Starting phenix.real_space_refine on Wed Mar 4 05:55:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oce_20017/03_2026/6oce_20017.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oce_20017/03_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_20017/03_2026/6oce_20017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oce_20017/03_2026/6oce_20017.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oce_20017/03_2026/6oce_20017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oce_20017/03_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-dev-5986/lib/python3.9/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: 2.58, per 1000 atoms: 0.23 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: 1.01 Conformation dependent library (CDL) restraints added in 445.6 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: 0.34 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: 1.51 Time building geometry restraints manager: 1.34 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.320 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.337 11542 Z= 0.274 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 covalent geometry : bond 0.00572 (11542) covalent geometry : angle 0.73199 (15700) hydrogen bonds : bond 0.21994 ( 464) hydrogen bonds : angle 6.78437 ( 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 : 0.168 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: 0.0795 time to fit residues: 20.6525 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 : 0.209 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 158 HIS B 422 GLN B 538 HIS B 570 GLN B 604 GLN B 607 ASN B 618 GLN B 682 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.087123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.073147 restraints weight = 27033.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.074893 restraints weight = 19041.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076093 restraints weight = 14450.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.077055 restraints weight = 11633.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.077766 restraints weight = 9719.263| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 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 7.829 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 B 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 covalent geometry : bond 0.00305 (11542) covalent geometry : angle 0.71253 (15700) hydrogen bonds : bond 0.04714 ( 464) hydrogen bonds : angle 4.39951 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ARG cc_start: 0.4331 (mtt90) cc_final: 0.4009 (tmm-80) REVERT: B 156 VAL cc_start: 0.7420 (t) cc_final: 0.7211 (p) REVERT: B 249 LYS cc_start: 0.8021 (mttm) cc_final: 0.7568 (tmtt) REVERT: B 250 LYS cc_start: 0.8480 (pttt) cc_final: 0.8143 (pptt) REVERT: B 303 ASP cc_start: 0.7305 (t70) cc_final: 0.7071 (m-30) REVERT: B 358 ASN cc_start: 0.8048 (m-40) cc_final: 0.7833 (m110) REVERT: B 444 MET cc_start: 0.8063 (ptp) cc_final: 0.7296 (ptp) REVERT: B 457 GLU cc_start: 0.8100 (tt0) cc_final: 0.7010 (tm-30) REVERT: B 464 TYR cc_start: 0.7874 (t80) cc_final: 0.7183 (t80) REVERT: B 513 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7736 (mt) REVERT: B 514 THR cc_start: 0.8512 (p) cc_final: 0.8124 (t) REVERT: B 552 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6794 (mp0) REVERT: B 564 TRP cc_start: 0.6271 (m-10) cc_final: 0.5956 (m-90) REVERT: B 585 LEU cc_start: 0.8008 (mt) cc_final: 0.7730 (tp) REVERT: B 601 TYR cc_start: 0.7223 (m-80) cc_final: 0.7011 (m-80) REVERT: B 631 LEU cc_start: 0.7771 (mm) cc_final: 0.7268 (mm) REVERT: B 666 LYS cc_start: 0.7195 (mmpt) cc_final: 0.6373 (pttt) REVERT: B 671 ARG cc_start: 0.6436 (ttt180) cc_final: 0.5990 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.0831 time to fit residues: 17.0570 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 : 0.201 ------------------------------------------------------------------------------- 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: 0.0470 chunk 114 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 0.0270 chunk 82 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 84 optimal weight: 0.0070 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN B 485 GLN B 603 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.087314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.073901 restraints weight = 25943.