Starting phenix.real_space_refine on Fri Mar 15 09:25:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/03_2024/6oce_20017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/03_2024/6oce_20017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/03_2024/6oce_20017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/03_2024/6oce_20017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/03_2024/6oce_20017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/03_2024/6oce_20017.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 40 5.16 5 C 7432 2.51 5 N 1830 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B ARG 678": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11228 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5614 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 650} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 5614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5614 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 650} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 6.10, per 1000 atoms: 0.54 Number of scatterers: 11228 At special positions: 0 Unit cell: (144.9, 120.06, 106.26, 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 40 16.00 O 1926 8.00 N 1830 7.00 C 7432 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: 4.16 Conformation dependent library (CDL) restraints added in 1.9 seconds 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 2 sheets defined 65.2% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.829A pdb=" N LEU A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 28 removed outlier: 4.167A pdb=" N VAL A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 38 through 42 removed outlier: 4.171A pdb=" N TRP A 42 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.753A pdb=" N SER A 74 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TRP A 75 " --> pdb=" O PHE A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 75' Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.803A pdb=" N MET A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 89 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 102 through 127 Proline residue: A 111 - end of helix removed outlier: 3.854A pdb=" N LEU A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 154 through 189 removed outlier: 3.691A pdb=" N HIS A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A 162 " --> pdb=" O HIS A 158 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 4.125A pdb=" N PHE A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.760A pdb=" N GLU A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 223 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 269 removed outlier: 4.311A pdb=" N LEU A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 296 through 309 removed outlier: 3.503A pdb=" N GLU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 363 through 385 removed outlier: 4.012A pdb=" N THR A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 removed outlier: 3.517A pdb=" N ALA A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 424 through 433 removed outlier: 4.130A pdb=" N LYS A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 3.724A pdb=" N ILE A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 473 removed outlier: 3.713A pdb=" N ARG A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 486 removed outlier: 3.600A pdb=" N ILE A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 removed outlier: 3.532A pdb=" N THR A 514 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.548A pdb=" N ALA A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 542 removed outlier: 3.538A pdb=" N ILE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 542 " --> pdb=" O HIS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.674A pdb=" N ALA A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 583 Proline residue: A 567 - end of helix removed outlier: 3.800A pdb=" N GLN A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 607 removed outlier: 4.169A pdb=" N LEU A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 592 " --> pdb=" O PRO A 588 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 596 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 639 removed outlier: 3.563A pdb=" N VAL A 623 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 630 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 639 " --> pdb=" O GLN A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 672 Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 