Starting phenix.real_space_refine on Wed Sep 25 21:52:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/09_2024/6oce_20017.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/09_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_20017/09_2024/6oce_20017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/09_2024/6oce_20017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/09_2024/6oce_20017.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oce_20017/09_2024/6oce_20017.cif" } 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. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.01, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 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: 3.01 Conformation dependent library (CDL) restraints added in 1.5 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: 1.19 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: 3.11 Time building geometry restraints manager: 3.48 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: 0.00 - 3.08: 15569 3.08 - 6.16: 117 6.16 - 9.24: 7 9.24 - 12.33: 2 12.33 - 15.41: 5 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 3.040 nonbonded pdb=" OG1 THR B 126 " pdb=" OG SER B 144 " model vdw 2.231 3.040 nonbonded pdb=" O PRO B 122 " pdb=" OG1 THR B 126 " model vdw 2.241 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.790 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.250 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- 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 : 0.641 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: 0.1905 time to fit residues: 49.0815 Evaluate side-chains 111 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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: 6.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 607 ASN B 618 GLN B 682 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.3910 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= 0.194 Angle : 0.708 7.753 15700 Z= 0.360 Chirality : 0.045 0.237 1776 Planarity : 0.006 0.070 1954 Dihedral : 3.917 19.605 1506 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.07 % Favored : 89.34 % Rotamer: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.39 % 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: -3.20 (0.21), residues: 1370 helix: -1.10 (0.18), residues: 718 sheet: 0.29 (1.80), residues: 10 loop : -3.48 (0.22), residues: 642 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 0.020 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 164 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ARG cc_start: 0.4213 (mtt90) cc_final: 0.3946 (tmm-80) REVERT: B 82 MET cc_start: 0.5864 (tpt) cc_final: 0.5654 (tpt) REVERT: B 249 LYS cc_start: 0.8041 (mttm) cc_final: 0.7601 (tmtt) REVERT: B 250 LYS cc_start: 0.8441 (pttt) cc_final: 0.8123 (pptt) REVERT: B 264 ARG cc_start: 0.3276 (mtm180) cc_final: 0.2788 (mtt180) REVERT: B 303 ASP cc_start: 0.7255 (t70) cc_final: 0.7025 (m-30) REVERT: B 358 ASN cc_start: 0.8193 (m-40) cc_final: 0.7990 (m110) REVERT: B 444 MET cc_start: 0.8206 (ptp) cc_final: 0.7461 (ptp) REVERT: B 457 GLU cc_start: 0.8467 (tt0) cc_final: 0.7342 (tm-30) REVERT: B 464 TYR cc_start: 0.8031 (t80) cc_final: 0.7382 (t80) REVERT: B 513 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7920 (mt) REVERT: B 514 THR cc_start: 0.8567 (p) cc_final: 0.8180 (t) REVERT: B 552 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6843 (mp0) REVERT: B 564 TRP cc_start: 0.6495 (m-10) cc_final: 0.6018 (m-90) REVERT: B 568 ARG cc_start: 0.8364 (ttt90) cc_final: 0.8149 (mtp-110) REVERT: B 585 LEU cc_start: 0.7995 (mt) cc_final: 0.7673 (tp) REVERT: B 631 LEU cc_start: 0.7719 (mm) cc_final: 0.7297 (mm) REVERT: B 666 LYS cc_start: 0.7478 (mmpt) cc_final: 0.6570 (pttt) REVERT: B 671 ARG cc_start: 0.6444 (ttt180) cc_final: 0.6020 (tpp-160) REVERT: B 673 GLU cc_start: 0.9136 (tp30) cc_final: 0.8863 (tp30) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1988 time to fit residues: 40.6731 Evaluate side-chains 107 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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: 7.