Starting phenix.real_space_refine on Fri Sep 11 20:00:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oce_20017/09_2026/6oce_20017.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oce_20017/09_2026/6oce_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 { model { file = "/net/cci-nas-00/data/ceres_data/6oce_20017/09_2026/6oce_20017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oce_20017/09_2026/6oce_20017.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oce_20017/09_2026/6oce_20017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oce_20017/09_2026/6oce_20017.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 2.29, per 1000 atoms: 0.20 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: 0.79 Conformation dependent library (CDL) restraints added in 499.3 milliseconds 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: 0.29 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: 1.52 Time building geometry restraints manager: 1.04 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: 0.02 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: 1.130 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 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= 0.274 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 305 TYR 0.006 0.001 TYR A 464 PHE 0.027 0.001 PHE B 593 TRP 0.003 0.000 TRP A 42 HIS 0.019 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.27 (11542) covalent geometry : angle 0.73199 / 0.46 (15700) hydrogen bonds : bond 0.21994 / 13.75 ( 464) hydrogen bonds : angle 6.78437 / 4.67 ( 1347) *********************** 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 to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.160 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: 0.6802 (p) cc_final: 0.6499 (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: 0.7429 (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: 0.7439 (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: 0.0748 time to fit residues: 19.7126 Evaluate side-chains 111 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.0010 chunk 55 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 HIS A 422 GLN A 538 HIS A 570 GLN A 604 GLN A 607 ASN A 618 GLN A 682 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.086745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072979 restraints weight = 26460.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074653 restraints weight = 18653.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.075885 restraints weight = 14075.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.076734 restraints weight = 11227.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077428 restraints weight = 9433.854| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11542 Z= 0.144 Angle : 0.713 7.830 15700 Z= 0.361 Chirality : 0.045 0.234 1776 Planarity : 0.006 0.066 1954 Dihedral : 3.936 19.670 1506 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.07 % Favored : 89.34 % Rotamer: Outliers : 0.16 % Allowed : 2.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.21), residues: 1370 helix: -1.13 (0.18), residues: 724 sheet: 0.13 (1.78), residues: 10 loop : -3.53 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 508 TYR 0.011 0.001 TYR A 601 PHE 0.022 0.001 PHE B 698 TRP 0.020 0.001 TRP B 75 HIS 0.007 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (11542) covalent geometry : angle 0.71256 / 0.36 (15700) hydrogen bonds : bond 0.04714 / 3.04 ( 464) hydrogen bonds : angle 4.39945 / 3.11 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 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 155 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.4975 (ttp) cc_final: 0.4639 (ttt) REVERT: A 67 ARG cc_start: 0.4454 (mtt90) cc_final: 0.3950 (tmm-80) REVERT: A 87 LEU cc_start: 0.7272 (mt) cc_final: 0.6869 (mt) REVERT: A 205 ILE cc_start: 0.8889 (mp) cc_final: 0.8520 (mp) REVERT: A 249 LYS cc_start: 0.8010 (mttm) cc_final: 0.7533 (tmtt) REVERT: A 250 LYS cc_start: 0.8468 (pttt) cc_final: 0.8198 (pptt) REVERT: A 303 ASP cc_start: 0.7160 (t70) cc_final: 0.6927 (m-30) REVERT: A 344 TRP cc_start: 0.7780 (m100) cc_final: 0.6778 (m-10) REVERT: A 379 PHE cc_start: 0.7485 (t80) cc_final: 0.7195 (t80) REVERT: A 431 LYS cc_start: 0.4605 (pttt) cc_final: 0.4229 (pttp) REVERT: A 457 GLU cc_start: 0.8375 (tt0) cc_final: 0.7319 (tm-30) REVERT: A 464 TYR cc_start: 0.7820 (t80) cc_final: 0.7086 (t80) REVERT: A 513 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7634 (mt) REVERT: A 514 THR cc_start: 0.8331 (p) cc_final: 0.7891 (t) REVERT: A 552 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6911 (mp0) REVERT: A 564 TRP cc_start: 0.6303 (m-10) cc_final: 0.6040 (m-90) REVERT: A 568 ARG cc_start: 0.8366 (ttt90) cc_final: 0.8118 (mtp-110) REVERT: A 585 LEU cc_start: 0.7982 (mt) cc_final: 0.7682 (tp) REVERT: A 598 TYR cc_start: 0.8065 (t80) cc_final: 0.7855 (t80) REVERT: A 631 LEU cc_start: 0.7706 (mm) cc_final: 0.7214 (mm) REVERT: A 671 ARG cc_start: 0.6394 (ttt180) cc_final: 0.5845 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.0807 time to fit residues: 16.0307 Evaluate side-chains 103 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 115 optimal weight: 1.9990 chunk 114 optimal weight: 0.0170 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.0870 chunk 82 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN A 485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.086289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072459 restraints weight = 27120.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.074092 restraints weight = 19384.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075319 restraints weight = 14787.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.076096 restraints weight = 11889.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.076785 restraints weight = 10113.322| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.4589 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= 0.124 Angle : 0.663 8.441 15700 Z= 0.339 Chirality : 0.044 0.217 1776 Planarity : 0.006 0.065 1954 Dihedral : 4.155 21.809 1506 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.22 % Favored : 89.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.22), residues: 1370 helix: -0.70 (0.19), residues: 750 sheet: 0.64 (1.88), residues: 10 loop : -3.50 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 305 TYR 0.021 0.001 TYR A 258 PHE 0.034 0.001 PHE B 109 TRP 0.010 0.001 TRP A 620 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11542) covalent geometry : angle 0.66339 / 0.34 (15700) hydrogen bonds : bond 0.04181 / 2.70 ( 464) hydrogen bonds : angle 4.11666 / 2.86 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 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 157 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 TYR cc_start: 0.5797 (m-80) cc_final: 0.5579 (m-80) REVERT: B 156 VAL cc_start: 0.7383 (t) cc_final: 0.7174 (p) REVERT: B 201 LEU cc_start: 0.7460 (pp) cc_final: 0.6631 (pp) REVERT: B 249 LYS cc_start: 0.8217 (mttm) cc_final: 0.7829 (tmtt) REVERT: B 379 PHE cc_start: 0.7685 (t80) cc_final: 0.7132 (t80) REVERT: B 380 PHE cc_start: 0.7233 (m-80) cc_final: 0.6759 (m-80) REVERT: B 444 MET cc_start: 0.8076 (ptp) cc_final: 0.7283 (ptp) REVERT: B 457 GLU cc_start: 0.8475 (tt0) cc_final: 0.7383 (tm-30) REVERT: B 464 TYR cc_start: 0.7959 (t80) cc_final: 0.7313 (t80) REVERT: B 513 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7256 (tp) REVERT: B 514 THR cc_start: 0.8451 (p) cc_final: 0.8173 (t) REVERT: B 552 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7046 (mp0) REVERT: B 581 VAL cc_start: 0.8084 (p) cc_final: 0.7698 (p) REVERT: B 585 LEU cc_start: 0.8013 (mt) cc_final: 0.7718 (tp) REVERT: B 604 GLN cc_start: 0.8426 (tp40) cc_final: 0.8023 (tp40) REVERT: B 631 LEU cc_start: 0.8043 (mm) cc_final: 0.7593 (mm) REVERT: B 663 TRP cc_start: 0.8300 (t-100) cc_final: 0.7911 (t-100) REVERT: B 666 LYS cc_start: 0.7261 (mmpt) cc_final: 0.6491 (pttt) REVERT: B 671 ARG cc_start: 0.6268 (ttt180) cc_final: 0.5879 (tpp-160) REVERT: B 709 LEU cc_start: 0.7569 (mt) cc_final: 0.7351 (mt) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.0755 time to fit residues: 15.3083 Evaluate side-chains 107 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 106 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 101 optimal weight: 0.0170 chunk 46 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 306 GLN B 393 GLN B 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.086191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.073242 restraints weight = 26981.