673 through 678 removed outlier: 3.504A pdb=" N VAL A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 678 " --> pdb=" O PRO A 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 678' Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.975A pdb=" N MET A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 4.053A pdb=" N ASN A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 9 removed outlier: 3.828A pdb=" N LEU B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 4.169A pdb=" N VAL B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 38 through 42 removed outlier: 4.161A pdb=" N TRP B 42 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 removed outlier: 3.744A pdb=" N SER B 74 " --> pdb=" O LYS B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 75 through 80 removed outlier: 4.398A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 127 removed outlier: 3.796A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.728A pdb=" N LEU B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 154 through 189 removed outlier: 3.700A pdb=" N HIS B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 169 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 4.110A pdb=" N PHE B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 224 removed outlier: 3.663A pdb=" N PHE B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 223 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 260 removed outlier: 4.376A pdb=" N LEU B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 removed outlier: 4.042A pdb=" N LYS B 268 " --> pdb=" O ARG B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.529A pdb=" N GLU B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 363 through 385 removed outlier: 3.989A pdb=" N THR B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 382 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 393 removed outlier: 3.535A pdb=" N ALA B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 424 through 433 removed outlier: 4.136A pdb=" N LYS B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 449 removed outlier: 3.723A pdb=" N ILE B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 473 removed outlier: 3.710A pdb=" N ARG B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 471 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 473 " --> pdb=" O PHE B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 486 removed outlier: 3.623A pdb=" N ILE B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 520 removed outlier: 3.557A pdb=" N THR B 514 " --> pdb=" O THR B 510 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 529 removed outlier: 3.611A pdb=" N ALA B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 529 " --> pdb=" O ALA B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 542 removed outlier: 4.025A pdb=" N ILE B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 542 " --> pdb=" O HIS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 554 removed outlier: 3.682A pdb=" N ALA B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 583 Proline residue: B 567 - end of helix removed outlier: 3.772A pdb=" N GLN B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B 582 " --> pdb=" O VAL B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 607 removed outlier: 4.165A pdb=" N LEU B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL B 592 " --> pdb=" O PRO B 588 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 596 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 606 " --> pdb=" O ARG B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 639 removed outlier: 3.553A pdb=" N VAL B 623 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 639 " --> pdb=" O GLN B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 645 removed outlier: 3.665A pdb=" N THR B 644 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS B 645 " --> pdb=" O LEU B 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 641 through 645' Processing helix chain 'B' and resid 650 through 672 Proline residue: B 658 - end of helix Processing helix chain 'B' and resid 673 through 678 removed outlier: 3.620A pdb=" N VAL B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 678 " --> pdb=" O PRO B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 678' Processing helix chain 'B' and resid 681 through 695 removed outlier: 3.741A pdb=" N MET B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 removed outlier: 4.077A pdb=" N ASN B 706 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 