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN B 485 GLN ** B 603 HIS ** 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: 0.6280 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11542 Z= 0.185 Angle : 0.652 7.302 15700 Z= 0.331 Chirality : 0.044 0.151 1776 Planarity : 0.005 0.054 1954 Dihedral : 4.056 17.608 1506 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.97 % Favored : 87.74 % 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: -3.10 (0.21), residues: 1370 helix: -1.02 (0.18), residues: 752 sheet: 0.03 (1.65), residues: 10 loop : -3.53 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 620 HIS 0.006 0.001 HIS B 603 PHE 0.034 0.002 PHE B 109 TYR 0.013 0.001 TYR A 598 ARG 0.004 0.000 ARG A 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 146 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 LYS cc_start: 0.8102 (mttm) cc_final: 0.7694 (tmtt) REVERT: B 343 VAL cc_start: 0.6352 (t) cc_final: 0.6099 (t) REVERT: B 379 PHE cc_start: 0.7792 (t80) cc_final: 0.7543 (t80) REVERT: B 421 ILE cc_start: 0.5538 (tt) cc_final: 0.5204 (pt) REVERT: B 444 MET cc_start: 0.8243 (ptp) cc_final: 0.7949 (ptm) REVERT: B 457 GLU cc_start: 0.8657 (tt0) cc_final: 0.7458 (tm-30) REVERT: B 464 TYR cc_start: 0.8045 (t80) cc_final: 0.7482 (t80) REVERT: B 513 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7658 (tp) REVERT: B 514 THR cc_start: 0.8517 (p) cc_final: 0.8231 (t) REVERT: B 552 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6924 (mp0) REVERT: B 564 TRP cc_start: 0.6306 (m-10) cc_final: 0.5893 (m-90) REVERT: B 581 VAL cc_start: 0.8148 (p) cc_final: 0.7843 (p) REVERT: B 585 LEU cc_start: 0.7999 (mt) cc_final: 0.7666 (tp) REVERT: B 604 GLN cc_start: 0.8338 (tp40) cc_final: 0.8125 (tp40) REVERT: B 631 LEU cc_start: 0.7971 (mm) cc_final: 0.7538 (mm) REVERT: B 671 ARG cc_start: 0.6513 (ttt180) cc_final: 0.5918 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1816 time to fit residues: 33.9826 Evaluate side-chains 110 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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: 5.9990 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 117 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11542 Z= 0.156 Angle : 0.627 6.885 15700 Z= 0.309 Chirality : 0.042 0.152 1776 Planarity : 0.005 0.053 1954 Dihedral : 4.018 16.878 1506 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.06 % 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: -0.94 (0.18), residues: 756 sheet: -0.22 (1.55), residues: 10 loop : -3.60 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 75 HIS 0.009 0.001 HIS B 603 PHE 0.015 0.001 PHE A 593 TYR 0.019 0.001 TYR B 258 ARG 0.003 0.000 ARG A 67 *********************** 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 145 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 PHE cc_start: 0.8695 (m-10) cc_final: 0.8210 (m-10) REVERT: B 247 LYS cc_start: 0.8429 (tmmt) cc_final: 0.7950 (tmtt) REVERT: B 249 LYS cc_start: 0.8240 (mttm) cc_final: 0.7778 (tmtt) REVERT: B 250 LYS cc_start: 0.8089 (pttm) cc_final: 0.7550 (tptp) REVERT: B 379 PHE cc_start: 0.7776 (t80) cc_final: 0.7494 (t80) REVERT: B 421 ILE cc_start: 0.5505 (tt) cc_final: 0.5183 (pt) REVERT: B 444 MET cc_start: 0.8420 (ptp) cc_final: 0.7634 (ptp) REVERT: B 457 GLU cc_start: 0.8541 (tt0) cc_final: 0.7308 (tm-30) REVERT: B 464 TYR cc_start: 0.8074 (t80) cc_final: 0.7493 (t80) REVERT: B 513 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7682 (mt) REVERT: B 514 THR cc_start: 0.8505 (p) cc_final: 0.8114 (t) REVERT: B 552 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6840 (mp0) REVERT: B 