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.074840 restraints weight = 18900.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076005 restraints weight = 14281.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076804 restraints weight = 11428.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.077457 restraints weight = 9695.016| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11542 Z= 0.121 Angle : 0.661 7.010 15700 Z= 0.330 Chirality : 0.043 0.168 1776 Planarity : 0.006 0.078 1954 Dihedral : 4.067 18.737 1506 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.66 % Favored : 89.20 % Rotamer: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.22), residues: 1370 helix: -0.49 (0.19), residues: 764 sheet: 1.38 (2.09), residues: 10 loop : -3.63 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 508 TYR 0.008 0.001 TYR A 579 PHE 0.025 0.001 PHE B 594 TRP 0.025 0.001 TRP B 564 HIS 0.002 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (11542) covalent geometry : angle 0.66091 / 0.33 (15700) hydrogen bonds : bond 0.03792 / 2.46 ( 464) hydrogen bonds : angle 4.04068 / 2.79 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 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 145 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 THR cc_start: 0.8069 (p) cc_final: 0.7758 (p) REVERT: B 156 VAL cc_start: 0.7435 (t) cc_final: 0.7205 (p) REVERT: B 166 THR cc_start: 0.8105 (p) cc_final: 0.7703 (p) REVERT: B 167 PHE cc_start: 0.8552 (m-10) cc_final: 0.8330 (m-10) REVERT: B 170 CYS cc_start: 0.8839 (m) cc_final: 0.8393 (m) REVERT: B 249 LYS cc_start: 0.8238 (mttm) cc_final: 0.7852 (tmtt) REVERT: B 250 LYS cc_start: 0.8081 (pttm) cc_final: 0.7500 (tptp) REVERT: B 343 VAL cc_start: 0.6618 (t) cc_final: 0.6361 (t) REVERT: B 457 GLU cc_start: 0.8498 (tt0) cc_final: 0.7386 (tm-30) REVERT: B 464 TYR cc_start: 0.8000 (t80) cc_final: 0.7472 (t80) REVERT: B 479 THR cc_start: 0.7826 (p) cc_final: 0.7612 (p) REVERT: B 513 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7558 (mt) REVERT: B 514 THR cc_start: 0.8426 (p) cc_final: 0.8048 (t) REVERT: B 552 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6812 (mp0) REVERT: B 581 VAL cc_start: 0.8254 (p) cc_final: 0.7878 (p) REVERT: B 585 LEU cc_start: 0.8002 (mt) cc_final: 0.7721 (tp) REVERT: B 604 GLN cc_start: 0.8376 (tp40) cc_final: 0.7969 (tp40) REVERT: B 631 LEU cc_start: 0.8039 (mm) cc_final: 0.7609 (mm) REVERT: B 663 TRP cc_start: 0.8333 (t-100) cc_final: 0.7829 (t60) REVERT: B 666 LYS cc_start: 0.7302 (mmpt) cc_final: 0.6515 (pttt) REVERT: B 671 ARG cc_start: 0.6153 (ttt180) cc_final: 0.5917 (tpp-160) REVERT: B 676 PHE cc_start: 0.8331 (t80) cc_final: 0.8013 (t80) REVERT: B 709 LEU cc_start: 0.7517 (mt) cc_final: 0.7160 (mp) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.0714 time to fit residues: 13.4297 Evaluate side-chains 112 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 121 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 113 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 80 optimal weight: 0.0370 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 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 = 0.3660 r_free = 0.3660 target = 0.085193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071919 restraints weight = 27384.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073580 restraints weight = 18869.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.074808 restraints weight = 14077.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.075738 restraints weight = 11186.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076397 restraints weight = 9217.259| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11542 Z= 0.119 Angle : 0.643 7.016 15700 Z= 0.319 Chirality : 0.043 0.160 1776 Planarity : 0.005 0.056 1954 Dihedral : 4.167 18.040 1506 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.23), residues: 1370 helix: -0.34 (0.19), residues: 770 sheet: 1.86 (2.20), residues: 10 loop : -3.46 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 508 TYR 0.008 0.001 TYR A 150 PHE 0.014 0.001 PHE B 593 TRP 0.015 0.001 TRP A 564 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (11542) covalent geometry : angle 0.64261 / 0.32 (15700) hydrogen bonds : bond 0.03588 / 2.38 ( 