.8195 (mtt) REVERT: A 702 GLU cc_start: 0.9495 (mp0) cc_final: 0.9093 (mp0) REVERT: A 706 MET cc_start: 0.8734 (ttp) cc_final: 0.8038 (ptm) REVERT: A 716 ARG cc_start: 0.8683 (pmt170) cc_final: 0.8436 (pmt170) REVERT: B 178 ASN cc_start: 0.9094 (t0) cc_final: 0.8504 (p0) REVERT: B 210 GLU cc_start: 0.7727 (tt0) cc_final: 0.7489 (tt0) REVERT: B 407 ILE cc_start: 0.8375 (tp) cc_final: 0.7837 (tt) REVERT: B 695 GLN cc_start: 0.8915 (mt0) cc_final: 0.8538 (mm110) REVERT: B 729 ARG cc_start: 0.7834 (mpt180) cc_final: 0.7465 (mmt180) REVERT: C 159 MET cc_start: 0.9404 (mmt) cc_final: 0.8917 (mtp) REVERT: C 169 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8241 (mtpp) REVERT: C 176 LEU cc_start: 0.9588 (mm) cc_final: 0.8663 (tt) REVERT: C 221 ILE cc_start: 0.9603 (mp) cc_final: 0.9237 (mp) REVERT: C 309 ASP cc_start: 0.8699 (p0) cc_final: 0.8195 (m-30) REVERT: C 347 LEU cc_start: 0.9703 (tt) cc_final: 0.9212 (tt) REVERT: C 351 MET cc_start: 0.9311 (mpp) cc_final: 0.8591 (mpp) REVERT: C 404 LEU cc_start: 0.9472 (mm) cc_final: 0.9132 (mt) REVERT: C 417 HIS cc_start: 0.9154 (p-80) cc_final: 0.8378 (p-80) REVERT: C 419 MET cc_start: 0.8554 (mtm) cc_final: 0.8158 (mtt) REVERT: C 436 PHE cc_start: 0.8423 (p90) cc_final: 0.8214 (p90) REVERT: C 694 LEU cc_start: 0.9545 (mt) cc_final: 0.9271 (pp) REVERT: C 706 MET cc_start: 0.8743 (ttp) cc_final: 0.8146 (ptm) REVERT: C 716 ARG cc_start: 0.8505 (pmt170) cc_final: 0.8147 (ptp90) REVERT: C 732 LEU cc_start: 0.8830 (mt) cc_final: 0.8521 (mt) REVERT: C 733 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7585 (mmp-170) REVERT: D 174 LYS cc_start: 0.9491 (tptt) cc_final: 0.9252 (tppt) REVERT: D 178 ASN cc_start: 0.9061 (t0) cc_final: 0.8488 (p0) REVERT: D 220 ASN cc_start: 0.9431 (m110) cc_final: 0.9077 (m110) REVERT: D 408 VAL cc_start: 0.8877 (t) cc_final: 0.8605 (t) REVERT: D 416 ARG cc_start: 0.8097 (mmt-90) cc_final: 0.7834 (mmt180) REVERT: D 695 GLN cc_start: 0.8927 (mt0) cc_final: 0.8576 (mm110) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2838 time to fit residues: 132.3607 Evaluate side-chains 242 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 220 ASN A 242 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN C 220 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 18028 Z= 0.334 Angle : 0.775 10.344 24396 Z= 0.396 Chirality : 0.046 0.193 2728 Planarity : 0.005 0.073 3092 Dihedral : 5.936 38.690 2360 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.16 % Favored : 84.65 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.58 (0.17), residues: 2144 helix: -0.27 (0.15), residues: 1162 sheet: -3.67 (0.54), residues: 62 loop : -3.60 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 742 HIS 0.006 0.002 HIS D 301 PHE 0.020 0.002 PHE B 124 TYR 0.023 0.002 TYR A 359 ARG 0.007 0.001 ARG A 733 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.9578 (mmt) cc_final: 0.9134 (mtp) REVERT: A 176 LEU cc_start: 0.9618 (mm) cc_final: 0.8509 (tp) REVERT: A 401 ASN cc_start: 0.8744 (t0) cc_final: 0.8543 (p0) REVERT: A 404 LEU cc_start: 0.9486 (mm) cc_final: 0.9187 (mt) REVERT: A 419 MET cc_start: 0.8851 (mtm) cc_final: 0.8453 (mtt) REVERT: A 694 LEU cc_start: 0.9662 (mp) cc_final: 0.9292 (pp) REVERT: A 716 ARG cc_start: 0.8758 (pmt170) cc_final: 0.8322 (pmt170) REVERT: B 178 ASN cc_start: 0.9072 (t0) cc_final: 0.8510 (p0) REVERT: B 210 GLU cc_start: 0.7764 (tt0) cc_final: 0.7563 (mt-10) REVERT: B 407 ILE cc_start: 0.8320 (tp) cc_final: 0.7884 (tp) REVERT: B 415 ASN cc_start: 0.7948 (p0) cc_final: 0.7734 (p0) REVERT: B 695 GLN cc_start: 0.9004 (mt0) cc_final: 