234 removed outlier: 4.388A pdb=" N GLN A 233 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 234 removed outlier: 4.311A pdb=" N GLN B 233 " --> pdb=" O PHE B 320 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1347 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: 3.31 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1720 1.29 - 1.42: 3174 1.42 - 1.55: 6578 1.55 - 1.68: 2 1.68 - 1.81: 68 Bond restraints: 11542 Sorted by residual: bond pdb=" CB PRO A 111 " pdb=" CG PRO A 111 " ideal model delta sigma weight residual 1.492 1.155 0.337 5.00e-02 4.00e+02 4.55e+01 bond pdb=" CB PRO B 111 " pdb=" CG PRO B 111 " ideal model delta sigma weight residual 1.492 1.227 0.265 5.00e-02 4.00e+02 2.81e+01 bond pdb=" CA PRO A 206 " pdb=" C PRO A 206 " ideal model delta sigma weight residual 1.514 1.531 -0.016 5.50e-03 3.31e+04 8.73e+00 bond pdb=" CB PRO B 498 " pdb=" CG PRO B 498 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.73e+00 bond pdb=" CA HIS B 624 " pdb=" CB HIS B 624 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.55e-02 4.16e+03 3.50e+00 ... (remaining 11537 not shown) Histogram of bond angle deviations from ideal: 96.97 - 105.66: 292 105.66 - 114.34: 6813 114.34 - 123.03: 7964 123.03 - 131.72: 600 131.72 - 140.41: 31 Bond angle restraints: 15700 Sorted by residual: angle pdb=" N ASP A 285 " pdb=" CA ASP A 285 " pdb=" C ASP A 285 " ideal model delta sigma weight residual 111.24 125.95 -14.71 1.29e+00 6.01e-01 1.30e+02 angle pdb=" CA PRO A 111 " pdb=" N PRO A 111 " pdb=" CD PRO A 111 " ideal model delta sigma weight residual 112.00 97.80 14.20 1.40e+00 5.10e-01 1.03e+02 angle pdb=" CA PRO B 111 " pdb=" N PRO B 111 " pdb=" CD PRO B 111 " ideal model delta sigma weight residual 112.00 98.69 13.31 1.40e+00 5.10e-01 9.03e+01 angle pdb=" N ASP B 285 " pdb=" CA ASP B 285 " pdb=" C ASP B 285 " ideal model delta sigma weight residual 111.24 121.76 -10.52 1.29e+00 6.01e-01 6.66e+01 angle pdb=" N LYS A 296 " pdb=" CA LYS A 296 " pdb=" C LYS A 296 " ideal model delta sigma weight residual 108.67 96.97 11.70 1.67e+00 3.59e-01 4.91e+01 ... (remaining 15695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.73: 6571 15.73 - 31.45: 223 31.45 - 47.18: 36 47.18 - 62.91: 3 62.91 - 78.63: 3 Dihedral angle restraints: 6836 sinusoidal: 2748 harmonic: 4088 Sorted by residual: dihedral pdb=" CA PRO B 498 " pdb=" C PRO B 498 " pdb=" N ARG B 499 " pdb=" CA ARG B 499 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PRO A 498 " pdb=" C PRO A 498 " pdb=" N ARG A 499 " pdb=" CA ARG A 499 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ILE B 497 " pdb=" C ILE B 497 " pdb=" N PRO B 498 " pdb=" CA PRO B 498 " ideal model delta harmonic sigma weight residual 180.00 -164.39 -15.61 0 5.00e+00 4.00e-02 9.75e+00 ... (remaining 6833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1610 0.066 - 0.131: 154 0.131 - 0.197: 10 0.197 - 0.263: 1 0.263 - 0.328: 1 Chirality restraints: 1776 Sorted by residual: chirality pdb=" CA ASP A 285 " pdb=" N ASP A 285 " pdb=" C ASP A 285 " pdb=" CB ASP A 285 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA ASP B 285 " pdb=" N ASP B 285 " pdb=" C ASP B 285 " pdb=" CB ASP B 285 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PHE A 593 " pdb=" N PHE A 593 " pdb=" C PHE A 593 " pdb=" CB PHE A 593 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 1773 not shown) Planarity restraints: 1954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 425 " 0.062 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO A 426 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 425 " -0.061 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO B 426 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 426 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 426 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 624 " -0.015 2.00e-02 2.50e+03 1.72e-02 4.43e+00 pdb=" CG HIS A 624 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 624 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS A 624 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS A 624 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 624 " -0.008 2.00e-02 2.50e+03 ... (remaining 1951 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 31 2.47 - 3.08: 8313 3.08 - 3.69: 15845 3.69 - 4.29: 22616 4.29 - 4.90: 36167 Nonbonded interactions: 82972 Sorted by model distance: nonbonded pdb=" O LYS B 107 " pdb=" CG2 VAL B 110 " model vdw 1.868 3.460 nonbonded pdb=" O LYS A 107 " pdb=" CG2 VAL A 110 " model vdw 1.932 3.460 nonbonded pdb=" OG SER A 282 " pdb=" OE1 GLU A 283 " model vdw 2.176 2.440 nonbonded pdb=" OG1 THR B 126 " pdb=" OG SER B 144 " model vdw 2.231 2.440 nonbonded pdb=" O PRO B 122 " pdb=" OG1 THR B 126 " model vdw 2.241 2.440 ... (remaining 82967 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' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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: 0.760 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: 0.010 Extract box with map and model: 3.650 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.080 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.337 11542 Z= 0.317 Angle : 0.732 15.407 15700 Z= 0.460 Chirality : 0.042 0.328 1776 Planarity : 0.006 0.093 1954 Dihedral : 8.069 78.634 4184 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.19), residues: 1370 helix: -2.24 (0.16), residues: 696 sheet: 0.34 (1.93), residues: 10 loop : -3.79 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 42 HIS 0.019 0.001 HIS A 624 PHE 0.027 0.001 PHE B 593 TYR 0.006 0.001 TYR A 464 ARG 0.002 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.694 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 37 VAL cc_start: 0.6801 (p) cc_final: 0.6498 (m) REVERT: A 66 MET cc_start: 0.5095 (ttp) cc_final: 0.4718 (ttt) REVERT: A 67 ARG cc_start: 0.4430 (mtt90) cc_final: 0.4007 (tmm-80) REVERT: A 87 LEU cc_start: 0.7561 (mt) cc_final: 0.7173 (mt) REVERT: A 109 PHE cc_start: 0.7130 (m-80) cc_final: 0.6792 (t80) REVERT: A 137 HIS cc_start: 0.4665 (m90) cc_final: 0.4337 (m-70) REVERT: A 167 PHE cc_start: 0.8569 (m-10) cc_final: 0.8271 (t80) REVERT: A 201 LEU cc_start: 0.8002 (tp) cc_final: 0.7428 (tp) REVERT: A 202 VAL cc_start: 0.7486 (t) cc_final: 0.7246 (t) REVERT: A 303 ASP cc_start: 0.7081 (t70) cc_final: 0.6876 (m-30) REVERT: A 373 ILE cc_start: 0.8455 (mm) cc_final: 0.8233 (tt) REVERT: A 457 GLU cc_start: 0.8301 (tt0) cc_final: 0.7644 (pt0) REVERT: A 464 TYR cc_start: 0.7955 (t80) cc_final: 0.7256 (t80) REVERT: A 514 THR cc_start: 0.8577 (p) cc_final: 0.8261 (t) REVERT: A 552 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7022 (mp0) REVERT: A 564 TRP cc_start: 0.6832 (m-10) cc_final: 0.6271 (m-90) REVERT: A 567 PRO cc_start: 0.8073 (Cg_exo) cc_final: 0.7440 (Cg_endo) REVERT: A 568 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7563 (mtm180) REVERT: A 585 LEU cc_start: 0.7966 (mt) cc_final: 0.7688 (tp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2130 time to fit residues: 55.0917 Evaluate side-chains 111 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS B 422 GLN B 538 HIS B 570 GLN B 604 GLN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11542 Z= 0.201 Angle : 0.700 7.986 15700 Z= 0.355 Chirality : 0.045 0.258 1776 Planarity : 0.006 0.065 1954 Dihedral : 3.831 18.633 1506 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.07 % Favored : 89.20 % Rotamer: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.21), residues: 1370 helix: -1.03 (0.18), residues: 714 sheet: 0.60 (1.92), residues: 10 loop : -3.49 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 75 HIS 0.006 0.001 HIS A 538 PHE 0.019 0.002 PHE A 698 TYR 0.010 0.001 TYR A 465 ARG 0.002 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ARG cc_start: 0.4211 (mtt90) cc_final: 0.3951 (tmm-80) REVERT: B 76 MET cc_start: 0.8337 (mmm) cc_final: 0.7669 (mtt) REVERT: B 249 LYS cc_start: 0.8051 (mttm) cc_final: 0.7610 (tmtt) REVERT: B 250 LYS cc_start: 0.8445 (pttt) cc_final: 0.8125 (pptt) REVERT: B 264 ARG cc_start: 0.3282 (mtm180) cc_final: 0.2819 (mtt180) REVERT: B 303 ASP cc_start: 0.7277 (t70) cc_final: 0.7014 (m-30) REVERT: B 358 ASN cc_start: 0.8182 (m-40) cc_final: 0.7966 (m110) REVERT: B 444 MET cc_start: 0.8201 (ptp) cc_final: 0.7891 (ptm) REVERT: B 457 GLU cc_start: 0.8443 (tt0) cc_final: 0.7366 (tm-30) REVERT: B 464 TYR cc_start: 0.8034 (t80) cc_final: 0.7381 (t80) REVERT: B 513 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7997 (mt) REVERT: B 514 THR cc_start: 0.8533 (p) cc_final: 0.8161 (t) REVERT: B 552 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6859 (mp0) REVERT: B 564 TRP cc_start: 0.6539 (m-10) cc_final: 0.6008 (m-90) REVERT: B 585 LEU cc_start: 0.7983 (mt) cc_final: 0.7679 (tp) REVERT: B 631 LEU cc_start: 0.7726 (mm) cc_final: 0.7313 (mm) REVERT: B 666 LYS cc_start: 0.7399 (mmpt) cc_final: 0.6464 (pttt) REVERT: B 671 ARG cc_start: 0.6421 (ttt180) cc_final: 0.5983 (tpp-160) REVERT: B 673 GLU