Starting phenix.real_space_refine on Fri Aug 7 08:31:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13ls_77143/08_2026/13ls_77143.cif Found real_map, /net/cci-nas-00/data/ceres_data/13ls_77143/08_2026/13ls_77143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13ls_77143/08_2026/13ls_77143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13ls_77143/08_2026/13ls_77143.map" model { file = "/net/cci-nas-00/data/ceres_data/13ls_77143/08_2026/13ls_77143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13ls_77143/08_2026/13ls_77143.cif" } resolution = 3.02 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= 0.008 sd= 0.026 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 120 5.16 5 C 13058 2.51 5 N 3230 2.21 5 O 3516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19932 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4743 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 11, 'TRANS': 567} Chain breaks: 2 Chain: "B" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 5015 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 17, 'TRANS': 597} Chain breaks: 4 Chain: "C" Number of atoms: 4743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4743 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 11, 'TRANS': 567} Chain breaks: 2 Chain: "D" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 5015 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 17, 'TRANS': 597} Chain breaks: 4 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.94, per 1000 atoms: 0.20 Number of scatterers: 19932 At special positions: 0 Unit cell: (142.245, 155.979, 121.644, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 8 15.00 O 3516 8.00 N 3230 7.00 C 13058 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: 1.25 Conformation dependent library (CDL) restraints added in 770.1 milliseconds 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4580 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 4 sheets defined 62.5% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.538A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.902A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.658A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.726A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.855A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.930A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.785A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.556A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.608A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.648A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.568A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.617A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 423 through 434 removed outlier: 3.997A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.622A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 506 removed outlier: 3.839A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 541 removed outlier: 4.345A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.573A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 removed outlier: 4.168A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 561 through 566' Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 590 through 609 removed outlier: 3.747A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 677 removed outlier: 3.712A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 671 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 707 removed outlier: 3.523A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 738 through 749 removed outlier: 3.558A pdb=" N PHE A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.610A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 147 removed outlier: 3.594A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 162 removed outlier: 3.737A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.696A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.552A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.588A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.544A pdb=" N LEU B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.728A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 4.024A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.515A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.519A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.686A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.563A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 542 removed outlier: 4.075A pdb=" N PHE B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.551A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 4.176A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 596 removed outlier: 3.605A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 651 through 676 removed outlier: 3.501A pdb=" N LEU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 696 removed outlier: 3.550A pdb=" N SER B 688 " --> pdb=" O VAL B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.692A pdb=" N ILE B 700 " --> pdb=" O ARG B 696 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.507A pdb=" N ARG B 712 " --> pdb=" O PRO B 708 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 708 through 