464) hydrogen bonds : angle 3.90234 / 2.76 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 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 145 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 VAL cc_start: 0.7502 (t) cc_final: 0.7260 (p) REVERT: B 166 THR cc_start: 0.8241 (p) cc_final: 0.7676 (p) REVERT: B 170 CYS cc_start: 0.8704 (m) cc_final: 0.8429 (m) REVERT: B 249 LYS cc_start: 0.8256 (mttm) cc_final: 0.7946 (tmtt) REVERT: B 250 LYS cc_start: 0.8041 (pttm) cc_final: 0.7416 (tptp) REVERT: B 295 GLU cc_start: 0.8303 (mp0) cc_final: 0.8012 (mp0) REVERT: B 457 GLU cc_start: 0.8524 (tt0) cc_final: 0.7471 (tm-30) REVERT: B 464 TYR cc_start: 0.7961 (t80) cc_final: 0.7410 (t80) REVERT: B 479 THR cc_start: 0.7789 (p) cc_final: 0.7531 (p) REVERT: B 513 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7338 (mt) REVERT: B 514 THR cc_start: 0.8418 (p) cc_final: 0.8197 (t) REVERT: B 534 LEU cc_start: 0.9053 (tp) cc_final: 0.8810 (tp) REVERT: B 552 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6852 (mp0) REVERT: B 581 VAL cc_start: 0.8269 (p) cc_final: 0.7921 (p) REVERT: B 585 LEU cc_start: 0.7988 (mt) cc_final: 0.7706 (tp) REVERT: B 631 LEU cc_start: 0.8030 (mm) cc_final: 0.7689 (mm) REVERT: B 663 TRP cc_start: 0.8297 (t-100) cc_final: 0.7817 (t60) REVERT: B 666 LYS cc_start: 0.7067 (mmpt) cc_final: 0.6424 (pttt) REVERT: B 671 ARG cc_start: 0.6334 (ttt180) cc_final: 0.5854 (tpp-160) REVERT: B 676 PHE cc_start: 0.8412 (t80) cc_final: 0.8034 (t80) REVERT: B 709 LEU cc_start: 0.7685 (mt) cc_final: 0.7345 (mp) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.0686 time to fit residues: 12.7919 Evaluate side-chains 106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 35 optimal weight: 0.7980 chunk 85 optimal weight: 0.0170 chunk 72 optimal weight: 0.0370 chunk 68 optimal weight: 20.0000 chunk 124 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 89 optimal weight: 0.0030 chunk 40 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 overall best weight: 0.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.072959 restraints weight = 26904.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074603 restraints weight = 18793.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.075801 restraints weight = 14147.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.076665 restraints weight = 11277.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077370 restraints weight = 9343.227| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11542 Z= 0.117 Angle : 0.632 6.698 15700 Z= 0.312 Chirality : 0.043 0.179 1776 Planarity : 0.005 0.051 1954 Dihedral : 4.139 17.394 1506 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.23), residues: 1370 helix: -0.22 (0.19), residues: 780 sheet: 1.96 (2.21), residues: 10 loop : -3.43 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 678 TYR 0.018 0.001 TYR B 258 PHE 0.017 0.001 PHE A 593 TRP 0.014 0.001 TRP B 564 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (11542) covalent geometry : angle 0.63227 / 0.31 (15700) hydrogen bonds : bond 0.03356 / 2.26 ( 464) hydrogen bonds : angle 4.00208 / 2.84 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 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 150 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 THR cc_start: 0.8236 (p) cc_final: 0.7660 (p) REVERT: B 170 CYS cc_start: 0.8440 (m) cc_final: 0.8138 (m) REVERT: B 249 LYS cc_start: 0.8265 (mttm) cc_final: 0.7991 (tmtt) REVERT: B 250 LYS cc_start: 0.8076 (pttm) cc_final: 0.7861 (pptt) REVERT: B 457 GLU cc_start: 0.8489 (tt0) cc_final: 0.7385 (tm-30) REVERT: B 464 TYR cc_start: 0.7965 (t80) cc_final: 0.7440 (t80) REVERT: B 479 THR cc_start: 0.7750 (p) cc_final: 0.7530 (p) REVERT: B 552 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7073 (mp0) REVERT: B 564 TRP cc_start: 0.7233 (m-90) cc_final: 0.6939 (m-90) REVERT: B 581 VAL cc_start: 0.8290 (p) cc_final: 0.7918 (p) REVERT: B 585 LEU cc_start: 0.8020 (mt) cc_final: 0.7710 (tp) REVERT: B 604 GLN cc_start: 0.8530 (tp40) cc_final: 0.8203 (tp40) REVERT: B 631 LEU cc_start: 0.7958 (mm) cc_final: 0.7658 (mm) REVERT: B 663 TRP cc_start: 0.8291 (t-100) cc_final: 0.7815 (t60) REVERT: B 666 LYS cc_start: 0.7091 (mmpt) cc_final: 0.6404 (pttt) REVERT: B 671 ARG cc_start: 0.6402 (ttt180) cc_final: 0.5957 (tpt170) REVERT: B 673 GLU cc_start: 0.8830 (tp30) cc_final: 0.8545 (tp30) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0604 time to fit residues: 12.1597 Evaluate side-chains 114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 9 optimal weight: 0.0980 chunk 132 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 1 optimal weight: 20.0000 overall best weight: 2.