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075468 restraints weight = 18314.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076702 restraints weight = 14111.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077607 restraints weight = 11227.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.078367 restraints weight = 9360.453| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11542 Z= 0.123 Angle : 0.650 7.159 15700 Z= 0.330 Chirality : 0.044 0.200 1776 Planarity : 0.005 0.053 1954 Dihedral : 4.031 17.348 1506 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.82 % Favored : 87.88 % 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: -3.28 (0.21), residues: 1370 helix: -1.14 (0.18), residues: 756 sheet: -0.39 (1.54), residues: 10 loop : -3.65 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 305 TYR 0.014 0.001 TYR B 598 PHE 0.036 0.002 PHE B 109 TRP 0.010 0.001 TRP B 620 HIS 0.006 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00260 (11542) covalent geometry : angle 0.64974 (15700) hydrogen bonds : bond 0.03928 ( 464) hydrogen bonds : angle 3.99305 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ARG cc_start: 0.4242 (mtt90) cc_final: 0.4028 (tmm-80) REVERT: B 76 MET cc_start: 0.7743 (mmm) cc_final: 0.7536 (mtt) REVERT: B 102 TYR cc_start: 0.6239 (m-80) cc_final: 0.6028 (m-80) REVERT: B 156 VAL cc_start: 0.7337 (t) cc_final: 0.7111 (p) REVERT: B 249 LYS cc_start: 0.8175 (mttm) cc_final: 0.7744 (tmtt) REVERT: B 379 PHE cc_start: 0.7674 (t80) cc_final: 0.7471 (t80) REVERT: B 444 MET cc_start: 0.8076 (ptp) cc_final: 0.7265 (ptp) REVERT: B 457 GLU cc_start: 0.8535 (tt0) cc_final: 0.7219 (tm-30) REVERT: B 464 TYR cc_start: 0.7955 (t80) cc_final: 0.7344 (t80) REVERT: B 513 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7517 (mt) REVERT: B 514 THR cc_start: 0.8495 (p) cc_final: 0.8123 (t) REVERT: B 552 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7019 (mp0) REVERT: B 564 TRP cc_start: 0.6352 (m-10) cc_final: 0.6133 (m-90) REVERT: B 581 VAL cc_start: 0.8089 (p) cc_final: 0.7713 (p) REVERT: B 585 LEU cc_start: 0.8073 (mt) cc_final: 0.7758 (tp) REVERT: B 604 GLN cc_start: 0.8451 (tp40) cc_final: 0.7949 (tp40) REVERT: B 631 LEU cc_start: 0.7990 (mm) cc_final: 0.7531 (mm) REVERT: B 663 TRP cc_start: 0.8365 (t-100) cc_final: 0.7963 (t-100) REVERT: B 666 LYS cc_start: 0.7260 (mmpt) cc_final: 0.6502 (pttt) REVERT: B 671 ARG cc_start: 0.6288 (ttt180) cc_final: 0.5875 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.0818 time to fit residues: 15.2323 Evaluate side-chains 110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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: 0.8980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 61 optimal weight: 0.0670 chunk 81 optimal weight: 8.9990 chunk 101 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.086671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073240 restraints weight = 26722.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.074870 restraints weight = 18974.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076084 restraints weight = 14422.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.077015 restraints weight = 11567.