Starting phenix.real_space_refine on Sat Dec 9 13:44:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/12_2023/6oce_20017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/12_2023/6oce_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_20017/12_2023/6oce_20017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/12_2023/6oce_20017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/12_2023/6oce_20017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/12_2023/6oce_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-1.21rc1-5172/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: 5.79, per 1000 atoms: 0.52 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: 4.01 Conformation dependent library (CDL) restraints added in 2.0 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: 1.08 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: 2.93 Time building geometry restraints manager: 4.38 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: 0.720 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: 30.520 Find NCS groups from input model: 0.580 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.580 ------------------------------------------------------------------------------- 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 : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1960 time to fit residues: 50.1705 Evaluate side-chains 98 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9092 ------------------------------------------------------------------------------- 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: 0.3980 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 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: 0.8980 chunk 123 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 B 682 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11542 Z= 0.197 Angle : 0.710 7.968 15700 Z= 0.361 Chirality : 0.045 0.254 1776 Planarity : 0.006 0.067 1954 Dihedral : 3.888 18.804 1506 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.07 % Favored : 89.20 % Rotamer: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.22 % 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: -3.24 (0.21), residues: 1370 helix: -1.09 (0.18), residues: 752 sheet: 0.23 (1.79), residues: 10 loop : -3.68 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 75 HIS 0.007 0.001 HIS B 538 PHE 0.019 0.001 PHE B 698 TYR 0.010 0.001 TYR B 601 ARG 0.002 0.000 ARG B 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 160 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1990 time to fit residues: 39.9465 Evaluate side-chains 95 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9175 ------------------------------------------------------------------------------- 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: 20.0000 chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 133 optimal weight: 0.1980 chunk 110 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 306 GLN B 393 GLN B 485 GLN B 603 HIS ** B 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11542 Z= 0.157 Angle : 0.642 6.958 15700 Z= 0.322 Chirality : 0.042 0.148 1776 Planarity : 0.005 0.057 1954 Dihedral : 4.006 19.450 1506 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.55 % Favored : 87.15 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: -3.13 (0.21), residues: 1370 helix: -1.07 (0.18), residues: 752 sheet: -0.20 (1.64), residues: 10 loop : -3.51 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 663 HIS 0.006 0.001 HIS B 603 PHE 0.031 0.001 PHE B 109 TYR 0.012 0.001 TYR A 150 ARG 0.003 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 136 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1740 time to fit residues: 30.9000 Evaluate side-chains 101 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.704 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0199 ------------------------------------------------------------------------------- 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: 0.5980 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 0.2980 chunk 131 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.6237 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11542 Z= 0.154 Angle : 0.625 6.862 15700 Z= 0.309 Chirality : 0.041 0.146 1776 Planarity : 0.006 0.065 1954 Dihedral : 3.963 16.995 1506 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % 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: -3.06 (0.21), residues: 1370 helix: -0.98 (0.18), residues: 754 sheet: -0.18 (1.55), residues: 10 loop : -3.53 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 75 HIS 0.008 0.001 HIS B 232 PHE 0.016 0.001 PHE A 364 TYR 0.017 0.001 TYR B 258 ARG 0.002 0.000 ARG B 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 141 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1733 time to fit residues: 32.0076 Evaluate side-chains 91 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8098 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 0.0970 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 393 GLN A 603 HIS ** 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: 0.6282 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11542 Z= 0.165 Angle : 0.630 6.793 15700 Z= 0.313 Chirality : 0.042 0.181 1776 Planarity : 0.005 0.053 1954 Dihedral : 4.001 15.190 1506 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.22), residues: 1370 helix: -0.93 (0.18), residues: 762 sheet: 0.02 (1.58), residues: 10 loop : -3.43 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 564 HIS 0.005 0.001 HIS B 232 PHE 0.017 0.001 PHE B 391 TYR 0.011 0.001 TYR B 258 ARG 0.004 0.000 ARG A 508 *********************** 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 130 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1704 time to fit residues: 29.2757 Evaluate side-chains 87 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8981 ------------------------------------------------------------------------------- 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: 0.0470 chunk 25 optimal weight: 0.0020 chunk 77 optimal weight: 0.0020 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 0.1980 chunk 109 optimal weight: 0.3980 chunk 60 optimal weight: 0.0570 chunk 10 optimal weight: 0.0050 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 overall best weight: 0.0226 ------------------------------------------------------------------------------- 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 224 ASN B 393 GLN ** B 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: 0.6242 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11542 