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 393 GLN ** B 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.081847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068942 restraints weight = 28086.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070538 restraints weight = 19362.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.071695 restraints weight = 14442.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072381 restraints weight = 11446.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.072700 restraints weight = 9711.062| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11542 Z= 0.129 Angle : 0.648 6.940 15700 Z= 0.323 Chirality : 0.043 0.157 1776 Planarity : 0.005 0.053 1954 Dihedral : 4.257 17.969 1506 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.16 % Allowed : 0.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.23), residues: 1370 helix: 0.04 (0.19), residues: 774 sheet: 2.12 (2.32), residues: 10 loop : -3.14 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 508 TYR 0.010 0.001 TYR B 515 PHE 0.014 0.001 PHE B 562 TRP 0.016 0.002 TRP A 168 HIS 0.010 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11542) covalent geometry : angle 0.64847 / 0.32 (15700) hydrogen bonds : bond 0.03340 / 2.25 ( 464) hydrogen bonds : angle 4.02491 / 2.87 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 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 150 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.7818 (mtm) cc_final: 0.7132 (mmm) REVERT: B 82 MET cc_start: 0.6568 (tpt) cc_final: 0.6168 (tpp) REVERT: B 86 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7683 (tp30) REVERT: B 102 TYR cc_start: 0.5758 (m-80) cc_final: 0.5493 (m-80) REVERT: B 156 VAL cc_start: 0.7671 (t) cc_final: 0.7459 (p) REVERT: B 167 PHE cc_start: 0.8574 (m-10) cc_final: 0.8010 (m-80) REVERT: B 241 LEU cc_start: 0.8046 (mm) cc_final: 0.7688 (pt) REVERT: B 249 LYS cc_start: 0.8205 (mttm) cc_final: 0.7818 (tmtt) REVERT: B 280 PHE cc_start: 0.5644 (m-80) cc_final: 0.4976 (t80) REVERT: B 457 GLU cc_start: 0.8420 (tt0) cc_final: 0.7402 (tm-30) REVERT: B 464 TYR cc_start: 0.7878 (t80) cc_final: 0.7313 (t80) REVERT: B 552 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6716 (mp0) REVERT: B 585 LEU cc_start: 0.7970 (mt) cc_final: 0.7683 (tp) REVERT: B 631 LEU cc_start: 0.8052 (mm) cc_final: 0.7720 (mm) REVERT: B 663 TRP cc_start: 0.8252 (t-100) cc_final: 0.7759 (t60) REVERT: B 666 LYS cc_start: 0.7227 (mmpt) cc_final: 0.6385 (pttt) REVERT: B 671 ARG cc_start: 0.6297 (ttt180) cc_final: 0.5751 (tpp-160) REVERT: B 676 PHE cc_start: 0.8023 (t80) cc_final: 0.7704 (t80) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.0688 time to fit residues: 13.6148 Evaluate side-chains 100 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 chunk 118 optimal weight: 0.0980 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 393 GLN ** B 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.082878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.069585 restraints weight = 27216.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071229 restraints weight = 18778.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072447 restraints weight = 13991.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073351 restraints weight = 11105.