cc_start: 0.9179 (tp30) cc_final: 0.8898 (tp30) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1945 time to fit residues: 39.1293 Evaluate side-chains 102 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.9990 chunk 38 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 0.0270 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN B 485 GLN ** B 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11542 Z= 0.172 Angle : 0.640 7.123 15700 Z= 0.323 Chirality : 0.042 0.151 1776 Planarity : 0.005 0.057 1954 Dihedral : 3.956 18.194 1506 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.70 % Favored : 87.01 % Rotamer: Outliers : 0.16 % Allowed : 2.94 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.21), residues: 1370 helix: -0.99 (0.18), residues: 744 sheet: 0.06 (1.69), residues: 10 loop : -3.57 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 620 HIS 0.006 0.001 HIS B 603 PHE 0.019 0.001 PHE B 594 TYR 0.011 0.001 TYR B 150 ARG 0.005 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 LYS cc_start: 0.8095 (mttm) cc_final: 0.7690 (tmtt) REVERT: B 303 ASP cc_start: 0.7189 (t70) cc_final: 0.6953 (m-30) REVERT: B 343 VAL cc_start: 0.6145 (t) cc_final: 0.5914 (t) REVERT: B 379 PHE cc_start: 0.7801 (t80) cc_final: 0.7244 (t80) REVERT: B 421 ILE cc_start: 0.5554 (tt) cc_final: 0.5237 (pt) REVERT: B 444 MET cc_start: 0.8231 (ptp) cc_final: 0.7464 (ptp) REVERT: B 457 GLU cc_start: 0.8565 (tt0) cc_final: 0.7302 (tm-30) REVERT: B 464 TYR cc_start: 0.8019 (t80) cc_final: 0.7467 (t80) REVERT: B 479 THR cc_start: 0.8079 (p) cc_final: 0.7813 (p) REVERT: B 513 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7880 (mt) REVERT: B 514 THR cc_start: 0.8555 (p) cc_final: 0.8176 (t) REVERT: B 552 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6917 (mp0) REVERT: B 564 TRP cc_start: 0.6323 (m-10) cc_final: 0.5843 (m-90) REVERT: B 581 VAL cc_start: 0.8146 (p) cc_final: 0.7827 (p) REVERT: B 585 LEU cc_start: 0.7989 (mt) cc_final: 0.7686 (tp) REVERT: B 604 GLN cc_start: 0.8065 (tp40) cc_final: 0.7790 (tp40) REVERT: B 631 LEU cc_start: 0.7947 (mm) cc_final: 0.7548 (mm) REVERT: B 671 ARG cc_start: 0.6502 (ttt180) cc_final: 0.5935 (tpp-160) REVERT: B 673 GLU cc_start: 0.9065 (tp30) cc_final: 0.8809 (tp30) REVERT: B 709 LEU cc_start: 0.7595 (mt) cc_final: 0.7389 (mt) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.1807 time to fit residues: 34.2407 Evaluate side-chains 109 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 228 HIS B 306 GLN B 337 GLN B 393 GLN B 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11542 Z= 0.206 Angle : 0.661 7.047 15700 Z= 0.330 Chirality : 0.043 0.150 1776 Planarity : 0.006 0.072 1954 Dihedral : 4.265 18.303 1506 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.43 % Favored : 86.57 % Rotamer: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.22), residues: 1370 helix: -0.66 (0.19), residues: 740 sheet: 0.39 (1.77), residues: 10 loop : -3.38 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 75 HIS 0.012 0.002 HIS A 232 PHE 0.014 0.001 PHE B 698 TYR 0.017 0.002 TYR B 258 ARG 0.003 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 THR cc_start: 0.7937 (p) cc_final: 0.7580 (p) REVERT: B 167 PHE cc_start: 0.8754 (m-10) cc_final: 0.8283 (m-10) REVERT: B 170 CYS cc_start: 0.8868 (m) cc_final: 0.8596 (p) REVERT: B 241 LEU cc_start: 0.8295 (mm) cc_final: 0.7819 (pt) REVERT: B 249 LYS cc_start: 0.8146 (mttm) cc_final: 0.7787 (tmtt) REVERT: B 250 LYS cc_start: 0.8027 (pttm) cc_final: 0.7515 (tptp) REVERT: B 379 PHE cc_start: 0.7740 (t80) cc_final: 0.7498 (t80) REVERT: B 402 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6821 (mm-30) REVERT: B 406 PRO cc_start: 0.2781 (Cg_exo) cc_final: 0.2539 (Cg_endo) REVERT: B 444 MET cc_start: 0.8302 (ptp) cc_final: 0.7507 (ptp) REVERT: B 464 TYR cc_start: 0.8029 (t80) cc_final: 0.7387 (t80) REVERT: B 479 THR cc_start: 0.7970 (p) cc_final: 0.7734 (p) REVERT: B 552 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6761 (mp0) REVERT: B 564 TRP cc_start: 0.6393 (m-10) cc_final: 0.5827 (m-90) REVERT: B 579 TYR cc_start: 0.6920 (m-80) cc_final: 0.6705 (m-10) REVERT: B 581 VAL cc_start: 0.8325 (p) cc_final: 0.8060 (p) REVERT: B 585 LEU cc_start: 0.7936 (mt) cc_final: 0.7590 (tp) REVERT: B 604 GLN cc_start: 0.8200 (tp40) cc_final: 0.7914 (tp40) REVERT: B 631 LEU cc_start: 0.8107 (mm) cc_final: 0.7740 (mm) REVERT: B 676 PHE cc_start: 0.7804 (t80) cc_final: 0.7584 (t80) REVERT: B 709 LEU cc_start: 0.7191 (mt) cc_final: 