564 TRP cc_start: 0.6326 (m-10) cc_final: 0.5970 (m-90) REVERT: B 579 TYR cc_start: 0.6732 (m-80) cc_final: 0.6513 (m-10) REVERT: B 581 VAL cc_start: 0.8259 (p) cc_final: 0.7931 (p) REVERT: B 585 LEU cc_start: 0.7965 (mt) cc_final: 0.7607 (tp) REVERT: B 604 GLN cc_start: 0.8445 (tp40) cc_final: 0.8064 (tp40) REVERT: B 631 LEU cc_start: 0.8006 (mm) cc_final: 0.7653 (mm) REVERT: B 671 ARG cc_start: 0.6506 (ttt180) cc_final: 0.5885 (tpp-160) REVERT: B 673 GLU cc_start: 0.9035 (tp30) cc_final: 0.8757 (tp30) REVERT: B 676 PHE cc_start: 0.8075 (t80) cc_final: 0.7845 (t80) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1983 time to fit residues: 37.6963 Evaluate side-chains 110 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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: 9.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 33 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN B 393 GLN B 618 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11542 Z= 0.214 Angle : 0.655 6.892 15700 Z= 0.326 Chirality : 0.042 0.152 1776 Planarity : 0.006 0.123 1954 Dihedral : 4.149 18.514 1506 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % 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: -2.78 (0.22), residues: 1370 helix: -0.75 (0.18), residues: 748 sheet: 0.42 (1.67), residues: 10 loop : -3.38 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 620 HIS 0.003 0.001 HIS B 603 PHE 0.015 0.001 PHE B 364 TYR 0.009 0.001 TYR B 613 ARG 0.008 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 135 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 THR cc_start: 0.8155 (p) cc_final: 0.7796 (p) REVERT: B 241 LEU cc_start: 0.8245 (mm) cc_final: 0.7753 (pt) REVERT: B 249 LYS cc_start: 0.8207 (mttm) cc_final: 0.7718 (tmtt) REVERT: B 379 PHE cc_start: 0.7772 (t80) cc_final: 0.7506 (t80) REVERT: B 444 MET cc_start: 0.8417 (ptp) cc_final: 0.7648 (ptp) REVERT: B 457 GLU cc_start: 0.8563 (tt0) cc_final: 0.7415 (tm-30) REVERT: B 464 TYR cc_start: 0.8030 (t80) cc_final: 0.7408 (t80) REVERT: B 479 THR cc_start: 0.7904 (p) cc_final: 0.7667 (p) REVERT: B 513 ILE cc_start: 0.8264 (mp) cc_final: 0.7947 (mp) REVERT: B 514 THR cc_start: 0.8516 (p) cc_final: 0.8205 (t) REVERT: B 552 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6999 (mp0) REVERT: B 564 TRP cc_start: 0.6307 (m-10) cc_final: 0.5838 (m-90) REVERT: B 579 TYR cc_start: 0.6824 (m-80) cc_final: 0.6592 (m-10) REVERT: B 585 LEU cc_start: 0.7954 (mt) cc_final: 0.7611 (tp) REVERT: B 604 GLN cc_start: 0.8387 (tp40) cc_final: 0.8072 (tp40) REVERT: B 631 LEU cc_start: 0.8072 (mm) cc_final: 0.7676 (mm) REVERT: B 673 GLU cc_start: 0.9111 (tp30) cc_final: 0.8865 (tp30) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1664 time to fit residues: 29.7400 Evaluate side-chains 100 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 0.0670 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 20.0000 chunk 126 optimal weight: 0.4980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN B 603 HIS B 618 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.5644 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= 0.154 Angle : 0.617 6.737 15700 Z= 0.305 Chirality : 0.042 0.149 1776 Planarity : 0.005 0.054 1954 Dihedral : 4.108 16.451 1506 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -2.80 (0.22), residues: 1370 helix: -0.85 (0.18), residues: 774 sheet: -0.09 (1.53), residues: 10 loop : -3.35 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.003 0.001 HIS A 225 PHE 0.017 0.001 PHE B 593 TYR 0.007 0.001 TYR A 703 ARG 0.006 0.000 ARG A 508 *********************** 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 139 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 PRO cc_start: 0.6923 (Cg_exo) cc_final: 0.6681 (Cg_endo) REVERT: B 241 LEU cc_start: 0.8341 (mm) cc_final: 0.7664 (pt) REVERT: B 247 LYS cc_start: 0.8415 (tmmt) cc_final: 