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.074031 restraints weight = 9235.772| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11542 Z= 0.117 Angle : 0.660 6.901 15700 Z= 0.328 Chirality : 0.043 0.190 1776 Planarity : 0.005 0.055 1954 Dihedral : 4.162 17.248 1506 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.23), residues: 1370 helix: 0.07 (0.19), residues: 784 sheet: 1.96 (2.29), residues: 10 loop : -3.21 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 508 TYR 0.018 0.001 TYR A 98 PHE 0.020 0.001 PHE B 364 TRP 0.013 0.001 TRP B 620 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11542) covalent geometry : angle 0.65962 / 0.33 (15700) hydrogen bonds : bond 0.03316 / 2.20 ( 464) hydrogen bonds : angle 3.98341 / 2.87 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 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 140 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7666 (mtm) cc_final: 0.7167 (mmm) REVERT: A 167 PHE cc_start: 0.8280 (m-10) cc_final: 0.7949 (t80) REVERT: A 241 LEU cc_start: 0.8174 (mm) cc_final: 0.7939 (pt) REVERT: A 249 LYS cc_start: 0.8206 (mttm) cc_final: 0.7983 (tttt) REVERT: A 250 LYS cc_start: 0.8168 (pttm) cc_final: 0.7575 (tptp) REVERT: A 280 PHE cc_start: 0.5332 (m-80) cc_final: 0.4928 (t80) REVERT: A 407 PHE cc_start: 0.6994 (m-80) cc_final: 0.6755 (p90) REVERT: A 444 MET cc_start: 0.8185 (ptp) cc_final: 0.7558 (ptp) REVERT: A 457 GLU cc_start: 0.8441 (tt0) cc_final: 0.7892 (tt0) REVERT: A 464 TYR cc_start: 0.7946 (t80) cc_final: 0.7293 (t80) REVERT: A 555 MET cc_start: 0.3904 (mpp) cc_final: 0.3557 (mpp) REVERT: A 581 VAL cc_start: 0.8348 (p) cc_final: 0.7993 (p) REVERT: A 585 LEU cc_start: 0.8008 (mt) cc_final: 0.7706 (tp) REVERT: A 598 TYR cc_start: 0.8163 (t80) cc_final: 0.7957 (t80) REVERT: A 604 GLN cc_start: 0.7558 (tp40) cc_final: 0.7129 (tp40) REVERT: A 631 LEU cc_start: 0.8000 (mm) cc_final: 0.7748 (mm) REVERT: A 671 ARG cc_start: 0.6279 (ttt180) cc_final: 0.5699 (tpp-160) REVERT: A 709 LEU cc_start: 0.7812 (mt) cc_final: 0.7559 (mp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0778 time to fit residues: 14.0864 Evaluate side-chains 97 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 85 optimal weight: 0.0870 chunk 22 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN A 393 GLN ** A 603 HIS ** 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 = 0.3627 r_free = 0.3627 target = 0.082865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.069147 restraints weight = 27717.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.070854 restraints weight = 18935.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072039 restraints weight = 14071.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072870 restraints weight = 11116.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.073528 restraints weight = 9315.311| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11542 Z= 0.115 Angle : 0.683 8.955 15700 Z= 0.334 Chirality : 0.043 0.177 1776 Planarity : 0.005 0.058 1954 Dihedral : 4.175 16.872 1506 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.23), residues: 1370 helix: 0.01 (0.19), residues: 794 sheet: 2.20 (2.33), residues: 10 loop : -3.15 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 370 TYR 0.006 0.001 TYR B 515 PHE 0.017 0.001 PHE B 593 TRP 0.010 0.001 TRP B 564 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (11542) covalent geometry : angle 0.68309 / 0.33 (15700) hydrogen bonds : bond 0.03079 / 2.06 ( 464) hydrogen bonds : angle 4.00119 / 2.87 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 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 136 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7600 (mtm) cc_final: 0.7165 (mmm) REVERT: A 88 ILE cc_start: 0.8235 (mm) cc_final: 0.7966 (mm) REVERT: A 167 PHE cc_start: 0.8210 (m-10) cc_final: 0.7902 (t80) REVERT: A 250 LYS cc_start: 0.8150 (pttm) cc_final: 0.7694 (tptp) REVERT: A 280 PHE cc_start: 0.5301 (m-80) cc_final: 0.4891 (t80) REVERT: A 336 GLN cc_start: 0.6806 (tt0) cc_final: 0.5923 (pp30) REVERT: A 407 PHE cc_start: 0.6433 (m-80) cc_final: 0.6230 (p90) REVERT: A 444 MET cc_start: 0.8175 (ptp) cc_final: 0.7489 (ptp) REVERT: A 464 TYR cc_start: 0.7943 (t80) cc_final: 0.7301 (t80) REVERT: A 552 GLU cc_start: 0.7175 (pm20) cc_final: 0.6395 (mm-30) REVERT: A 581 VAL cc_start: 0.8339 (p) cc_final: 0.7988 (p) REVERT: A 585 LEU cc_start: 0.7996 (mt) cc_final: 0.7693 (tp) REVERT: A 604 GLN cc_start: 0.7638 (tp40) cc_final: 0.7231 (tp40) REVERT: A 637 LEU cc_start: 0.6991 (mm) cc_final: 0.6579 (mm) REVERT: A 671 ARG cc_start: 0.6196 (ttt180) cc_final: 0.5704 (tpp-160) REVERT: A 709 LEU cc_start: 0.7712 (mt) cc_final: 0.7462 (mp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0674 time to fit residues: 12.1486 Evaluate side-chains 90 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 43 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 106 optimal weight: 0.0010 chunk 33 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 chunk 119 optimal weight: 5.9990 chunk 96 optimal weight: 0.0040 chunk 11 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 0.1676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS A 359 ASN A 393 GLN ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.083859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070224 restraints weight = 27450.