713' Processing helix chain 'C' and resid 119 through 129 removed outlier: 3.539A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.901A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 162 removed outlier: 3.658A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.726A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.855A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.929A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.786A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.555A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.608A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.648A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.567A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.617A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 423 through 434 removed outlier: 3.924A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.622A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 506 removed outlier: 3.839A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 541 removed outlier: 4.345A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 532 " --> pdb=" O ILE C 528 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 535 " --> pdb=" O VAL C 531 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.573A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 566 removed outlier: 4.169A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 561 through 566' Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 590 through 609 removed outlier: 3.747A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER C 607 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 677 removed outlier: 3.712A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 671 " --> pdb=" O VAL C 667 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 707 removed outlier: 3.522A pdb=" N ARG C 690 " --> pdb=" O LYS C 686 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'C' and resid 738 through 749 removed outlier: 3.558A pdb=" N PHE C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.611A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 147 removed outlier: 3.594A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 162 removed outlier: 3.737A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.697A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.552A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.587A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.544A pdb=" N LEU D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.728A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 4.024A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.516A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.519A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.685A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.564A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D 494 " --> pdb=" O VAL D 490 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 542 removed outlier: 4.075A pdb=" N PHE D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS D 523 " --> pdb=" O ASP D 519 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.551A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.700A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 596 removed outlier: 3.605A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 639 Processing helix chain 'D' and resid 651 through 676 removed outlier: 3.501A pdb=" N LEU D 655 " --> pdb=" O PRO D 651 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 696 removed outlier: 3.551A pdb=" N SER D 688 " --> pdb=" O VAL D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.693A pdb=" N ILE D 700 " --> pdb=" O ARG D 696 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 704 " --> pdb=" O ILE D 700 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.508A pdb=" N ARG D 712 " --> pdb=" O PRO D 708 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 708 through 713' Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.864A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 381 removed outlier: 7.034A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.864A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 381 removed outlier: 7.034A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3266 1.32 - 1.44: 5351 1.44 - 1.57: 11515 1.57 - 1.69: 16 1.69 - 1.81: 202 Bond restraints: 20350 Sorted by residual: bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.25e-02 6.40e+03 1.37e+01 bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.25e-02 6.40e+03 1.37e+01 bond pdb=" O12 POV D1102 " pdb=" P POV D1102 " ideal model delta sigma weight residual 1.657 1.593 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O12 POV B1101 " pdb=" P POV B1101 " ideal model delta sigma weight residual 1.657 1.593 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C GLU B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.337 1.372 -0.035 1.11e-02 8.12e+03 1.01e+01 ... (remaining 20345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 26673 2.60 - 5.19: 673 5.19 - 7.79: 84 7.79 - 10.39: 13 10.39 - 12.99: 3 Bond angle restraints: 27446 Sorted by residual: angle pdb=" N GLN B 570 " pdb=" CA GLN B 570 " pdb=" C GLN B 570 " ideal model delta sigma weight