0.6904 (mp) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1707 time to fit residues: 31.5420 Evaluate side-chains 98 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11542 Z= 0.158 Angle : 0.625 6.904 15700 Z= 0.309 Chirality : 0.042 0.162 1776 Planarity : 0.005 0.055 1954 Dihedral : 4.079 16.226 1506 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.87 % Favored : 86.13 % Rotamer: Outliers : 0.16 % Allowed : 1.96 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.22), residues: 1370 helix: -0.79 (0.18), residues: 770 sheet: 0.37 (1.70), residues: 10 loop : -3.23 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 168 HIS 0.003 0.001 HIS A 232 PHE 0.023 0.001 PHE B 593 TYR 0.026 0.001 TYR A 613 ARG 0.004 0.000 ARG B 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 THR cc_start: 0.8067 (p) cc_final: 0.7614 (p) REVERT: A 167 PHE cc_start: 0.8612 (m-10) cc_final: 0.8403 (m-10) REVERT: A 170 CYS cc_start: 0.8835 (m) cc_final: 0.8574 (m) REVERT: A 241 LEU cc_start: 0.8120 (mm) cc_final: 0.7553 (pt) REVERT: A 249 LYS cc_start: 0.8122 (mttm) cc_final: 0.7878 (tmtt) REVERT: A 280 PHE cc_start: 0.5474 (m-80) cc_final: 0.4967 (t80) REVERT: A 406 PRO cc_start: 0.2091 (Cg_exo) cc_final: 0.1288 (Cg_endo) REVERT: A 444 MET cc_start: 0.8310 (ptp) cc_final: 0.7768 (ptp) REVERT: A 464 TYR cc_start: 0.7960 (t80) cc_final: 0.7235 (t80) REVERT: A 552 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6812 (mp0) REVERT: A 564 TRP cc_start: 0.6421 (m-10) cc_final: 0.5896 (m-90) REVERT: A 579 TYR cc_start: 0.6906 (m-80) cc_final: 0.6648 (m-10) REVERT: A 581 VAL cc_start: 0.8418 (p) cc_final: 0.8119 (p) REVERT: A 585 LEU cc_start: 0.7990 (mt) cc_final: 0.7686 (tp) REVERT: A 604 GLN cc_start: 0.8043 (tp40) cc_final: 0.7741 (tp40) REVERT: A 613 TYR cc_start: 0.6360 (t80) cc_final: 0.5704 (t80) REVERT: A 615 SER cc_start: 0.7625 (t) cc_final: 0.7026 (p) REVERT: A 631 LEU cc_start: 0.8146 (mm) cc_final: 0.7767 (mm) REVERT: A 657 LEU cc_start: 0.7598 (mt) cc_final: 0.7386 (mt) REVERT: A 676 PHE cc_start: 0.7824 (t80) cc_final: 0.7434 (t80) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1680 time to fit residues: 30.6688 Evaluate side-chains 92 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.0060 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS A 393 GLN A 603 HIS A 618 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11542 Z= 0.143 Angle : 0.616 6.865 15700 Z= 0.299 Chirality : 0.041 0.176 1776 Planarity : 0.005 0.057 1954 Dihedral : 4.037 16.214 1506 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.22), residues: 1370 helix: -0.74 (0.18), residues: 772 sheet: 0.12 (1.56), residues: 10 loop : -3.25 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 168 HIS 0.004 0.001 HIS A 225 PHE 0.017 0.001 PHE A 593 TYR 0.021 0.001 TYR B 613 ARG 0.003 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 166 THR cc_start: 0.8238 (p) cc_final: 0.8022 (p) REVERT: A 167 PHE cc_start: 0.8844 (m-10) cc_final: 0.8212 (m-80) REVERT: A 241 LEU cc_start: 0.8152 (mm) cc_final: 0.7572 (pt) REVERT: A 247 LYS cc_start: 0.8453 (tmmt) cc_final: 0.7851 (tmtt) REVERT: A 250 LYS cc_start: 0.8329 (pttm) cc_final: 0.7821 (tptp) REVERT: A 280 PHE cc_start: 0.5421 (m-80) cc_final: 0.4954 (t80) REVERT: A 444 MET cc_start: 0.8314 (ptp) cc_final: 0.7777 (ptp) REVERT: A 464 TYR cc_start: 0.7990 (t80) cc_final: 0.7273 (t80) REVERT: A 552 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6837 (mp0) REVERT: A 564 TRP cc_start: 0.6465 (m-10) cc_final: 0.5926 (m-90) REVERT: A 579 TYR cc_start: 0.6887 (m-80) cc_final: 0.6580 (m-10) REVERT: A 585 LEU cc_start: 0.7979 (mt) cc_final: 0.7677 (tp) REVERT: A 604 GLN cc_start: 0.8073 (tp40) cc_final: 0.7791 (tp40) REVERT: A 613 TYR cc_start: 0.6278 (t80) cc_final: 0.5619 (t80) REVERT: A 664 PHE cc_start: 0.8553 (t80) cc_final: 0.8326 (t80) REVERT: A 671 ARG cc_start: 0.6754 (ttt180) cc_final: 0.5903 (tpt170) REVERT: A 676 PHE cc_start: 0.7779 (t80) cc_final: 0.7510 (t80) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1583 time to fit residues: 29.8895 Evaluate side-chains 99 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 96 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 131 optimal weight: 0.0270 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 60 optimal weight: 0.0370 chunk 81 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11542 Z= 0.142 Angle : 0.616 7.480 15700 Z= 0.295 Chirality : 0.041 0.170 1776 Planarity : 0.005 0.056 1954 Dihedral : 3.885 