Starting phenix.real_space_refine on Fri Aug 7 16:01:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13lj_77134/08_2026/13lj_77134.cif Found real_map, /net/cci-nas-00/data/ceres_data/13lj_77134/08_2026/13lj_77134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13lj_77134/08_2026/13lj_77134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13lj_77134/08_2026/13lj_77134.map" model { file = "/net/cci-nas-00/data/ceres_data/13lj_77134/08_2026/13lj_77134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13lj_77134/08_2026/13lj_77134.cif" } resolution = 2.86 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= 0.002 sd= 0.021 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: 6 Type Number sf(0) Gaussians P 32 5.49 5 S 128 5.16 5 Na 4 4.78 5 C 14584 2.51 5 N 3396 2.21 5 O 4033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s 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: 22177 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "B" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "C" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "D" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 471 Unusual residues: {' NA': 3, 'POV': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 365 Unusual residues: {' NA': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Time building chain proxies: 4.07, per 1000 atoms: 0.18 Number of scatterers: 22177 At special positions: 0 Unit cell: (152.28, 153.126, 128.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 32 15.00 Na 4 11.00 O 4033 8.00 N 3396 7.00 C 14584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 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: 1.43 Conformation dependent library (CDL) restraints added in 920.6 milliseconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4784 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 4 sheets defined 64.3% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 4.082A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.533A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 153 through 161 removed outlier: 3.758A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.553A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.518A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.665A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.565A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.817A pdb=" N LEU A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.605A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.556A pdb=" N THR A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.742A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.685A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 461 removed outlier: 3.567A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.685A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 507 removed outlier: 3.844A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.767A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.930A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.509A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.510A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 666 removed outlier: 3.566A pdb=" N LEU A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 685 removed outlier: 3.603A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.582A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.698A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 4.082A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 removed outlier: 3.533A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.757A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.554A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.519A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.666A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.566A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.817A pdb=" N LEU B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.605A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.556A pdb=" N THR B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.741A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.679A 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 415 through 419 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.686A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 461 removed outlier: 3.567A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.686A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 