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.077443 restraints weight = 9637.672| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11542 Z= 0.115 Angle : 0.615 6.705 15700 Z= 0.306 Chirality : 0.042 0.174 1776 Planarity : 0.006 0.060 1954 Dihedral : 3.976 17.159 1506 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.26 % Favored : 87.59 % 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: -2.99 (0.21), residues: 1370 helix: -0.84 (0.18), residues: 754 sheet: -0.56 (1.45), residues: 10 loop : -3.62 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 231 TYR 0.020 0.001 TYR A 258 PHE 0.017 0.001 PHE B 364 TRP 0.008 0.001 TRP B 620 HIS 0.006 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00238 (11542) covalent geometry : angle 0.61458 (15700) hydrogen bonds : bond 0.03424 ( 464) hydrogen bonds : angle 4.02370 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 THR cc_start: 0.7922 (p) cc_final: 0.7571 (p) REVERT: B 167 PHE cc_start: 0.8606 (m-10) cc_final: 0.8284 (m-10) REVERT: B 170 CYS cc_start: 0.8894 (m) cc_final: 0.8661 (p) REVERT: B 247 LYS cc_start: 0.7983 (pptt) cc_final: 0.7753 (ptmm) REVERT: B 249 LYS cc_start: 0.8235 (mttm) cc_final: 0.7827 (tmtt) REVERT: B 250 LYS cc_start: 0.8076 (pttm) cc_final: 0.7500 (tptp) REVERT: B 343 VAL cc_start: 0.6538 (t) cc_final: 0.6291 (t) REVERT: B 444 MET cc_start: 0.8258 (ptp) cc_final: 0.7476 (ptp) REVERT: B 457 GLU cc_start: 0.8535 (tt0) cc_final: 0.7451 (tm-30) REVERT: B 464 TYR cc_start: 0.7969 (t80) cc_final: 0.7441 (t80) REVERT: B 513 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7273 (tp) REVERT: B 514 THR cc_start: 0.8375 (p) cc_final: 0.8133 (t) REVERT: B 552 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6908 (mp0) REVERT: B 581 VAL cc_start: 0.8257 (p) cc_final: 0.7880 (p) REVERT: B 585 LEU cc_start: 0.7988 (mt) cc_final: 0.7654 (tp) REVERT: B 604 GLN cc_start: 0.8447 (tp40) cc_final: 0.7926 (tp40) REVERT: B 631 LEU cc_start: 0.8032 (mm) cc_final: 0.7618 (mm) REVERT: B 663 TRP cc_start: 0.8359 (t-100) cc_final: 0.7851 (t-100) REVERT: B 666 LYS cc_start: 0.7073 (mmpt) cc_final: 0.6435 (pttt) REVERT: B 676 PHE cc_start: 0.8329 (t80) cc_final: 0.7982 (t80) REVERT: B 709 LEU cc_start: 0.7631 (mt) cc_final: 0.7392 (mt) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.0732 time to fit residues: 13.8841 Evaluate side-chains 114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 95 optimal weight: 0.0670 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.087615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.073460 restraints weight = 28818.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075079 restraints weight = 20428.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076266 restraints weight = 15505.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077195 restraints weight = 12451.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.077652 restraints weight = 10405.552| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11542 Z= 0.113 Angle : 0.629 6.857 15700 Z= 0.309 Chirality : 0.043 0.170 1776 Planarity : 0.005 0.050 1954 Dihedral : 3.953 15.582 1506 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % 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: -2.81 (0.22), residues: 1370 helix: -0.68 (0.18), residues: 758 sheet: -0.27 (1.48), residues: 10 loop : -3.57 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 671 TYR 0.014 0.001 TYR A 598 PHE 0.015 0.001 PHE A 593 TRP 0.014 0.001 TRP A 75 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00249 (11542) covalent geometry : angle 0.62891 (15700) hydrogen bonds : bond 0.03157 ( 464) hydrogen bonds : angle 3.85352 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.7517 (mtm) cc_final: 0.6706 (mmm) REVERT: B 156 VAL cc_start: 0.7397 (t) cc_final: 0.7168 (p) REVERT: B 166 THR cc_start: 0.8219 (p) cc_final: 0.7880 (p) REVERT: B 167 PHE cc_start: 0.8599 (m-10) cc_final: 0.8300 (m-10) REVERT: B 249 LYS cc_start: 0.8251 (mttm) cc_final: 0.7906 (tmtt) REVERT: B 250 LYS cc_start: 0.7994 (pttm) cc_final: 0.7454 (tptp) REVERT: B 343 VAL cc_start: 0.6308 (t) cc_final: 0.6083 (t) REVERT: B 457 GLU cc_start: 0.8419 (tt0) cc_final: 0.7412 (tm-30) REVERT: B 464 TYR cc_start: 0.7818 (t80) cc_final: 0.7240 (t80) REVERT: B 513 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7159 (mt) REVERT: B 514 THR cc_start: 0.8408 (p) cc_final: 0.8158 (t) REVERT: B 581 VAL cc_start: 0.8282 (p) cc_final: 0.7937 (p) REVERT: B 585 LEU cc_start: 0.7979 (mt) cc_final: 0.7702 (tp) REVERT: B 631 LEU cc_start: 0.8065 (mm) cc_final: 0.7737 (mm) REVERT: B 635 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7915 (mm-40) REVERT: B 663 TRP cc_start: 0.8225 (t-100) cc_final: 0.7765 (t60) REVERT: B 666 LYS cc_start: 0.7025 (mmpt) cc_final: 0.6346 (pttt) REVERT: B 676 PHE cc_start: 0.8385 (t80) cc_final: 0.7966 (t80) REVERT: B 709 LEU cc_start: 0.7739 (mt) cc_final: 0.7460 (mt) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.0715 time to fit residues: 13.0434 Evaluate side-chains 105 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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: 0.0030 chunk 85 optimal weight: 2.9990 chunk 72 optimal weight: 0.0040 chunk 68 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 90 optimal weight: 6.9990 chunk 89 optimal weight: 0.0370 chunk 40 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 overall best weight: 0.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.088509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.074592 restraints weight = 27874.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076190 restraints weight = 19594.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.077402 restraints weight = 14884.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.078204 restraints weight = 11885.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.078858 restraints weight = 10087.661| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11542 Z= 0.113 Angle : 0.619 6.864 15700 Z= 0.308 Chirality : 0.042 0.179 1776 Planarity : 0.006 0.054 1954 Dihedral : 4.020 16.988 1506 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.89 (0.21), residues: 1370 helix: -0.80 (0.18), residues: 770 sheet: -0.45 (1.41), residues: 10 loop : -3.57 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 671 TYR 0.008 0.001 TYR B 356 PHE 0.017 0.001 PHE B 364 TRP 0.009 0.001 TRP A 168 HIS 0.004 0.001 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00245 (11542) covalent geometry : angle 0.61933 (15700) hydrogen bonds : bond 0.03207 ( 464) hydrogen bonds : angle 4.00477 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.7758 (mtm) cc_final: 0.6879 (mmm) REVERT: B 102 TYR cc_start: 0.5893 (m-80) cc_final: 0.5620 (m-80) REVERT: B 166 THR cc_start: 0.8168 (p) cc_final: 0.7864 (p) REVERT: B 249 LYS cc_start: 0.8223 (mttm) cc_final: 0.7887 (tmtt) REVERT: B 250 LYS cc_start: 0.8037 (pttm) cc_final: 0.7415 (tptp) REVERT: B 457 GLU cc_start: 0.8429 (tt0) cc_final: 0.7403 (tm-30) REVERT: B 464 TYR cc_start: 0.7854 (t80) cc_final: 0.7258 (t80) REVERT: B 552 GLU cc_start: 0.7123 (pm20) cc_final: 0.6301 (mm-30) REVERT: B 581 VAL cc_start: 0.8287 (p) cc_final: 0.7947 (p) REVERT: B 585 LEU cc_start: 0.8000 (mt) cc_final: 0.7674 (tp) REVERT: B 604 GLN cc_start: 0.8357 (tp40) cc_final: 0.8091 (tp40) REVERT: B 631 LEU cc_start: 0.7953 (mm) cc_final: 0.7704 (mm) REVERT: B 635 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7721 (mm-40) REVERT: B 663 TRP cc_start: 0.8221 (t-100) cc_final: 0.7761 (t60) REVERT: B 666 LYS cc_start: 0.6918 (mmpt) cc_final: 0.6341 (pttt) REVERT: B 676 PHE cc_start: 0.8365 (t80) cc_final: 0.7980 (t80) REVERT: B 709 LEU cc_start: 0.7684 (mt) cc_final: 0.7317 (mp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0803 time to fit residues: 14.4622 Evaluate side-chains 103 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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: 3.9990 chunk 45 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.0070 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.082573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069455 restraints weight = 28133.