0.8678 (mm110) REVERT: B 729 ARG cc_start: 0.7837 (mpt180) cc_final: 0.7401 (mmt180) REVERT: C 176 LEU cc_start: 0.9609 (mm) cc_final: 0.8660 (tt) REVERT: C 221 ILE cc_start: 0.9667 (mp) cc_final: 0.9305 (mp) REVERT: C 339 ASN cc_start: 0.9264 (t0) cc_final: 0.8941 (m110) REVERT: C 401 ASN cc_start: 0.8989 (t0) cc_final: 0.8514 (p0) REVERT: C 404 LEU cc_start: 0.9473 (mm) cc_final: 0.9250 (mm) REVERT: C 419 MET cc_start: 0.8776 (mtm) cc_final: 0.8432 (mtt) REVERT: C 694 LEU cc_start: 0.9571 (mt) cc_final: 0.9307 (pp) REVERT: C 702 GLU cc_start: 0.9502 (mp0) cc_final: 0.9295 (mp0) REVERT: C 706 MET cc_start: 0.8823 (ttp) cc_final: 0.8225 (ptm) REVERT: C 732 LEU cc_start: 0.8825 (mt) cc_final: 0.8549 (mt) REVERT: C 733 ARG cc_start: 0.7866 (mmm160) cc_final: 0.7437 (mmp-170) REVERT: D 174 LYS cc_start: 0.9522 (tptt) cc_final: 0.8783 (tttt) REVERT: D 178 ASN cc_start: 0.9044 (t0) cc_final: 0.8535 (p0) REVERT: D 220 ASN cc_start: 0.9431 (m110) cc_final: 0.9109 (m110) REVERT: D 415 ASN cc_start: 0.8052 (p0) cc_final: 0.7670 (p0) REVERT: D 416 ARG cc_start: 0.8281 (mmt-90) cc_final: 0.8033 (mmt180) REVERT: D 695 GLN cc_start: 0.8995 (mt0) cc_final: 0.8650 (mm110) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.3018 time to fit residues: 132.9657 Evaluate side-chains 226 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.527 > 50: distance: 4 - 21: 20.393 distance: 9 - 29: 25.274 distance: 13 - 34: 26.089 distance: 19 - 21: 22.198 distance: 21 - 22: 33.185 distance: 22 - 23: 34.296 distance: 22 - 25: 15.891 distance: 23 - 24: 8.971 distance: 23 - 29: 49.628 distance: 25 - 26: 56.527 distance: 25 - 27: 29.050 distance: 26 - 28: 25.764 distance: 29 - 30: 21.674 distance: 30 - 31: 19.228 distance: 30 - 33: 37.708 distance: 31 - 32: 13.672 distance: 31 - 34: 34.781 distance: 34 - 35: 20.720 distance: 35 - 36: 28.029 distance: 35 - 38: 5.378 distance: 36 - 37: 14.770 distance: 36 - 42: 33.368 distance: 38 - 39: 9.696 distance: 38 - 40: 16.066 distance: 39 - 41: 12.215 distance: 42 - 43: 21.756 distance: 43 - 44: 5.453 distance: 43 - 46: 12.849 distance: 44 - 45: 21.835 distance: 44 - 53: 19.121 distance: 46 - 47: 10.626 distance: 47 - 48: 17.025 distance: 47 - 49: 11.955 distance: 48 - 50: 17.604 distance: 49 - 51: 8.249 distance: 50 - 52: 7.599 distance: 51 - 52: 14.897 distance: 53 - 54: 15.695 distance: 54 - 55: 22.143 distance: 54 - 57: 27.029 distance: 55 - 56: 31.312 distance: 55 - 61: 19.112 distance: 57 - 58: 28.828 distance: 58 - 59: 20.005 distance: 58 - 60: 30.926 distance: 61 - 62: 8.604 distance: 62 - 63: 14.656 distance: 62 - 65: 21.505 distance: 63 - 64: 13.156 distance: 63 - 69: 23.167 distance: 65 - 66: 24.776 distance: 66 - 67: 27.945 distance: 66 - 68: 17.656 distance: 69 - 70: 14.168 distance: 70 - 71: 28.596 distance: 70 - 73: 19.212 distance: 71 - 72: 27.337 distance: 71 - 80: 15.096 distance: 73 - 74: 10.914 distance: 74 - 75: 8.363 distance: 75 - 76: 13.368 distance: 76 - 77: 4.283 distance: 77 - 78: 7.387 distance: 77 - 79: 6.158 distance: 80 - 81: 14.215 distance: 80 - 86: 13.806 distance: 81 - 82: 10.054 distance: 81 - 84: 10.949 distance: 82 - 83: 26.631 distance: 82 - 87: 17.987 distance: 84 - 85: 15.500 distance: 85 - 86: 14.595 distance: 87 - 88: 26.961 distance: 88 - 89: 11.631 distance: 88 - 91: 30.458 distance: 89 - 90: 6.546 distance: 89 - 93: 15.061 distance: 91 - 92: 8.606 distance: 93 - 94: 8.242 distance: 94 - 95: 18.686 distance: 94 - 97: 13.258 distance: 95 - 96: 16.388 distance: 95 - 101: 24.571 distance: 97 - 98: 6.448 distance: 98 - 99: 9.737 distance: 98 - 100: 7.340