residual 113.23 100.24 12.99 1.24e+00 6.50e-01 1.10e+02 angle pdb=" N GLN D 570 " pdb=" CA GLN D 570 " pdb=" C GLN D 570 " ideal model delta sigma weight residual 112.90 101.26 11.64 1.31e+00 5.83e-01 7.90e+01 angle pdb=" C ASP D 153 " pdb=" N VAL D 154 " pdb=" CA VAL D 154 " ideal model delta sigma weight residual 120.33 125.15 -4.82 8.00e-01 1.56e+00 3.64e+01 angle pdb=" C ASP B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta sigma weight residual 120.33 125.14 -4.81 8.00e-01 1.56e+00 3.61e+01 angle pdb=" C LYS A 368 " pdb=" N ARG A 369 " pdb=" CA ARG A 369 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 ... (remaining 27441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 12000 35.59 - 71.17: 172 71.17 - 106.76: 25 106.76 - 142.34: 5 142.34 - 177.93: 6 Dihedral angle restraints: 12208 sinusoidal: 5168 harmonic: 7040 Sorted by residual: dihedral pdb=" CA ARG A 369 " pdb=" C ARG A 369 " pdb=" N LEU A 370 " pdb=" CA LEU A 370 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA ARG C 369 " pdb=" C ARG C 369 " pdb=" N LEU C 370 " pdb=" CA LEU C 370 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PHE D 601 " pdb=" C PHE D 601 " pdb=" N GLY D 602 " pdb=" CA GLY D 602 " ideal model delta harmonic sigma weight residual 180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 12205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2578 0.060 - 0.121: 444 0.121 - 0.181: 51 0.181 - 0.242: 9 0.242 - 0.302: 6 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CG LEU A 535 " pdb=" CB LEU A 535 " pdb=" CD1 LEU A 535 " pdb=" CD2 LEU A 535 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C2 POV B1103 " pdb=" C1 POV B1103 " pdb=" C3 POV B1103 " pdb=" O21 POV B1103 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2 POV D1101 " pdb=" C1 POV D1101 " pdb=" C3 POV D1101 " pdb=" O21 POV D1101 " both_signs ideal model delta sigma weight residual False 2.43 2.17 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3085 not shown) Planarity restraints: 3374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 71 " -0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ASN B 71 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN B 71 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE B 72 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 71 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ASN D 71 " -0.066 2.00e-02 2.50e+03 pdb=" O ASN D 71 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE D 72 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 73 " 0.271 9.50e-02 1.11e+02 1.21e-01 9.04e+00 pdb=" NE ARG D 73 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 73 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 73 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 73 " 0.010 2.00e-02 2.50e+03 ... (remaining 3371 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5416 2.80 - 3.32: 16875 3.32 - 3.85: 30603 3.85 - 4.37: 36746 4.37 - 4.90: 62350 Nonbonded interactions: 151990 Sorted by model distance: nonbonded pdb=" O21 POV B1102 " pdb=" O31 POV B1102 " model vdw 2.274 2.432 nonbonded pdb=" O21 POV D1103 " pdb=" O31 POV D1103 " model vdw 2.276 2.432 nonbonded pdb=" O GLU A 334 " pdb=" OG1 THR A 343 " model vdw 2.278 3.040 nonbonded pdb=" O GLU C 334 " pdb=" OG1 THR C 343 " model vdw 2.279 3.040 nonbonded pdb=" OG SER D 444 " pdb=" O14 POV D1102 " model vdw 2.319 3.040 ... (remaining 151985 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.990 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.005 0.064 20350 Z= 0.251 Angle : 1.021 12.986 27446 Z= 0.611 Chirality : 0.047 0.302 3088 Planarity : 0.006 0.121 3374 Dihedral : 13.955 177.927 7628 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.49 % Favored : 92.95 % Rotamer: Outliers : 0.71 % Allowed : 5.94 % Favored : 93.36 % 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: -6.60 (0.10), residues: 2356 helix: -4.67 (0.05), residues: 1516 sheet: -1.65 (0.49), residues: 76 loop : -3.48 (0.17), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 693 TYR 0.017 0.002 TYR D 575 PHE 0.030 0.002 PHE D 445 TRP 0.026 0.002 TRP B 692 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.25 (20350) covalent geometry : angle 1.02105 / 0.61 (27446) hydrogen bonds : bond 0.33541 / 21.71 ( 879) hydrogen bonds : angle 9.72459 / 6.67 ( 2607) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 349 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8815 (mmmt) REVERT: A 422 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7315 (mt) REVERT: A 555 MET cc_start: 0.6940 (mtp) cc_final: 0.6591 (ttp) REVERT: B 121 LYS cc_start: 0.7645 (mmpt) cc_final: 0.7395 (mttm) REVERT: B 131 CYS cc_start: 0.9117 (m) cc_final: 0.8712 (m) REVERT: B 320 MET cc_start: 0.9271 (mmt) cc_final: 0.9043 (mmt) REVERT: B 545 LYS cc_start: 0.8028 (pmmt) cc_final: 0.7619 (mmmm) REVERT: B 599 LEU cc_start: 0.7145 (tt) cc_final: 0.6600 (mp) REVERT: C 152 GLU cc_start: 0.7602 (pt0) cc_final: 0.7033 (tm-30) REVERT: D 211 GLU cc_start: 0.7904 (pp20) cc_final: 0.7397 (pp20) REVERT: D 514 GLN cc_start: 0.7841 (tt0) cc_final: 0.7635 (mp10) outliers start: 15 outliers final: 3 residues processed: 357 average time/residue: 0.1841 time to fit residues: 94.5336 Evaluate