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071025 restraints weight = 19581.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072184 restraints weight = 14629.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.072981 restraints weight = 11580.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.073628 restraints weight = 9737.234| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.5975 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= 0.141 Angle : 0.673 12.078 15700 Z= 0.333 Chirality : 0.043 0.181 1776 Planarity : 0.007 0.139 1954 Dihedral : 4.202 16.101 1506 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -2.73 (0.22), residues: 1370 helix: -0.71 (0.18), residues: 780 sheet: -1.14 (1.13), residues: 20 loop : -3.49 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 508 TYR 0.009 0.001 TYR B 515 PHE 0.011 0.001 PHE A 593 TRP 0.031 0.002 TRP B 564 HIS 0.004 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00309 (11542) covalent geometry : angle 0.67330 (15700) hydrogen bonds : bond 0.03226 ( 464) hydrogen bonds : angle 4.09993 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TYR cc_start: 0.6384 (m-80) cc_final: 0.6182 (m-80) REVERT: B 104 THR cc_start: 0.8553 (p) cc_final: 0.7843 (p) REVERT: B 167 PHE cc_start: 0.8111 (m-10) cc_final: 0.7787 (t80) REVERT: B 241 LEU cc_start: 0.8434 (mm) cc_final: 0.7823 (pt) REVERT: B 343 VAL cc_start: 0.6808 (t) cc_final: 0.6561 (t) REVERT: B 457 GLU cc_start: 0.8404 (tt0) cc_final: 0.7950 (tt0) REVERT: B 464 TYR cc_start: 0.7987 (t80) cc_final: 0.7408 (t80) REVERT: B 585 LEU cc_start: 0.7942 (mt) cc_final: 0.7654 (tp) REVERT: B 631 LEU cc_start: 0.8203 (mm) cc_final: 0.7865 (mm) REVERT: B 662 PHE cc_start: 0.6708 (t80) cc_final: 0.6394 (t80) REVERT: B 663 TRP cc_start: 0.8298 (t-100) cc_final: 0.7794 (t60) REVERT: B 666 LYS cc_start: 0.7122 (mmpt) cc_final: 0.6258 (pttt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0695 time to fit residues: 12.7291 Evaluate side-chains 102 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 HIS B 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.081628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068805 restraints weight = 28076.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.070321 restraints weight = 19402.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071421 restraints weight = 14513.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072141 restraints weight = 11573.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072789 restraints weight = 9826.204| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11542 Z= 0.139 Angle : 0.665 10.276 15700 Z= 0.328 Chirality : 0.044 0.179 1776 Planarity : 0.006 0.086 1954 Dihedral : 4.246 15.509 1506 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.63 (0.22), residues: 1370 helix: -0.68 (0.18), residues: 776 sheet: 0.70 (1.62), residues: 10 loop : -3.34 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 678 TYR 0.012 0.001 TYR B 98 PHE 0.013 0.001 PHE B 593 TRP 0.015 0.002 TRP B 564 HIS 0.011 0.002 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00311 (11542) covalent geometry : angle 0.66451 (15700) hydrogen bonds : bond 0.03214 ( 464) hydrogen bonds : angle 4.07725 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.8051 (t80) cc_final: 0.7712 (t80) REVERT: B 167 PHE cc_start: 0.8166 (m-10) cc_final: 0.7848 (t80) REVERT: B 241 LEU cc_start: 0.8378 (mm) cc_final: 0.7796 (pt) REVERT: B 280 PHE cc_start: 0.5683 (m-80) cc_final: 0.5003 (t80) REVERT: B 387 ILE cc_start: 0.8287 (pt) cc_final: 0.8079 (tp) REVERT: B 406 PRO cc_start: 0.3493 (Cg_exo) cc_final: 0.3241 (Cg_endo) REVERT: B 444 MET cc_start: 0.8197 (ptp) cc_final: 0.7854 (ptm) REVERT: B 457 GLU cc_start: 0.8341 (tt0) cc_final: 0.8101 (tt0) REVERT: B 464 TYR cc_start: 0.7920 (t80) cc_final: 0.7303 (t80) REVERT: B 552 GLU cc_start: 0.6768 (pm20) cc_final: 0.5910 (mm-30) REVERT: B 