Z= 0.153 Angle : 0.639 8.468 15700 Z= 0.314 Chirality : 0.042 0.170 1776 Planarity : 0.005 0.058 1954 Dihedral : 3.970 16.738 1506 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -2.92 (0.22), residues: 1370 helix: -0.89 (0.18), residues: 770 sheet: -0.19 (1.49), residues: 10 loop : -3.49 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 564 HIS 0.005 0.001 HIS A 232 PHE 0.021 0.001 PHE B 364 TYR 0.012 0.001 TYR A 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 144 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1798 time to fit residues: 33.4195 Evaluate side-chains 96 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8945 ------------------------------------------------------------------------------- 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: 0.8980 chunk 74 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11542 Z= 0.156 Angle : 0.641 11.231 15700 Z= 0.311 Chirality : 0.041 0.158 1776 Planarity : 0.005 0.052 1954 Dihedral : 3.982 16.152 1506 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -2.70 (0.22), residues: 1370 helix: -0.76 (0.18), residues: 754 sheet: -0.22 (1.43), residues: 10 loop : -3.25 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 564 HIS 0.005 0.001 HIS B 603 PHE 0.015 0.001 PHE A 593 TYR 0.012 0.001 TYR B 163 ARG 0.004 0.000 ARG A 568 *********************** 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 135 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1671 time to fit residues: 29.7592 Evaluate side-chains 87 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.643 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9460 ------------------------------------------------------------------------------- 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: 0.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 64 optimal weight: 0.3980 chunk 12 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 359 ASN A 393 GLN A 603 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11542 Z= 0.155 Angle : 0.643 10.166 15700 Z= 0.314 Chirality : 0.042 0.187 1776 Planarity : 0.005 0.055 1954 Dihedral : 3.975 14.996 1506 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -2.82 (0.22), residues: 1370 helix: -0.88 (0.18), residues: 760 sheet: -0.25 (1.43), residues: 10 loop : -3.28 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 564 HIS 0.008 0.001 HIS A 232 PHE 0.016 0.001 PHE A 562 TYR 0.014 0.001 TYR B 163 ARG 0.004 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 128 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1785 time to fit residues: 29.9679 Evaluate side-chains 84 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9883 ------------------------------------------------------------------------------- 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: 0.9990 chunk 125 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 95 optimal weight: 8.9990 chunk 37 optimal weight: 0.0270 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 121 optimal weight: 0.0470 chunk 80 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 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 393 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.6200 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= 0.143 Angle : 0.643 10.142 15700 Z= 0.310 Chirality : 0.042 0.190 1776 Planarity : 0.005 0.055 1954 Dihedral : 3.942 13.873 1506 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % 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: -2.78 (0.22), residues: 1370 helix: -0.83 (0.18), residues: 760 sheet: -0.36 (1.44), residues: 10 loop : -3.29 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 564 HIS 0.006 0.001 HIS B 603 PHE 0.017 0.001 PHE B 593 TYR 0.005 0.001 TYR A 290 ARG 0.003 0.000 ARG B 568 *********************** 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 128 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1538 time to fit residues: 26.5833 Evaluate side-chains 88 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9072 ------------------------------------------------------------------------------- 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: 9.9990 chunk 61 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 107 optimal weight: 0.0570 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 603 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.6789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11542 Z= 0.269 Angle : 0.770 9.294 15700 Z= 0.382 Chirality : 0.046 0.174 1776 Planarity : 0.006 0.062 1954 Dihedral : 4.733 18.475 1506 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.01 % Favored : 85.99 % 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: -3.11 (0.21), residues: 1370 helix: -1.26 (0.17), residues: 796 sheet: 0.42 (1.53), residues: 10 loop : -3.30 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 357 HIS 0.009 0.002 HIS A 232 PHE 0.021 0.002 PHE A 562 TYR 0.012 0.002 TYR A 515 ARG 0.006 0.001 ARG A 508 ********************** 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 119 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.694 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1683 time to fit residues: 26.5320 Evaluate side-chains 83 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8385 ------------------------------------------------------------------------------- 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: 0.0030 chunk 99 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- 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 603 HIS ** B 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 = 0.3596 r_free = 0.3596 target = 0.081022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066619 restraints weight = 28593.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.068300 restraints weight = 19624.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.069466 restraints weight = 14708.362| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11542 Z= 0.169 Angle : 0.693 10.852 15700 Z= 0.338 Chirality : 0.044 0.192 1776 Planarity : 0.006 0.061 1954 Dihedral : 4.421 16.703 1506 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.97 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: -2.82 (0.22), residues: 1370 helix: -1.02 (0.17), residues: 790 sheet: -0.25 (1.38), residues: 10 loop : -3.16 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 564 HIS 0.009 0.001 HIS A 232 PHE 0.027 0.001 PHE A 676 TYR 0.012 0.001 TYR A 515 ARG 0.006 0.001 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.22 seconds wall clock time: 35 minutes 10.48 seconds (2110.48 seconds total)