0.7869 (tmtt) REVERT: B 249 LYS cc_start: 0.8174 (mttm) cc_final: 0.7726 (tmtt) REVERT: B 250 LYS cc_start: 0.7949 (pttm) cc_final: 0.7401 (tptp) REVERT: B 387 ILE cc_start: 0.8362 (pt) cc_final: 0.8162 (tp) REVERT: B 457 GLU cc_start: 0.8400 (tt0) cc_final: 0.7247 (tm-30) REVERT: B 464 TYR cc_start: 0.8072 (t80) cc_final: 0.7522 (t80) REVERT: B 514 THR cc_start: 0.8480 (p) cc_final: 0.8141 (t) REVERT: B 552 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6769 (mp0) REVERT: B 564 TRP cc_start: 0.6323 (m-10) cc_final: 0.5843 (m-90) REVERT: B 579 TYR cc_start: 0.6862 (m-80) cc_final: 0.6520 (m-10) REVERT: B 581 VAL cc_start: 0.8378 (p) cc_final: 0.8069 (p) REVERT: B 585 LEU cc_start: 0.7949 (mt) cc_final: 0.7599 (tp) REVERT: B 631 LEU cc_start: 0.8092 (mm) cc_final: 0.7749 (mm) REVERT: B 650 THR cc_start: 0.7497 (p) cc_final: 0.7025 (p) REVERT: B 671 ARG cc_start: 0.6648 (ttt180) cc_final: 0.5817 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1645 time to fit residues: 30.0809 Evaluate side-chains 102 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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: 8.9990 chunk 74 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 0.0000 chunk 82 optimal weight: 8.9990 chunk 79 optimal weight: 0.0370 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 52 optimal weight: 0.0570 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.5756 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= 0.149 Angle : 0.618 6.896 15700 Z= 0.304 Chirality : 0.042 0.148 1776 Planarity : 0.005 0.053 1954 Dihedral : 4.079 17.027 1506 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % 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: -2.68 (0.22), residues: 1370 helix: -0.77 (0.18), residues: 776 sheet: -0.25 (1.38), residues: 10 loop : -3.26 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.008 0.001 HIS B 232 PHE 0.018 0.001 PHE B 109 TYR 0.009 0.001 TYR B 579 ARG 0.004 0.000 ARG B 678 *********************** 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 140 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 THR cc_start: 0.8285 (p) cc_final: 0.7621 (p) REVERT: B 241 LEU cc_start: 0.8114 (mm) cc_final: 0.7792 (pt) REVERT: B 247 LYS cc_start: 0.8418 (tmmt) cc_final: 0.7875 (tmtt) REVERT: B 249 LYS cc_start: 0.8152 (mttm) cc_final: 0.7771 (tmtt) REVERT: B 250 LYS cc_start: 0.7965 (pttm) cc_final: 0.7408 (tptp) REVERT: B 280 PHE cc_start: 0.5728 (m-80) cc_final: 0.5050 (t80) REVERT: B 457 GLU cc_start: 0.8415 (tt0) cc_final: 0.7374 (tm-30) REVERT: B 464 TYR cc_start: 0.8168 (t80) cc_final: 0.7573 (t80) REVERT: B 514 THR cc_start: 0.8664 (p) cc_final: 0.8290 (t) REVERT: B 516 VAL cc_start: 0.8197 (t) cc_final: 0.7853 (p) REVERT: B 552 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6936 (mp0) REVERT: B 564 TRP cc_start: 0.6372 (m-10) cc_final: 0.5928 (m-90) REVERT: B 579 TYR cc_start: 0.6828 (m-80) cc_final: 0.6534 (m-10) REVERT: B 581 VAL cc_start: 0.8384 (p) cc_final: 0.8095 (p) REVERT: B 585 LEU cc_start: 0.8019 (mt) cc_final: 0.7710 (tp) REVERT: B 604 GLN cc_start: 0.8284 (tp40) cc_final: 0.8074 (tp40) REVERT: B 631 LEU cc_start: 0.8038 (mm) cc_final: 0.7619 (mm) REVERT: B 671 ARG cc_start: 0.6417 (ttt180) cc_final: 0.5880 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1652 time to fit residues: 30.8638 Evaluate side-chains 103 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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: 0.0370 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 0.3980 chunk 125 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.5934 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= 0.144 Angle : 0.616 6.915 15700 Z= 0.300 Chirality : 0.041 0.148 1776 Planarity : 0.005 0.062 1954 Dihedral : 4.012 16.630 1506 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -0.64 (0.18), residues: 750 