side-chains 181 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 177 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain D residue 563 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN A 412 ASN A 452 ASN A 570 GLN A 683 ASN A 750 ASN B 143 GLN B 220 ASN B 314 ASN B 410 ASN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN C 220 ASN C 412 ASN C 430 HIS C 570 GLN C 683 ASN C 750 ASN D 143 GLN D 178 ASN D 220 ASN D 314 ASN D 410 ASN D 430 HIS D 750 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.121874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087647 restraints weight = 35084.024| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.21 r_work: 0.3113 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20350 Z= 0.127 Angle : 0.612 8.421 27446 Z= 0.318 Chirality : 0.038 0.160 3088 Planarity : 0.005 0.075 3374 Dihedral : 14.215 172.403 2945 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.46 % Rotamer: Outliers : 1.70 % Allowed : 8.20 % Favored : 90.10 % 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: -3.85 (0.14), residues: 2356 helix: -2.23 (0.10), residues: 1522 sheet: -0.40 (0.55), residues: 66 loop : -3.12 (0.18), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 567 TYR 0.019 0.001 TYR D 547 PHE 0.022 0.001 PHE B 445 TRP 0.018 0.001 TRP B 692 HIS 0.004 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (20350) covalent geometry : angle 0.61181 / 0.32 (27446) hydrogen bonds : bond 0.05112 / 3.25 ( 879) hydrogen bonds : angle 4.11906 / 2.84 ( 2607) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.9276 (mtmt) cc_final: 0.8859 (mmmt) REVERT: A 514 GLN cc_start: 0.7782 (pp30) cc_final: 0.7495 (pp30) REVERT: A 555 MET cc_start: 0.7160 (mtp) cc_final: 0.6734 (ttp) REVERT: B 121 LYS cc_start: 0.7083 (mmpt) cc_final: 0.6811 (mttm) REVERT: B 253 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8623 (mmpt) REVERT: B 516 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7767 (pp) REVERT: B 562 MET cc_start: 0.8775 (mmm) cc_final: 0.8565 (mmm) REVERT: C 443 LEU cc_start: 0.7536 (tt) cc_final: 0.7333 (mt) REVERT: C 562 MET cc_start: 0.8243 (tpp) cc_final: 0.7969 (mmm) REVERT: D 211 GLU cc_start: 0.8243 (pp20) cc_final: 0.7803 (tm-30) REVERT: D 514 GLN cc_start: 0.8065 (tt0) cc_final: 0.7496 (mp10) REVERT: D 516 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7574 (pp) outliers start: 36 outliers final: 14 residues processed: 223 average time/residue: 0.1405 time to fit residues: 49.3772 Evaluate side-chains 187 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 176 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 178 ASN B 430 HIS D 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.118620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.083408 restraints weight = 35138.731| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.21 r_work: 0.3039 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20350 Z= 0.137 Angle : 0.570 11.614 27446 Z= 0.289 Chirality : 0.038 0.171 3088 Planarity : 0.004 0.070 3374 Dihedral : 12.968 153.514 2940 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.49 % Favored : 93.29 % Rotamer: Outliers : 1.84 % Allowed : 10.04 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.16), residues: 2356 helix: -0.53 (0.13), residues: 1514 sheet: 0.57 (0.58), residues: 66 loop : -2.73 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 188 TYR 0.020 0.001 TYR D 547 PHE 0.028 0.001 PHE D 445 TRP 0.011 0.001 TRP C 742 HIS 0.004 0.001 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (20350) covalent geometry : angle 0.57006 / 0.29 (27446) hydrogen bonds : bond 0.04084 / 2.61 ( 879) hydrogen bonds : angle 3.49782 / 2.38 ( 2607) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: A 311 LYS cc_start: 0.9256 (mtmt) cc_final: 0.8997 (mmtt) REVERT: B 121 LYS cc_start: 0.7100 (mmpt) cc_final: 0.6846 (mttm) REVERT: B 253 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8733 (mmpt) REVERT: B 322 ASP cc_start: 0.8721 (t0) cc_final: 0.8381 (m-30) REVERT: B 431 MET cc_start: 0.8236 (mmm) cc_final: 0.7957 (mmm) REVERT: B 516 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7752 (pp) REVERT: C 283 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: D 211 GLU cc_start: 0.8347 (pp20) cc_final: 0.7983 (tm-30) REVERT: D 253 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8600 (mmpt) REVERT: D 324 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8083 (mp) REVERT: D 431 MET cc_start: 0.8297 (mmm) cc_final: 0.8084 (mmm) REVERT: D 514 GLN cc_start: 0.8185 (tt0) cc_final: 0.7729 (mp10) REVERT: D 516 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7601 (pp) REVERT: D 544 TYR cc_start: 0.5860 (m-80) cc_final: 0.5618 (m-80) REVERT: D 574 MET cc_start: 0.9008 (mtt) cc_final: 0.8787 (mtt) outliers start: 39 outliers final: 21 residues processed: 213 average time/residue: 0.1186 time to fit residues: 40.6794 Evaluate side-chains 197 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 653 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 147 optimal weight: 0.0570 chunk 20 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 76 optimal weight: 0.0470 chunk 197 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.121157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086210 