507 removed outlier: 3.844A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.767A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.930A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.509A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.510A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 650 through 666 removed outlier: 3.567A pdb=" N LEU B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.603A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.583A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.698A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 removed outlier: 4.082A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.534A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.758A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.554A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.519A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.665A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.565A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.816A pdb=" N LEU C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.605A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 removed outlier: 3.556A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.742A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.685A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 461 removed outlier: 3.567A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 488 Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.686A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 507 removed outlier: 3.844A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.767A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.930A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 removed outlier: 3.509A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.510A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 650 through 666 removed outlier: 3.568A pdb=" N LEU C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.602A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 705 removed outlier: 3.582A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.698A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 4.083A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 removed outlier: 3.534A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 153 through 161 removed outlier: 3.758A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.554A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.518A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.665A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.566A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.816A pdb=" N LEU D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.605A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 removed outlier: 3.556A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.741A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.679A 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 415 through 419 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.685A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 461 removed outlier: 3.568A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 488 Processing helix chain 'D' and resid 488 through 493 removed outlier: 3.686A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 507 removed outlier: 3.844A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 520 Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.767A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.929A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 removed outlier: 3.508A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.509A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 666 removed outlier: 3.567A pdb=" N LEU D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 662 " --> pdb=" O LEU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.604A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 705 removed outlier: 3.582A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.698A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.785A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.785A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 7.123A 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: 6.785A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.786A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2700 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: 2.96 Time building geometry