15.108 1506 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.22), residues: 1370 helix: -0.62 (0.18), residues: 758 sheet: -0.42 (1.35), residues: 10 loop : -3.11 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 168 HIS 0.010 0.001 HIS A 232 PHE 0.017 0.001 PHE A 593 TYR 0.018 0.001 TYR B 613 ARG 0.003 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 167 PHE cc_start: 0.8232 (m-10) cc_final: 0.7891 (t80) REVERT: B 247 LYS cc_start: 0.8389 (tmmt) cc_final: 0.7945 (tmtt) REVERT: B 250 LYS cc_start: 0.8107 (pttm) cc_final: 0.7699 (tptp) REVERT: B 280 PHE cc_start: 0.5698 (m-80) cc_final: 0.5013 (t80) REVERT: B 379 PHE cc_start: 0.7901 (t80) cc_final: 0.7537 (t80) REVERT: B 380 PHE cc_start: 0.6963 (m-80) cc_final: 0.6476 (m-80) REVERT: B 406 PRO cc_start: 0.2009 (Cg_endo) cc_final: 0.1769 (Cg_exo) REVERT: B 444 MET cc_start: 0.8453 (ptp) cc_final: 0.7730 (ptp) REVERT: B 464 TYR cc_start: 0.8156 (t80) cc_final: 0.7544 (t80) REVERT: B 552 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6931 (mp0) REVERT: B 564 TRP cc_start: 0.6476 (m-10) cc_final: 0.6028 (m-90) REVERT: B 581 VAL cc_start: 0.8394 (p) cc_final: 0.8115 (p) REVERT: B 585 LEU cc_start: 0.7864 (mt) cc_final: 0.7572 (tp) REVERT: B 631 LEU cc_start: 0.8080 (mm) cc_final: 0.7823 (mm) REVERT: B 650 THR cc_start: 0.7581 (p) cc_final: 0.7064 (p) REVERT: B 671 ARG cc_start: 0.6458 (ttt180) cc_final: 0.5804 (tpt170) REVERT: B 673 GLU cc_start: 0.9092 (tp30) cc_final: 0.8800 (tp30) REVERT: B 709 LEU cc_start: 0.7765 (mt) cc_final: 0.7414 (mp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1714 time to fit residues: 32.0617 Evaluate side-chains 101 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 8.9990 chunk 39 optimal weight: 0.0870 chunk 25 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 0.0970 chunk 114 optimal weight: 4.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS A 393 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11542 Z= 0.144 Angle : 0.624 6.920 15700 Z= 0.301 Chirality : 0.042 0.166 1776 Planarity : 0.005 0.056 1954 Dihedral : 3.926 15.621 1506 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.22), residues: 1370 helix: -0.59 (0.18), residues: 760 sheet: -0.30 (1.39), residues: 10 loop : -3.23 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 75 HIS 0.003 0.001 HIS B 232 PHE 0.019 0.001 PHE A 364 TYR 0.005 0.001 TYR A 464 ARG 0.003 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 77 PRO cc_start: 0.6721 (Cg_exo) cc_final: 0.6453 (Cg_endo) REVERT: A 167 PHE cc_start: 0.8207 (m-10) cc_final: 0.7876 (t80) REVERT: A 241 LEU cc_start: 0.7012 (pt) cc_final: 0.6812 (mm) REVERT: A 280 PHE cc_start: 0.5460 (m-80) cc_final: 0.4970 (t80) REVERT: A 379 PHE cc_start: 0.7739 (t80) cc_final: 0.7323 (t80) REVERT: A 444 MET cc_start: 0.8269 (ptp) cc_final: 0.7803 (ptp) REVERT: A 464 TYR cc_start: 0.8012 (t80) cc_final: 0.7340 (t80) REVERT: A 511 PHE cc_start: 0.6923 (t80) cc_final: 0.6665 (t80) REVERT: A 552 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6994 (mp0) REVERT: A 555 MET cc_start: 0.3464 (mpp) cc_final: 0.3075 (mpp) REVERT: A 564 TRP cc_start: 0.6474 (m-10) cc_final: 0.5955 (m-90) REVERT: A 581 VAL cc_start: 0.8393 (p) cc_final: 0.8100 (p) REVERT: A 585 LEU cc_start: 0.7894 (mt) cc_final: 0.7569 (tp) REVERT: A 604 GLN cc_start: 0.8100 (tp40) cc_final: 0.7629 (tp40) REVERT: A 671 ARG cc_start: 0.6648 (ttt180) cc_final: 0.5745 (tpp-160) REVERT: A 673 GLU cc_start: 0.9065 (tp30) cc_final: 0.8830 (tp30) REVERT: A 709 LEU cc_start: 0.7641 (mt) cc_final: 0.7338 (mp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1664 time to fit residues: 31.2257 Evaluate side-chains 101 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 9.9990 chunk 125 optimal weight: 0.0970 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 0.0980 chunk 37 optimal weight: 0.0270 chunk 110 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 121 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 228 HIS A 393 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11542 Z= 0.144 Angle : 0.642 7.080 15700 Z= 0.305 Chirality : 0.042 0.224 1776 Planarity : 0.005 0.055 1954 Dihedral : 3.900 15.212 1506 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.22), residues: 1370 helix: -0.70 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -3.13 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 344 HIS 0.010 0.001 HIS B 232 PHE 0.015 0.001 PHE A 593 TYR 0.023 0.001 TYR B 98 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7561 (t80) cc_final: 0.7337 (t80) REVERT: A 167 PHE cc_start: 0.8381 (m-10) cc_final: 0.8027 (t80) REVERT: A 241 LEU cc_start: 0.7040 (pt) cc_final: 0.6782 (mm) REVERT: A 280 PHE cc_start: 0.5431 (m-80) cc_final: 0.4966 (t80) REVERT: A 379 PHE cc_start: 0.7742 (t80) cc_final: 0.7266 (t80) REVERT: A 406 PRO cc_start: 0.3931 (Cg_exo) cc_final: 0.3598 (Cg_endo) REVERT: A 464 TYR cc_start: 0.8083 (t80) cc_final: 0.7417 (t80) REVERT: A 511 PHE cc_start: 0.6928 (t80) cc_final: 0.6614 (t80) REVERT: A 552 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7102 (mp0) REVERT: A 555 MET cc_start: 0.3764 (mpp) cc_final: 0.3357 (mpp) REVERT: A 564 TRP cc_start: 0.6462 (m-10) cc_final: 0.5953 (m-90) REVERT: A 581 VAL cc_start: 0.8367 (p) cc_final: 0.8052 (p) REVERT: A 585 LEU cc_start: 0.7838 (mt) cc_final: 0.7608 (tp) REVERT: A 604 GLN cc_start: 0.8115 (tp40) cc_final: 0.7639 (tp40) REVERT: A 637 LEU cc_start: 0.6935 (mm) cc_final: 0.6508 (mm) REVERT: A 671 ARG cc_start: 0.6692 (ttt180) cc_final: 0.5620 (tpp-160) REVERT: A 672 PHE cc_start: 0.6683 (m-80) cc_final: 0.6093 (m-10) REVERT: A 673 GLU cc_start: 0.8984 (tp30) cc_final: 0.8729 (tp30) REVERT: A 709 LEU cc_start: 0.7652 (mt) cc_final: 0.7338 (mp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1529 time to fit residues: 27.8908 Evaluate side-chains 100 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 107 optimal weight: 0.0050 chunk 11 optimal weight: 0.0570 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 overall best weight: 1.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 603 HIS ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.6249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11542 Z= 0.145 Angle : 0.637 7.115 15700 Z= 0.303 Chirality : 0.042 0.145 1776 Planarity : 0.005 0.056 1954 Dihedral : 3.862 15.866 1506 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.22), residues: 1370 helix: -0.61 (0.18), residues: 772 sheet: -0.39 (1.38), residues: 10 loop : -3.09 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 620 HIS 0.008 0.001 HIS B 232 PHE 0.029 0.001 PHE A 109 TYR 0.018 0.001 TYR A 98 ARG 0.003 0.000 ARG A 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.7015 (pt) cc_final: 0.6739 (mm) REVERT: A 280 PHE cc_start: 0.5442 (m-80) cc_final: 0.4974 (t80) REVERT: A 379 PHE cc_start: 0.7781 (t80) cc_final: 0.7210 (t80) REVERT: A 406 PRO cc_start: 0.3908 (Cg_exo) cc_final: 0.3599 (Cg_endo) REVERT: A 464 TYR cc_start: 0.8028 (t80) cc_final: 0.7416 (t80) REVERT: A 511 PHE cc_start: 0.6957 (t80) cc_final: 0.6642 (t80) REVERT: A 552 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6926 (mp0) REVERT: A 555 MET cc_start: 0.3550 (mpp) cc_final: 0.3183 (mpp) REVERT: A 564 TRP cc_start: 0.6476 (m-10) cc_final: 0.5952 (m-90) REVERT: A 581 VAL cc_start: 0.8472 (p) cc_final: 0.8174 (p) REVERT: A 585 LEU cc_start: 0.7868 (mt) cc_final: 0.7595 (tp) REVERT: A 604 GLN cc_start: 0.8123 (tp40) cc_final: 0.7652 (tp40) REVERT: A 637 LEU cc_start: 0.6855 (mm) cc_final: 0.6436 (mm) REVERT: A 671 ARG cc_start: 0.6633 (ttt180) cc_final: 0.5722 (tpp-160) REVERT: A 673 GLU cc_start: 0.9027 (tp30) cc_final: 0.8790 (tp30) REVERT: A 709 LEU cc_start: 0.7669 (mt) cc_final: 0.7379 (mp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1522 time to fit residues: 27.2914 Evaluate side-chains 101 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 108 optimal weight: 0.2980 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 0.0770 chunk 94 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS A 393 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.082686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.070293 restraints weight = 27208.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.071849 restraints weight = 18758.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.072920 restraints weight = 13977.140| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11542 Z= 0.146 Angle : 0.637 7.095 15700 Z= 0.305 Chirality : 0.042 0.187 1776 Planarity : 0.005 0.056 1954 Dihedral : 3.878 15.728 1506 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.22), residues: 1370 helix: -0.61 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -3.12 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 75 HIS 0.003 0.001 HIS B 225 PHE 0.015 0.001 PHE A 676 TYR 0.039 0.001 TYR A 613 ARG 0.006 0.000 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1837.87 seconds wall clock time: 34 minutes 19.34 seconds (2059.34 seconds total)