restraints weight = 35089.843| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.23 r_work: 0.3087 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20350 Z= 0.086 Angle : 0.496 10.311 27446 Z= 0.251 Chirality : 0.036 0.129 3088 Planarity : 0.003 0.073 3374 Dihedral : 12.219 141.921 2940 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.15 % Favored : 93.68 % Rotamer: Outliers : 1.89 % Allowed : 10.18 % Favored : 87.94 % 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: -0.95 (0.17), residues: 2356 helix: 0.24 (0.13), residues: 1520 sheet: 0.93 (0.58), residues: 66 loop : -2.51 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.015 0.001 TYR D 547 PHE 0.016 0.001 PHE C 489 TRP 0.009 0.001 TRP B 739 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.09 (20350) covalent geometry : angle 0.49553 / 0.25 (27446) hydrogen bonds : bond 0.02937 / 1.88 ( 879) hydrogen bonds : angle 3.22475 / 2.19 ( 2607) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: A 311 LYS cc_start: 0.9200 (mtmt) cc_final: 0.8931 (mmtt) REVERT: A 320 MET cc_start: 0.8754 (mmm) cc_final: 0.8004 (mmm) REVERT: B 76 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6939 (tp) REVERT: B 121 LYS cc_start: 0.7093 (mmpt) cc_final: 0.6816 (mttm) REVERT: B 147 ARG cc_start: 0.8053 (mtt90) cc_final: 0.7810 (mtt90) REVERT: B 253 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8706 (mmpt) REVERT: B 431 MET cc_start: 0.8114 (mmm) cc_final: 0.7869 (mmm) REVERT: B 516 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7817 (pp) REVERT: B 562 MET cc_start: 0.9006 (mmt) cc_final: 0.8780 (mmt) REVERT: B 738 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8679 (mtpp) REVERT: B 741 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: C 283 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: C 320 MET cc_start: 0.8570 (mmm) cc_final: 0.7844 (mmm) REVERT: C 575 TYR cc_start: 0.3096 (OUTLIER) cc_final: 0.1342 (p90) REVERT: D 211 GLU cc_start: 0.8316 (pp20) cc_final: 0.7984 (tm-30) REVERT: D 253 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8600 (mmpt) REVERT: D 324 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8133 (mp) REVERT: D 431 MET cc_start: 0.8252 (mmm) cc_final: 0.8014 (mmm) REVERT: D 514 GLN cc_start: 0.8159 (tt0) cc_final: 0.7729 (mp10) REVERT: D 516 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7677 (pp) REVERT: D 574 MET cc_start: 0.8931 (mtt) cc_final: 0.8693 (mtt) outliers start: 40 outliers final: 18 residues processed: 211 average time/residue: 0.1211 time to fit residues: 40.6421 Evaluate side-chains 200 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS B 452 ASN C 150 HIS C 274 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.117227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.083278 restraints weight = 34733.779| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.19 r_work: 0.3039 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20350 Z= 0.114 Angle : 0.516 8.706 27446 Z= 0.261 Chirality : 0.037 0.132 3088 Planarity : 0.003 0.074 3374 Dihedral : 11.621 126.242 2938 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.58 % Favored : 93.25 % Rotamer: Outliers : 2.21 % Allowed : 10.84 % Favored : 86.95 % 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: -0.35 (0.17), residues: 2356 helix: 0.74 (0.14), residues: 1522 sheet: 1.29 (0.56), residues: 66 loop : -2.39 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.017 0.001 TYR D 547 PHE 0.019 0.001 PHE D 445 TRP 0.008 0.001 TRP B 739 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (20350) covalent geometry : angle 0.51568 / 0.26 (27446) hydrogen bonds : bond 0.03160 / 2.02 ( 879) hydrogen bonds : angle 3.22046 / 2.18 ( 2607) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7833 (mm-30) REVERT: A 311 LYS cc_start: 0.9189 (mtmt) cc_final: 0.8902 (mmtt) REVERT: B 121 LYS cc_start: 0.7073 (mmpt) cc_final: 0.6829 (mttm) REVERT: B 159 MET cc_start: 0.8083 (mmm) cc_final: 0.7866 (mmm) REVERT: B 253 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8757 (mmpt) REVERT: B 431 MET cc_start: 0.8198 (mmm) cc_final: 0.7957 (mmm) REVERT: B 516 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7800 (pp) REVERT: B 738 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9074 (mtpp) REVERT: C 283 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: C 575 TYR cc_start: 0.3138 (OUTLIER) cc_final: 0.1401 (p90) REVERT: D 211 GLU cc_start: 0.8400 (pp20) cc_final: 0.8121 (tm-30) REVERT: D 253 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8609 (mmpt) REVERT: D 324 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8057 (mp) REVERT: D 431 MET cc_start: 0.8252 (mmm) cc_final: 0.8018 (mmm) REVERT: D 514 GLN cc_start: 0.8259 (tt0) cc_final: 0.7838 (mp10) REVERT: D 516 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7665 (pp) REVERT: D 574 MET cc_start: 0.9020 (mtt) cc_final: 0.8762 (mtt) outliers start: 47 outliers final: 20 residues processed: 215 average time/residue: 0.1234 time to fit residues: 42.1578 Evaluate side-chains 195 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 65 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 206 