restraints manager: 2.01 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: 3540 1.32 - 1.44: 5571 1.44 - 1.56: 13049 1.56 - 1.69: 68 1.69 - 1.81: 208 Bond restraints: 22436 Sorted by residual: bond pdb=" O12 POV D1108 " pdb=" P POV D1108 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O12 POV C1105 " pdb=" P POV C1105 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O12 POV B1106 " pdb=" P POV B1106 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O12 POV A1105 " pdb=" P POV A1105 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O12 POV B1103 " pdb=" P POV B1103 " ideal model delta sigma weight residual 1.657 1.590 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 22431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 28164 1.93 - 3.86: 1547 3.86 - 5.79: 207 5.79 - 7.72: 94 7.72 - 9.65: 20 Bond angle restraints: 30032 Sorted by residual: angle pdb=" C ASP A 153 " pdb=" N VAL A 154 " pdb=" CA VAL A 154 " ideal model delta sigma weight residual 120.33 123.95 -3.62 8.00e-01 1.56e+00 2.04e+01 angle pdb=" C ASP D 153 " pdb=" N VAL D 154 " pdb=" CA VAL D 154 " ideal model delta sigma weight residual 120.33 123.93 -3.60 8.00e-01 1.56e+00 2.03e+01 angle pdb=" C ASP C 153 " pdb=" N VAL C 154 " pdb=" CA VAL C 154 " ideal model delta sigma weight residual 120.33 123.89 -3.56 8.00e-01 1.56e+00 1.99e+01 angle pdb=" C ASP B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta sigma weight residual 120.33 123.89 -3.56 8.00e-01 1.56e+00 1.98e+01 angle pdb=" C GLN A 313 " pdb=" N ASN A 314 " pdb=" CA ASN A 314 " ideal model delta sigma weight residual 120.89 114.57 6.32 1.50e+00 4.44e-01 1.77e+01 ... (remaining 30027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 13290 35.18 - 70.37: 378 70.37 - 105.55: 57 105.55 - 140.73: 34 140.73 - 175.92: 37 Dihedral angle restraints: 13796 sinusoidal: 6428 harmonic: 7368 Sorted by residual: dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual 93.00 -176.77 -90.23 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 -176.79 -90.21 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual 93.00 -176.79 -90.21 1 1.00e+01 1.00e-02 9.63e+01 ... (remaining 13793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2791 0.069 - 0.138: 382 0.138 - 0.206: 56 0.206 - 0.275: 0 0.275 - 0.344: 7 Chirality restraints: 3236 Sorted by residual: chirality pdb=" CG LEU D 429 " pdb=" CB LEU D 429 " pdb=" CD1 LEU D 429 " pdb=" CD2 LEU D 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CG LEU B 429 " pdb=" CB LEU B 429 " pdb=" CD1 LEU B 429 " pdb=" CD2 LEU B 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CG LEU A 429 " pdb=" CB LEU A 429 " pdb=" CD1 LEU A 429 " pdb=" CD2 LEU A 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 3233 not shown) Planarity restraints: 3608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 622 " 0.010 2.00e-02 2.50e+03 1.68e-02 5.62e+00 pdb=" CG TYR A 622 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 622 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 622 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 622 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 622 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 622 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 622 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 622 " -0.010 2.00e-02 2.50e+03 1.68e-02 5.61e+00 pdb=" CG TYR B 622 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 622 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 622 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 622 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 622 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 622 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 622 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 622 " -0.010 2.00e-02 2.50e+03 1.67e-02 5.56e+00 pdb=" CG TYR C 622 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR C 622 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR C 622 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 622 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR C 622 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 622 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 622 " 0.000 2.00e-02 2.50e+03 ... (remaining 3605 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 166 2.61 - 3.18: 16717 3.18 - 3.75: 32021 3.75 - 4.33: 48820 4.33 - 4.90: 79961 Nonbonded interactions: 177685 Sorted by model distance: nonbonded pdb="NA NA