sheet: -0.50 (1.28), residues: 10 loop : -3.31 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 344 HIS 0.003 0.001 HIS B 232 PHE 0.018 0.001 PHE A 593 TYR 0.019 0.001 TYR A 98 ARG 0.003 0.000 ARG B 678 *********************** 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 137 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 LEU cc_start: 0.7882 (mm) cc_final: 0.7488 (pt) REVERT: B 247 LYS cc_start: 0.8345 (tmmt) cc_final: 0.7842 (tmtt) REVERT: B 249 LYS cc_start: 0.8144 (mttm) cc_final: 0.7790 (tmtt) REVERT: B 250 LYS cc_start: 0.8043 (pttm) cc_final: 0.7396 (tptp) REVERT: B 280 PHE cc_start: 0.5724 (m-80) cc_final: 0.5064 (t80) REVERT: B 457 GLU cc_start: 0.8370 (tt0) cc_final: 0.7436 (tm-30) REVERT: B 464 TYR cc_start: 0.8122 (t80) cc_final: 0.7552 (t80) REVERT: B 513 ILE cc_start: 0.8006 (mm) cc_final: 0.7713 (mm) REVERT: B 514 THR cc_start: 0.8662 (p) cc_final: 0.8311 (t) REVERT: B 515 TYR cc_start: 0.7343 (t80) cc_final: 0.7091 (t80) REVERT: B 552 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6927 (mp0) REVERT: B 564 TRP cc_start: 0.6406 (m-10) cc_final: 0.5988 (m-90) REVERT: B 579 TYR cc_start: 0.6823 (m-80) cc_final: 0.6527 (m-10) REVERT: B 581 VAL cc_start: 0.8394 (p) cc_final: 0.8118 (p) REVERT: B 585 LEU cc_start: 0.7988 (mt) cc_final: 0.7696 (tp) REVERT: B 604 GLN cc_start: 0.8484 (tp40) cc_final: 0.8214 (tp40) REVERT: B 631 LEU cc_start: 0.8007 (mm) cc_final: 0.7623 (mm) REVERT: B 671 ARG cc_start: 0.6450 (ttt180) cc_final: 0.5812 (tpt170) REVERT: B 673 GLU cc_start: 0.9041 (tp30) cc_final: 0.8832 (tp30) REVERT: B 709 LEU cc_start: 0.7791 (mt) cc_final: 0.7433 (mp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1548 time to fit residues: 28.1763 Evaluate side-chains 108 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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: 0.0570 chunk 125 optimal weight: 0.3980 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 0.1980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.1980 chunk 80 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.5991 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 : 0.625 6.906 15700 Z= 0.301 Chirality : 0.042 0.150 1776 Planarity : 0.005 0.053 1954 Dihedral : 3.931 16.000 1506 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % 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: -2.58 (0.22), residues: 1370 helix: -0.59 (0.18), residues: 754 sheet: -0.50 (1.27), residues: 10 loop : -3.30 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 344 HIS 0.003 0.001 HIS A 225 PHE 0.019 0.001 PHE B 364 TYR 0.020 0.001 TYR A 98 ARG 0.003 0.000 ARG A 678 *********************** 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 148 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 THR cc_start: 0.7847 (p) cc_final: 0.7315 (p) REVERT: A 241 LEU cc_start: 0.7648 (mm) cc_final: 0.6998 (pt) REVERT: A 249 LYS cc_start: 0.8220 (mttm) cc_final: 0.7934 (tmtt) REVERT: A 280 PHE cc_start: 0.5379 (m-80) cc_final: 0.4961 (t80) REVERT: A 285 ASP cc_start: 0.7571 (m-30) cc_final: 0.7275 (m-30) REVERT: A 444 MET cc_start: 0.8249 (ptp) cc_final: 0.7521 (ptp) REVERT: A 457 GLU cc_start: 0.8524 (tt0) cc_final: 0.7378 (tm-30) REVERT: A 464 TYR cc_start: 0.8089 (t80) cc_final: 0.7462 (t80) REVERT: A 513 ILE cc_start: 0.7956 (mm) cc_final: 0.7576 (mm) REVERT: A 514 THR cc_start: 0.8579 (p) cc_final: 0.8230 (t) REVERT: A 516 VAL cc_start: 0.8409 (t) cc_final: 0.8083 (p) REVERT: A 552 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7048 (mp0) REVERT: A 555 MET cc_start: 0.4085 (mpp) cc_final: 0.3654 (mpp) REVERT: A 579 TYR cc_start: 0.6813 (m-80) cc_final: 0.6541 (m-10) REVERT: A 581 VAL cc_start: 0.8376 (p) cc_final: 0.8077 (p) REVERT: A 585 LEU cc_start: 0.8006 (mt) cc_final: 0.7727 (tp) REVERT: A 604 GLN cc_start: 0.8398 (tp40) cc_final: 0.8098 (tp40) REVERT: A 631 LEU cc_start: 0.8103 (mm) cc_final: 0.7829 (mm) REVERT: A 671 ARG cc_start: 0.6639 (ttt180) cc_final: 0.5726 (tpp-160) REVERT: A 672 PHE cc_start: 0.6616 (m-80) cc_final: 0.6029 (m-10) REVERT: A 673 GLU cc_start: 0.8961 (tp30) cc_final: 0.8755 (tp30) REVERT: A 709 LEU cc_start: 0.7503 (mt) cc_final: 0.7251 (mp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1804 time to fit residues: 34.2519 Evaluate side-chains 108 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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: 6.9990 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 0.0040 chunk 114 optimal weight: 7.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11542 Z= 0.152 Angle : 0.642 6.931 15700 Z= 0.307 Chirality : 0.042 0.148 1776 Planarity : 0.005 0.053 1954 Dihedral : 3.921 15.193 1506 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % 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: -2.63 (0.22), residues: 1370 helix: -0.64 (0.18), residues: 754 sheet: -0.44 (1.25), residues: 10 loop : -3.31 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 357 HIS 0.012 0.001 HIS A 232 PHE 0.015 0.001 PHE B 593 TYR 0.018 0.001 TYR B 98 ARG 0.003 0.000 ARG B 678 ********************** 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 136 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TRP cc_start: 0.5714 (t-100) cc_final: 0.5498 (t-100) REVERT: A 241 LEU cc_start: 0.7667 (mm) cc_final: 0.7172 (pt) REVERT: A 249 LYS cc_start: 0.8182 (mttm) cc_final: 0.7965 (tmtt) REVERT: A 250 LYS cc_start: 0.8104 (pttm) cc_final: 0.7550 (tptp) REVERT: A 280 PHE cc_start: 0.5387 (m-80) cc_final: 0.4972 (t80) REVERT: A 285 ASP cc_start: 0.7563 (m-30) cc_final: 0.7326 (m-30) REVERT: A 444 MET cc_start: 0.8263 (ptp) cc_final: 0.7524 (ptp) REVERT: A 457 GLU cc_start: 0.8528 (tt0) cc_final: 0.7561 (tm-30) REVERT: A 464 TYR cc_start: 0.8125 (t80) cc_final: 0.7477 (t80) REVERT: A 514 THR cc_start: 0.8563 (p) cc_final: 0.8223 (t) REVERT: A 515 TYR cc_start: 0.7378 (t80) cc_final: 0.7139 (t80) REVERT: A 516 VAL cc_start: 0.8437 (t) cc_final: 0.7992 (p) REVERT: A 552 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7052 (mp0) REVERT: A 555 MET cc_start: 0.3847 (mpp) cc_final: 0.3440 (mpp) REVERT: A 579 TYR cc_start: 0.6795 (m-80) cc_final: 0.6469 (m-10) REVERT: A 581 VAL cc_start: 0.8382 (p) cc_final: 0.8095 (p) REVERT: A 585 LEU cc_start: 0.7996 (mt) cc_final: 0.7710 (tp) REVERT: A 604 GLN cc_start: 0.8408 (tp40) cc_final: 0.8109 (tp40) REVERT: A 631 LEU cc_start: 0.8077 (mm) cc_final: 0.7721 (mm) REVERT: A 671 ARG cc_start: 0.6338 (ttt180) cc_final: 0.5799 (tpp-160) REVERT: A 709 LEU cc_start: 0.7503 (mt) cc_final: 0.7262 (mp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1687 time to fit residues: 30.3080 Evaluate side-chains 101 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 0.0370 chunk 99 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.083612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070037 restraints weight = 27293.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.071727 restraints weight = 18860.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.072837 restraints weight = 14040.525| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11542 Z= 0.153 Angle : 0.647 11.462 15700 Z= 0.306 Chirality : 0.042 0.147 1776 Planarity : 0.005 0.058 1954 Dihedral : 3.937 15.068 1506 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.78 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: -2.58 (0.22), residues: 1370 helix: -0.58 (0.18), residues: 756 sheet: -1.46 (0.96), residues: 20 loop : -3.33 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 357 HIS 0.003 0.001 HIS A 225 PHE 0.014 0.001 PHE B 593 TYR 0.016 0.001 TYR A 98 ARG 0.002 0.000 ARG A 678 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.62 seconds wall clock time: 34 minutes 17.94 seconds (2057.94 seconds total)