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.119251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084339 restraints weight = 34887.744| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.19 r_work: 0.3054 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20350 Z= 0.098 Angle : 0.503 8.709 27446 Z= 0.251 Chirality : 0.036 0.128 3088 Planarity : 0.003 0.073 3374 Dihedral : 11.110 125.911 2936 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.11 % Favored : 93.72 % Rotamer: Outliers : 2.21 % Allowed : 11.45 % Favored : 86.33 % 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: 0.04 (0.17), residues: 2356 helix: 1.06 (0.14), residues: 1520 sheet: 1.48 (0.55), residues: 66 loop : -2.28 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 690 TYR 0.013 0.001 TYR D 547 PHE 0.016 0.001 PHE C 316 TRP 0.008 0.001 TRP B 739 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (20350) covalent geometry : angle 0.50252 / 0.25 (27446) hydrogen bonds : bond 0.02818 / 1.81 ( 879) hydrogen bonds : angle 3.11233 / 2.11 ( 2607) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7791 (mm-30) REVERT: A 286 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: A 311 LYS cc_start: 0.9151 (mtmt) cc_final: 0.8886 (mmtt) REVERT: A 578 MET cc_start: 0.4968 (OUTLIER) cc_final: 0.4206 (ptm) REVERT: B 121 LYS cc_start: 0.7037 (mmpt) cc_final: 0.6799 (mttm) REVERT: B 147 ARG cc_start: 0.7808 (mtt90) cc_final: 0.7570 (mtt90) REVERT: B 253 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8755 (mmpt) REVERT: B 431 MET cc_start: 0.8155 (mmm) cc_final: 0.7916 (mmm) REVERT: B 516 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7730 (pp) REVERT: B 738 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9054 (mtpp) REVERT: C 286 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: C 320 MET cc_start: 0.8431 (mmm) cc_final: 0.8063 (mmm) REVERT: C 575 TYR cc_start: 0.3075 (OUTLIER) cc_final: 0.1380 (p90) REVERT: D 211 GLU cc_start: 0.8371 (pp20) cc_final: 0.8101 (tm-30) REVERT: D 253 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8618 (mmpt) REVERT: D 431 MET cc_start: 0.8180 (mmm) cc_final: 0.7952 (mmm) REVERT: D 514 GLN cc_start: 0.8229 (tt0) cc_final: 0.7865 (mp10) REVERT: D 516 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7653 (pp) REVERT: D 574 MET cc_start: 0.8937 (mtt) cc_final: 0.8719 (mtt) outliers start: 47 outliers final: 25 residues processed: 207 average time/residue: 0.1276 time to fit residues: 42.4126 Evaluate side-chains 203 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 13 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 17 optimal weight: 0.0170 chunk 162 optimal weight: 1.9990 chunk 198 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 28 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 199 optimal weight: 0.6980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN B 452 ASN C 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085426 restraints weight = 34801.687| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.22 r_work: 0.3071 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20350 Z= 0.085 Angle : 0.489 8.773 27446 Z= 0.244 Chirality : 0.036 0.131 3088 Planarity : 0.003 0.077 3374 Dihedral : 10.845 124.685 2936 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.20 % Favored : 93.63 % Rotamer: Outliers : 1.84 % Allowed : 11.64 % Favored : 86.52 % 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: 0.37 (0.18), residues: 2356 helix: 1.34 (0.14), residues: 1518 sheet: 1.73 (0.54), residues: 66 loop : -2.20 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 690 TYR 0.013 0.001 TYR A 208 PHE 0.015 0.001 PHE C 316 TRP 0.009 0.001 TRP B 739 HIS 0.002 0.000 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 (20350) covalent geometry : angle 0.48882 / 0.24 (27446) hydrogen bonds : bond 0.02554 / 1.64 ( 879) hydrogen bonds : angle 3.02191 / 2.05 ( 2607) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7743 (mm-30) REVERT: A 286 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: A 311 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8752 (mmtt) REVERT: A 423 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6090 (mt-10) REVERT: A 431 MET cc_start: 0.7862 (ttm) cc_final: 0.7436 (ttm) REVERT: A 578 MET cc_start: 0.4846 (OUTLIER) cc_final: 0.4092 (ptm) REVERT: B 121 LYS cc_start: 0.7076 (mmpt) cc_final: 0.6828 (mttm) REVERT: B 159 MET cc_start: 0.8023 (mmm) cc_final: 0.7800 (mmm) REVERT: B 253 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8745 (mmpt) REVERT: B 514 GLN cc_start: 0.7794 (mp10) cc_final: 0.7533 (mp10) REVERT: B 516 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7741 (pp) REVERT: B 738 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9064 (mtpp) REVERT: C 286 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8222 (pm20) REVERT: C 320 MET cc_start: 0.8430 (mmm) cc_final: 0.7978 (mmm) REVERT: C 575 TYR cc_start: 0.2967 (OUTLIER) cc_final: 0.1208 (p90) REVERT: D 146 CYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8515 (p) REVERT: D 147 ARG cc_start: 0.8596 (mtt90) cc_final: 0.8152 (mtt90) REVERT: D 211 GLU cc_start: 0.8361 (pp20) cc_final: 0.8107 (tm-30) REVERT: D 253 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8638 (mmpt) REVERT: D 514 GLN cc_start: 0.8197 (tt0) cc_final: 0.7873 (mp10) REVERT: D 516 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7641 (pp) outliers start: 39 outliers final: 18 residues processed: 209 average time/residue: 0.1272 time to fit residues: 42.2984 Evaluate side-chains 201 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 214 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.119139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.083595 restraints weight = 34784.806| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.21 r_work: 0.3039 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20350 Z= 0.110 Angle : 0.503 8.018 27446 Z= 0.252 Chirality : 0.037 0.125 3088 Planarity : 0.003 0.076 3374 Dihedral : 10.725 122.911 2936 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.11 % Favored : 93.72 % Rotamer: Outliers : 1.98 % Allowed : 11.73 % Favored : 86.29 % 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: 0.50 (0.18), residues: 2356 helix: 1.43 (0.14), residues: 1518 sheet: 1.98 (0.53), residues: 66 loop : -2.14 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 690 TYR 0.014 0.001 TYR D 547 PHE 0.015 0.001 PHE B 445 TRP 0.007 0.001 TRP A 559 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (20350) covalent geometry : angle 0.50283 / 0.25 (27446) hydrogen bonds : bond 0.02800 / 1.80 ( 879) hydrogen bonds : angle 3.04830 / 2.06 ( 2607) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: A 286 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: A 311 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8731 (mmtt) REVERT: A 423 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6139 (mt-10) REVERT: A 578 MET cc_start: 0.4837 (OUTLIER) cc_final: 0.4081 (ptm) REVERT: B 121 LYS cc_start: 0.7071 (mmpt) cc_final: 0.6848 (mttm) REVERT: B 253 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8786 (mmpt) REVERT: B 514 GLN cc_start: 0.7787 (mp10) cc_final: 0.7531 (mp10) REVERT: B 516 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7678 (pp) REVERT: B 738 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8584 (mtpp) REVERT: B 741 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: C 286 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: C 575 TYR cc_start: 0.2945 (OUTLIER) cc_final: 0.1207 (p90) REVERT: D 146 CYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8505 (p) REVERT: D 147 ARG cc_start: 0.8469 (mtt90) cc_final: 0.8025 (mtt90) REVERT: D 159 MET cc_start: 0.7806 (mmm) cc_final: 0.7589 (mmm) REVERT: D 211 GLU cc_start: 0.8383 (pp20) cc_final: 0.8140 (tm-30) REVERT: D 253 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8660 (mmpt) REVERT: D 514 GLN cc_start: 0.8252 (tt0) cc_final: 0.7904 (mp10) REVERT: D 516 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7609 (pp) REVERT: D 574 MET cc_start: 0.8919 (mtt) cc_final: 0.8709 (mtt) outliers start: 42 outliers final: 25 residues processed: 206 average time/residue: 0.1364 time to fit residues: 44.3611 Evaluate side-chains 209 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 156 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 173 optimal weight: 0.0010 chunk 15 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 452 ASN C 160 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.119770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085745 restraints weight = 34609.150| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.21 r_work: 0.3078 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20350 Z= 0.083 Angle : 0.494 9.610 27446 Z= 0.245 Chirality : 0.036 0.133 3088 Planarity : 0.003 0.075 3374 Dihedral : 10.422 122.734 2936 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.15 % Favored : 93.72 % Rotamer: Outliers : 1.65 % Allowed : 12.06 % Favored : 86.29 % 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: 0.70 (0.18), residues: 2356 helix: 1.59 (0.14), residues: 1518 sheet: 2.18 (0.54), residues: 66 loop : -2.08 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 690 TYR 0.014 0.001 TYR D 547 PHE 0.016 0.001 PHE C 316 TRP 0.007 0.001 TRP A 710 HIS 0.006 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.08 (20350) covalent geometry : angle 0.49389 / 0.24 (27446) hydrogen bonds : bond 0.02420 / 1.56 ( 879) hydrogen bonds : angle 2.95912 / 2.01 ( 2607) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: A 286 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: A 311 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8713 (mmtt) REVERT: A 423 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6189 (mt-10) REVERT: A 514 GLN cc_start: 0.7554 (pp30) cc_final: 0.7335 (pp30) REVERT: A 578 MET cc_start: 0.4715 (OUTLIER) cc_final: 0.3997 (ptm) REVERT: B 121 LYS cc_start: 0.7076 (mmpt) cc_final: 0.6862 (mttm) REVERT: B 159 MET cc_start: 0.7972 (mmm) cc_final: 0.7712 (mmm) REVERT: B 253 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8714 (mmpt) REVERT: B 514 GLN cc_start: 0.7803 (mp10) cc_final: 0.7542 (mp10) REVERT: B 516 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7762 (pp) REVERT: B 738 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8572 (mtpp) REVERT: B 741 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: C 286 