A1110 " pdb="NA NA A1111 " model vdw 2.034 1.900 nonbonded pdb="NA NA A1110 " pdb="NA NA C1108 " model vdw 2.086 1.900 nonbonded pdb=" O PRO B 753 " pdb=" OH TYR C 213 " model vdw 2.140 3.040 nonbonded pdb=" O PRO C 753 " pdb=" OH TYR D 213 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO D 753 " model vdw 2.274 3.040 ... (remaining 177680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 118 through 1107) selection = (chain 'B' and resid 118 through 1107) selection = (chain 'C' and resid 118 through 1107) selection = (chain 'D' and resid 118 through 1107) } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.800 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.008 0.069 22440 Z= 0.357 Angle : 1.028 9.653 30040 Z= 0.509 Chirality : 0.053 0.344 3236 Planarity : 0.006 0.046 3608 Dihedral : 19.986 175.918 9000 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.11 % Favored : 94.57 % Rotamer: Outliers : 0.45 % Allowed : 3.15 % Favored : 96.40 % 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: -5.89 (0.11), residues: 2484 helix: -4.56 (0.05), residues: 1508 sheet: -0.73 (0.47), residues: 112 loop : -2.62 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 226 TYR 0.037 0.004 TYR D 622 PHE 0.020 0.003 PHE A 715 TRP 0.019 0.002 TRP D 692 HIS 0.011 0.003 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00802 / 0.36 (22436) covalent geometry : angle 1.02760 / 0.51 (30032) SS BOND : bond 0.00248 / 0.12 ( 4) SS BOND : angle 1.79587 / 1.10 ( 8) hydrogen bonds : bond 0.33373 / 21.89 ( 920) hydrogen bonds : angle 10.11090 / 7.01 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 443 time to evaluate : 0.713 Fit side-chains REVERT: A 174 LYS cc_start: 0.7449 (tptt) cc_final: 0.7053 (tptp) REVERT: A 202 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6568 (ptm160) REVERT: A 217 THR cc_start: 0.8344 (m) cc_final: 0.8140 (p) REVERT: A 282 MET cc_start: 0.8037 (mtm) cc_final: 0.7734 (mtp) REVERT: A 294 SER cc_start: 0.8453 (m) cc_final: 0.8040 (p) REVERT: A 311 LYS cc_start: 0.7767 (ptmm) cc_final: 0.7500 (mmtm) REVERT: A 315 ASP cc_start: 0.7664 (t0) cc_final: 0.6908 (t0) REVERT: A 332 GLU cc_start: 0.7341 (tt0) cc_final: 0.7087 (pt0) REVERT: A 355 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7186 (mp0) REVERT: A 371 ARG cc_start: 0.6852 (tmm-80) cc_final: 0.6466 (tpt170) REVERT: A 546 GLU cc_start: 0.7227 (mp0) cc_final: 0.6704 (mp0) REVERT: A 627 ASP cc_start: 0.8083 (m-30) cc_final: 0.7848 (m-30) REVERT: A 730 LEU cc_start: 0.8371 (mt) cc_final: 0.8060 (tp) REVERT: A 738 LYS cc_start: 0.8521 (tttp) cc_final: 0.8226 (ttmp) REVERT: B 174 LYS cc_start: 0.7507 (tptt) cc_final: 0.7054 (tptp) REVERT: B 202 ARG cc_start: 0.7134 (ttp-110) cc_final: 0.6584 (ptm160) REVERT: B 294 SER cc_start: 0.8472 (m) cc_final: 0.8085 (p) REVERT: B 308 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7518 (mm-30) REVERT: B 315 ASP cc_start: 0.7674 (t0) cc_final: 0.6899 (t0) REVERT: B 332 GLU cc_start: 0.7328 (tt0) cc_final: 0.7091 (pt0) REVERT: B 355 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7189 (mp0) REVERT: B 371 ARG cc_start: 0.6836 (tmm-80) cc_final: 0.6454 (tpt170) REVERT: B 546 GLU cc_start: 0.7188 (mp0) cc_final: 0.6861 (mp0) REVERT: B 627 ASP cc_start: 0.8076 (m-30) cc_final: 0.7844 (m-30) REVERT: B 691 ILE cc_start: 0.8258 (mt) cc_final: 0.8029 (mt) REVERT: B 730 LEU cc_start: 0.8312 (mt) cc_final: 0.8024 (tp) REVERT: B 738 LYS cc_start: 0.8559 (tttp) cc_final: 0.8307 (ttmp) REVERT: C 131 CYS cc_start: 0.8374 (m) cc_final: 0.7724 (m) REVERT: C 202 ARG cc_start: 0.7011 (ttp-110) cc_final: 0.6390 (ptm160) REVERT: C 217 THR cc_start: 0.8321 (m) cc_final: 0.8009 (p) REVERT: C 294 SER cc_start: 0.8363 (m) cc_final: 0.8130 (m) REVERT: C 315 ASP cc_start: 0.7527 (t0) cc_final: 0.6841 (t0) REVERT: C 355 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7180 (pm20) REVERT: C 371 ARG cc_start: 0.6877 (tmm-80) cc_final: 0.6196 (tpt170) REVERT: C 546 GLU cc_start: 0.7438 (mp0) cc_final: 0.6922 (mp0) REVERT: C 627 ASP cc_start: 0.8177 (m-30) cc_final: 0.7977 (m-30) REVERT: C 645 GLN cc_start: 0.7788 (mm110) cc_final: 0.7308 (mp10) REVERT: C 650 TYR cc_start: 0.8475 (m-80) cc_final: 0.8205 (m-80) REVERT: C 683 ASN cc_start: 0.8168 (m-40) cc_final: 0.7950 (m-40) REVERT: C 716 ARG cc_start: 0.6900 (ptp-110) cc_final: 0.6636 (mmt-90) REVERT: D 174 LYS cc_start: 0.7513 (tptt) cc_final: 0.7115 (tptp) REVERT: D 202 ARG cc_start: 0.7096 (ttp-110) cc_final: 