581 VAL cc_start: 0.8440 (p) cc_final: 0.8179 (p) REVERT: B 585 LEU cc_start: 0.7914 (mt) cc_final: 0.7653 (tp) REVERT: B 604 GLN cc_start: 0.7449 (tp40) cc_final: 0.7107 (tp40) REVERT: B 631 LEU cc_start: 0.8111 (mm) cc_final: 0.7838 (mm) REVERT: B 662 PHE cc_start: 0.6712 (t80) cc_final: 0.6442 (t80) REVERT: B 663 TRP cc_start: 0.8302 (t-100) cc_final: 0.7838 (t60) REVERT: B 666 LYS cc_start: 0.7187 (mmpt) cc_final: 0.6283 (pttt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0659 time to fit residues: 11.8843 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 : 0.252 ------------------------------------------------------------------------------- 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: 7.9990 chunk 57 optimal weight: 0.0470 chunk 134 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 85 optimal weight: 0.0870 chunk 22 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.0258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.082698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.069507 restraints weight = 28767.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.071049 restraints weight = 19665.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072193 restraints weight = 14573.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.073035 restraints weight = 11583.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073455 restraints weight = 9681.289| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11542 Z= 0.118 Angle : 0.678 10.447 15700 Z= 0.330 Chirality : 0.043 0.182 1776 Planarity : 0.006 0.076 1954 Dihedral : 4.162 15.533 1506 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.82 (0.22), residues: 1370 helix: -0.89 (0.18), residues: 778 sheet: 0.25 (1.54), residues: 10 loop : -3.34 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 184 TYR 0.022 0.001 TYR A 171 PHE 0.024 0.001 PHE A 109 TRP 0.023 0.001 TRP B 564 HIS 0.009 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00259 (11542) covalent geometry : angle 0.67814 (15700) hydrogen bonds : bond 0.03060 ( 464) hydrogen bonds : angle 4.00335 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 HIS cc_start: 0.5296 (m90) cc_final: 0.4976 (m-70) REVERT: B 241 LEU cc_start: 0.8404 (mm) cc_final: 0.7726 (pt) REVERT: B 280 PHE cc_start: 0.5660 (m-80) cc_final: 0.4978 (t80) REVERT: B 343 VAL cc_start: 0.6768 (t) cc_final: 0.6515 (t) REVERT: B 387 ILE cc_start: 0.8284 (pt) cc_final: 0.8079 (tp) REVERT: B 406 PRO cc_start: 0.2865 (Cg_exo) cc_final: 0.2631 (Cg_endo) REVERT: B 444 MET cc_start: 0.8264 (ptp) cc_final: 0.7922 (ptm) REVERT: B 457 GLU cc_start: 0.8237 (tt0) cc_final: 0.8009 (tt0) REVERT: B 464 TYR cc_start: 0.7817 (t80) cc_final: 0.7366 (t80) REVERT: B 552 GLU cc_start: 0.6678 (pm20) cc_final: 0.5867 (mm-30) REVERT: B 581 VAL cc_start: 0.8432 (p) cc_final: 0.8136 (p) REVERT: B 585 LEU cc_start: 0.7877 (mt) cc_final: 0.7636 (tp) REVERT: B 604 GLN cc_start: 0.7408 (tp40) cc_final: 0.7131 (tp40) REVERT: B 631 LEU cc_start: 0.8056 (mm) cc_final: 0.7703 (mm) REVERT: B 662 PHE cc_start: 0.6686 (t80) cc_final: 0.6439 (t80) REVERT: B 663 TRP cc_start: 0.8133 (t-100) cc_final: 0.7752 (t60) REVERT: B 666 LYS cc_start: 0.7101 (mmpt) cc_final: 0.6342 (pttt) REVERT: B 673 GLU cc_start: 0.8758 (tp30) cc_final: 0.8453 (tp30) REVERT: B 709 LEU cc_start: 0.7607 (mt) cc_final: 0.7308 (mp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0674 time to fit residues: 12.2694 Evaluate side-chains 103 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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: 4.9990 chunk 135 optimal weight: 0.0040 chunk 106 optimal weight: 0.0040 chunk 33 optimal weight: 5.9990 chunk 86 optimal weight: 0.0040 chunk 63 optimal weight: 0.0010 chunk 119 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 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 = 0.3603 r_free = 0.3603 target = 0.081790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.068518 restraints weight = 27869.