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: C 320 MET cc_start: 0.8443 (mmm) cc_final: 0.8018 (mmm) REVERT: C 514 GLN cc_start: 0.7060 (pp30) cc_final: 0.6835 (pp30) REVERT: C 575 TYR cc_start: 0.2863 (OUTLIER) cc_final: 0.1176 (p90) REVERT: D 146 CYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8585 (p) REVERT: D 147 ARG cc_start: 0.8472 (mtt90) cc_final: 0.8051 (mtt90) REVERT: D 211 GLU cc_start: 0.8354 (pp20) cc_final: 0.8122 (tm-30) REVERT: D 253 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8647 (mmpt) REVERT: D 514 GLN cc_start: 0.8236 (tt0) cc_final: 0.7910 (mp10) REVERT: D 516 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7634 (pp) outliers start: 35 outliers final: 20 residues processed: 206 average time/residue: 0.1294 time to fit residues: 41.8256 Evaluate side-chains 205 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 131 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 170 optimal weight: 0.6980 chunk 190 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.120983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085651 restraints weight = 34799.859| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.22 r_work: 0.3073 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20350 Z= 0.085 Angle : 0.499 11.045 27446 Z= 0.245 Chirality : 0.036 0.129 3088 Planarity : 0.003 0.070 3374 Dihedral : 10.207 121.233 2936 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.03 % Favored : 93.85 % Rotamer: Outliers : 1.51 % Allowed : 12.11 % Favored : 86.38 % 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: 0.82 (0.18), residues: 2356 helix: 1.68 (0.14), residues: 1516 sheet: 2.33 (0.54), residues: 66 loop : -2.03 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 690 TYR 0.014 0.001 TYR D 547 PHE 0.015 0.001 PHE C 316 TRP 0.007 0.001 TRP C 559 HIS 0.004 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 (20350) covalent geometry : angle 0.49950 / 0.24 (27446) hydrogen bonds : bond 0.02442 / 1.58 ( 879) hydrogen bonds : angle 2.94002 / 1.99 ( 2607) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: A 286 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: A 311 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8737 (mmtt) REVERT: A 423 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6209 (mt-10) REVERT: A 514 GLN cc_start: 0.7519 (pp30) cc_final: 0.7299 (pp30) REVERT: A 578 MET cc_start: 0.4681 (OUTLIER) cc_final: 0.3985 (ptm) REVERT: B 121 LYS cc_start: 0.7078 (mmpt) cc_final: 0.6862 (mttm) REVERT: B 159 MET cc_start: 0.7982 (mmm) cc_final: 0.7720 (mmm) REVERT: B 253 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8710 (mmpt) REVERT: B 514 GLN cc_start: 0.7802 (mp10) cc_final: 0.7542 (mp10) REVERT: B 516 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7729 (pp) REVERT: B 709 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7862 (pm20) REVERT: B 738 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8566 (mtpp) REVERT: B 741 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: C 286 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: C 311 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8455 (mmtt) REVERT: C 320 MET cc_start: 0.8446 (mmm) cc_final: 0.8005 (mmm) REVERT: C 514 GLN cc_start: 0.6936 (pp30) cc_final: 0.6689 (pp30) REVERT: C 575 TYR cc_start: 0.2930 (OUTLIER) cc_final: 0.1220 (p90) REVERT: D 146 CYS cc_start: 0.8852 (m) cc_final: 0.8573 (p) REVERT: D 147 ARG cc_start: 0.8442 (mtt90) cc_final: 0.8032 (mtt90) REVERT: D 253 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8651 (mmpt) REVERT: D 514 GLN cc_start: 0.8254 (tt0) cc_final: 0.7921 (mp10) REVERT: D 516 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7607 (pp) REVERT: D 709 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7905 (pm20) outliers start: 32 outliers final: 21 residues processed: 200 average time/residue: 0.1458 time to fit residues: 46.1847 Evaluate side-chains 206 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 99 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 47 optimal weight: 0.0270 chunk 24 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.121577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086325 restraints weight = 34815.112| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.23 r_work: 0.3085 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20350 Z= 0.081 Angle : 0.491 10.244 27446 Z= 0.241 Chirality : 0.036 0.148 3088 Planarity : 0.003 0.072 3374 Dihedral : 9.990 119.886 2936 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 1.46 % Allowed : 12.21 % Favored : 86.33 % 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: 0.94 (0.18), residues: 2356 helix: 1.76 (0.14), residues: 1518 sheet: 2.35 (0.54), residues: 66 loop : -1.97 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 690 TYR 0.014 0.001 TYR D 547 PHE 0.020 0.001 PHE A 489 TRP 0.009 0.001 TRP A 559 HIS 0.004 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.08 (20350) covalent geometry : angle 0.49121 / 0.24 (27446) hydrogen bonds : bond 0.02336 / 1.51 ( 879) hydrogen bonds : angle 2.90302 / 1.96 ( 2607) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.07 seconds wall clock time: 73 minutes 22.00 seconds (4402.00 seconds total)