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.071956 restraints weight = 18729.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073224 restraints weight = 13851.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074020 restraints weight = 10826.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.074747 restraints weight = 9070.379| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11542 Z= 0.123 Angle : 0.707 12.207 15700 Z= 0.341 Chirality : 0.044 0.256 1776 Planarity : 0.005 0.055 1954 Dihedral : 4.119 16.008 1506 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.23), residues: 1370 helix: 0.14 (0.19), residues: 778 sheet: 2.29 (2.35), residues: 10 loop : -2.95 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.007 0.001 TYR B 613 PHE 0.018 0.001 PHE B 593 TRP 0.012 0.001 TRP A 620 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11542) covalent geometry : angle 0.70693 / 0.34 (15700) hydrogen bonds : bond 0.03094 / 2.05 ( 464) hydrogen bonds : angle 4.02546 / 2.90 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 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 134 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7583 (mtm) cc_final: 0.7076 (mmm) REVERT: A 167 PHE cc_start: 0.8169 (m-10) cc_final: 0.7908 (t80) REVERT: A 280 PHE cc_start: 0.5711 (m-80) cc_final: 0.5224 (t80) REVERT: A 336 GLN cc_start: 0.6422 (tt0) cc_final: 0.5749 (pp30) REVERT: A 444 MET cc_start: 0.8148 (ptp) cc_final: 0.7476 (ptp) REVERT: A 453 GLN cc_start: 0.7227 (pp30) cc_final: 0.6989 (tm-30) REVERT: A 464 TYR cc_start: 0.7969 (t80) cc_final: 0.7353 (t80) REVERT: A 552 GLU cc_start: 0.7019 (pm20) cc_final: 0.6175 (mm-30) REVERT: A 581 VAL cc_start: 0.8305 (p) cc_final: 0.7947 (p) REVERT: A 585 LEU cc_start: 0.8015 (mt) cc_final: 0.7677 (tp) REVERT: A 604 GLN cc_start: 0.7649 (tp40) cc_final: 0.7253 (tp40) REVERT: A 637 LEU cc_start: 0.6889 (mm) cc_final: 0.6471 (mm) REVERT: A 661 THR cc_start: 0.8892 (m) cc_final: 0.8679 (p) REVERT: A 671 ARG cc_start: 0.6438 (ttt180) cc_final: 0.5636 (tpp-160) REVERT: A 672 PHE cc_start: 0.6142 (m-80) cc_final: 0.5806 (m-10) REVERT: A 709 LEU cc_start: 0.7665 (mt) cc_final: 0.7429 (mp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0629 time to fit residues: 11.3339 Evaluate side-chains 95 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 36 optimal weight: 0.0980 chunk 33 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 113 optimal weight: 0.0170 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS A 359 ASN A 393 GLN ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.084117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070908 restraints weight = 27314.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072516 restraints weight = 18971.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.073691 restraints weight = 14240.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.074550 restraints weight = 11300.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075063 restraints weight = 9411.617| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11542 Z= 0.119 Angle : 0.694 12.027 15700 Z= 0.333 Chirality : 0.044 0.244 1776 Planarity : 0.005 0.054 1954 Dihedral : 4.094 15.961 1506 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.23), residues: 1370 helix: 0.13 (0.19), residues: 778 sheet: 2.33 (2.34), residues: 10 loop : -2.91 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 184 TYR 0.011 0.001 TYR A 177 PHE 0.017 0.001 PHE B 593 TRP 0.013 0.001 TRP B 564 HIS 0.010 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (11542) covalent geometry : angle 0.69399 / 0.33 (15700) hydrogen bonds : bond 0.02984 / 1.97 ( 464) hydrogen bonds : angle 4.01052 / 2.88 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1179.84 seconds wall clock time: 21 minutes 17.13 seconds (1277.13 seconds total)