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070262 restraints weight = 18985.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071539 restraints weight = 13977.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072442 restraints weight = 10867.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073096 restraints weight = 8986.785| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.6637 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= 0.114 Angle : 0.669 10.243 15700 Z= 0.326 Chirality : 0.043 0.160 1776 Planarity : 0.006 0.059 1954 Dihedral : 4.097 15.122 1506 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % 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: -2.64 (0.22), residues: 1370 helix: -0.74 (0.18), residues: 768 sheet: 0.33 (1.52), residues: 10 loop : -3.24 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 678 TYR 0.017 0.001 TYR A 171 PHE 0.019 0.001 PHE B 676 TRP 0.018 0.001 TRP B 564 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00256 (11542) covalent geometry : angle 0.66945 (15700) hydrogen bonds : bond 0.02950 ( 464) hydrogen bonds : angle 3.97620 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TRP cc_start: 0.6107 (t-100) cc_final: 0.5387 (t-100) REVERT: A 241 LEU cc_start: 0.8187 (mm) cc_final: 0.7952 (pt) REVERT: A 251 LEU cc_start: 0.6676 (mt) cc_final: 0.6405 (pp) REVERT: A 280 PHE cc_start: 0.5642 (m-80) cc_final: 0.5153 (t80) REVERT: A 285 ASP cc_start: 0.7364 (m-30) cc_final: 0.7087 (m-30) REVERT: A 336 GLN cc_start: 0.6267 (tt0) cc_final: 0.5549 (pp30) REVERT: A 407 PHE cc_start: 0.6445 (m-80) cc_final: 0.6070 (p90) REVERT: A 464 TYR cc_start: 0.7941 (t80) cc_final: 0.7353 (t80) REVERT: A 552 GLU cc_start: 0.6570 (pm20) cc_final: 0.5844 (mm-30) REVERT: A 581 VAL cc_start: 0.8463 (p) cc_final: 0.8132 (p) REVERT: A 585 LEU cc_start: 0.7969 (mt) cc_final: 0.7653 (tp) REVERT: A 631 LEU cc_start: 0.7946 (mm) cc_final: 0.7589 (mm) REVERT: A 662 PHE cc_start: 0.6722 (t80) cc_final: 0.6433 (t80) REVERT: A 709 LEU cc_start: 0.7738 (mt) cc_final: 0.7436 (mp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0704 time to fit residues: 12.7142 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 : 0.236 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 39 optimal weight: 0.3980 chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 113 optimal weight: 0.0370 chunk 45 optimal weight: 0.0370 chunk 12 optimal weight: 7.9990 overall best weight: 1.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 228 HIS A 393 GLN A 603 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.081360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068022 restraints weight = 27588.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.069659 restraints weight = 19005.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.070831 restraints weight = 14095.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071724 restraints weight = 11164.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.072395 restraints weight = 9263.569| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11542 Z= 0.117 Angle : 0.683 9.933 15700 Z= 0.332 Chirality : 0.044 0.240 1776 Planarity : 0.005 0.061 1954 Dihedral : 4.120 15.245 1506 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 0.16 % Allowed : 0.49 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.68 (0.22), residues: 1370 helix: -0.78 (0.18), residues: 754 sheet: 0.28 (1.49), residues: 10 loop : -3.19 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 184 TYR 0.019 0.001 TYR A 98 PHE 0.014 0.001 PHE A 676 TRP 0.024 0.002 TRP B 564 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00262 (11542) covalent geometry : angle 0.68276 (15700) hydrogen bonds : bond 0.03074 ( 464) hydrogen bonds : angle 4.06959 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.63 seconds wall clock time: 21 minutes 3.34 seconds (1263.34 seconds total)