0.6555 (ptm160) REVERT: D 217 THR cc_start: 0.8332 (m) cc_final: 0.8130 (p) REVERT: D 282 MET cc_start: 0.7987 (mtm) cc_final: 0.7712 (mtp) REVERT: D 294 SER cc_start: 0.8465 (m) cc_final: 0.8045 (p) REVERT: D 311 LYS cc_start: 0.7741 (ptmm) cc_final: 0.7468 (mmtm) REVERT: D 315 ASP cc_start: 0.7666 (t0) cc_final: 0.6913 (t0) REVERT: D 332 GLU cc_start: 0.7370 (tt0) cc_final: 0.7096 (pt0) REVERT: D 355 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7092 (mp0) REVERT: D 371 ARG cc_start: 0.6860 (tmm-80) cc_final: 0.6464 (tpt170) REVERT: D 546 GLU cc_start: 0.7200 (mp0) cc_final: 0.6870 (mp0) REVERT: D 627 ASP cc_start: 0.8090 (m-30) cc_final: 0.7809 (m-30) REVERT: D 687 GLU cc_start: 0.8215 (pp20) cc_final: 0.7983 (pp20) REVERT: D 691 ILE cc_start: 0.8235 (mt) cc_final: 0.8015 (mt) REVERT: D 730 LEU cc_start: 0.8365 (mt) cc_final: 0.8058 (tp) REVERT: D 738 LYS cc_start: 0.8520 (tttp) cc_final: 0.8207 (ttmp) outliers start: 10 outliers final: 0 residues processed: 453 average time/residue: 0.6352 time to fit residues: 325.2971 Evaluate side-chains 306 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 410 ASN A 417 HIS A 426 HIS A 483 GLN A 616 ASN B 160 HIS B 220 ASN B 410 ASN B 417 HIS B 426 HIS B 616 ASN C 160 HIS C 410 ASN C 417 HIS C 426 HIS C 483 GLN C 616 ASN D 160 HIS D 410 ASN D 417 HIS D 426 HIS D 483 GLN D 616 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.165331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117107 restraints weight = 23853.775| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.24 r_work: 0.2997 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22440 Z= 0.164 Angle : 0.624 6.845 30040 Z= 0.322 Chirality : 0.040 0.172 3236 Planarity : 0.005 0.040 3608 Dihedral : 23.812 177.320 4092 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.15 % Favored : 94.69 % Rotamer: Outliers : 2.88 % Allowed : 7.84 % Favored : 89.28 % 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: -3.53 (0.14), residues: 2484 helix: -2.31 (0.11), residues: 1532 sheet: -0.35 (0.49), residues: 112 loop : -2.34 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 712 TYR 0.015 0.002 TYR C 622 PHE 0.016 0.002 PHE B 449 TRP 0.012 0.001 TRP C 559 HIS 0.008 0.002 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (22436) covalent geometry : angle 0.62340 / 0.32 (30032) SS BOND : bond 0.00509 / 0.25 ( 4) SS BOND : angle 1.77766 / 1.13 ( 8) hydrogen bonds : bond 0.04979 / 3.28 ( 920) hydrogen bonds : angle 4.44257 / 3.06 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 319 time to evaluate : 0.822 Fit side-chains REVERT: A 217 THR cc_start: 0.8029 (m) cc_final: 0.7772 (p) REVERT: A 257 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7395 (mp0) REVERT: A 315 ASP cc_start: 0.7401 (t0) cc_final: 0.6467 (t0) REVERT: A 332 GLU cc_start: 0.7962 (tt0) cc_final: 0.7499 (pt0) REVERT: A 355 GLU cc_start: 0.7980 (mm-30) cc_final: 0.6849 (mp0) REVERT: A 371 ARG cc_start: 0.7174 (tmm-80) cc_final: 0.6217 (tpt170) REVERT: A 508 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6248 (mm) REVERT: A 546 GLU cc_start: 0.7967 (mp0) cc_final: 0.7316 (mp0) REVERT: A 627 ASP cc_start: 0.8265 (m-30) cc_final: 0.7924 (m-30) REVERT: A 730 LEU cc_start: 0.8368 (mt) cc_final: 0.7983 (tp) REVERT: A 738 LYS cc_start: 0.8863 (tttp) cc_final: 0.8411 (ttmp) REVERT: B 257 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7345 (mp0) REVERT: B 315 ASP cc_start: 0.7498 (t0) cc_final: 0.6537 (t0) REVERT: B 332 GLU cc_start: 0.7956 (tt0) cc_final: 0.7465 (pt0) REVERT: B 355 GLU cc_start: 0.8026 (mm-30) cc_final: 0.6862 (mp0) REVERT: B 371 ARG cc_start: 0.7129 (tmm-80) cc_final: 0.6303 (tpt170) REVERT: B 508 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6218 (mm) REVERT: B 546 GLU cc_start: 0.8042 (mp0) cc_final: 0.7686 (mp0) REVERT: B 627 ASP cc_start: 0.8269 (m-30) cc_final: 0.7923 (m-30) REVERT: B 730 LEU cc_start: 0.8369 (mt) cc_final: 0.7987 (tp) REVERT: B 738 LYS cc_start: 0.8890 (tttp) cc_final: 0.8460 (ttmp) REVERT: C 161 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7404 (tppp) REVERT: C 217 THR cc_start: 0.7939 (m) cc_final: 0.7621 (p) REVERT: C 257 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7433 (mp0) REVERT: C 315 ASP cc_start: 0.7451 (t0) cc_final: 0.6529 (t0) REVERT: C 355 GLU cc_start: 0.8034 (mm-30) cc_final: 0.6958 (mp0) REVERT: C 371 ARG cc_start: 0.7190 (tmm-80) cc_final: 0.6154 (tpt170) REVERT: C 440 MET cc_start: 0.8778 (mtp) cc_final: 0.8509 (mtp) REVERT: C 508 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5817 (mm) REVERT: C 546 GLU cc_start: 0.8052 (mp0) cc_final: 0.7417 (mp0) REVERT: C 645 GLN cc_start: 0.8021 (mm110) cc_final: 0.7484 (mp10) REVERT: C 683 ASN cc_start: 0.7941 (m-40) cc_final: 0.7619 (m110) REVERT: C 716 ARG cc_start: 0.7071 (ptp-110) cc_final: 0.6639 (mmt-90) REVERT: D 217 THR cc_start: 0.8015 (m) cc_final: 0.7772 (p) REVERT: D 257 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7353 (mp0) REVERT: D 315 ASP cc_start: 0.7403 (t0) cc_final: 0.6465 (t0) REVERT: D 332 GLU cc_start: 0.7965 (tt0) cc_final: 0.7490 (pt0) REVERT: D 355 GLU cc_start: 0.7995 (mm-30) cc_final: 0.6854 (mp0) REVERT: D 371 ARG cc_start: 0.7164 (tmm-80) cc_final: 0.6205 (tpt170) REVERT: D 508 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6239 (mm) REVERT: D 546 GLU cc_start: 0.8092 (mp0) cc_final: 0.7717 (mp0) REVERT: D 627 ASP cc_start: 0.8260 (m-30) cc_final: 0.7919 (m-30) REVERT: D 687 GLU cc_start: 0.8403 (pp20) cc_final: 0.7983 (pp20) REVERT: D 730 LEU cc_start: 0.8322 (mt) cc_final: 0.7935 (tp) REVERT: D 738 LYS cc_start: 0.8881 (tttp) cc_final: 0.8428 (ttmp) outliers start: 64 outliers final: 20 residues processed: 357 average time/residue: 0.5961 time to fit residues: 243.8385 Evaluate side-chains 292 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 536 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 236 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 GLN C 483 GLN D 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.161797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113052 restraints weight = 23914.279| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.34 r_work: 0.2995 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22440 Z= 0.149 Angle : 0.555 6.401 30040 Z= 0.285 Chirality : 0.040 0.193 3236 Planarity : 0.004 0.037 3608 Dihedral : 22.189 175.139 4092 Min Nonbonded Distance : 1.490 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.79 % Favored : 95.05 % Rotamer: Outliers : 3.20 % Allowed : 10.05 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.16), residues: 2484 helix: -1.02 (0.12), residues: 1560 sheet: -0.34 (0.47), residues: 112 loop : -2.11 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 202 TYR 0.013 0.002 TYR D 451 PHE 0.012 0.001 PHE D 449 TRP 0.010 0.001 TRP C 559 HIS 0.007 0.002 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (22436) covalent geometry : angle 0.55498 / 0.29 (30032) SS BOND : bond 0.00277 / 0.14 ( 4) SS BOND : angle 1.31733 / 0.81 ( 8) hydrogen bonds : bond 0.04195 / 2.77 ( 920) hydrogen bonds : angle 3.93760 / 2.72 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 283 time to evaluate : 0.696 Fit side-chains REVERT: A 257 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7417 (mp0) REVERT: A 315 ASP cc_start: 0.7278 (t0) cc_final: 0.6283 (t0) REVERT: A 332 GLU cc_start: 0.8012 (tt0) cc_final: 0.7474 (pt0) REVERT: A 355 GLU cc_start: 0.7980 (mm-30) cc_final: 0.6743 (mp0) REVERT: A 371 ARG cc_start: 0.7169 (tmm-80) cc_final: 0.6140 (tpt170) REVERT: A 495 MET cc_start: 0.7312 (mtp) cc_final: 0.7091 (mtp) REVERT: A 508 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6095 (mm) REVERT: A 546 GLU cc_start: 0.8049 (mp0) cc_final: 0.7399 (mp0) REVERT: A 627 ASP cc_start: 0.8208 (m-30) cc_final: 0.7858 (m-30) REVERT: A 730 LEU cc_start: 0.8286 (mt) cc_final: 0.7894 (tp) REVERT: A 738 LYS cc_start: 0.8828 (tttp) cc_final: 0.8322 (ttmp) REVERT: B 257 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7298 (mp0) REVERT: B 315 ASP cc_start: 0.7328 (t0) cc_final: 0.6308 (t0) REVERT: B 332 GLU cc_start: 0.8047 (tt0) cc_final: 0.7490 (pt0) REVERT: B 355 GLU cc_start: 0.7990 (mm-30) cc_final: 0.6741 (mp0) REVERT: B 371 ARG cc_start: 0.7153 (tmm-80) cc_final: 0.6052 (tpt170) REVERT: B 495 MET cc_start: 0.7290 (mtp) cc_final: 0.7071 (mtp) REVERT: B 508 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6091 (mm) REVERT: B 546 GLU cc_start: 0.8103 (mp0) cc_final: 0.7447 (mp0) REVERT: B 627 ASP cc_start: 0.8204 (m-30) cc_final: 0.7854 (m-30) REVERT: B 730 LEU cc_start: 0.8294 (mt) cc_final: 0.7874 (tp) REVERT: B 738 LYS cc_start: 0.8856 (tttp) cc_final: 0.8358 (ttmp) REVERT: C 161 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7352 (tppp) REVERT: C 167 THR cc_start: 0.7552 (p) cc_final: 0.7255 (t) REVERT: C 217 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7681 (p) REVERT: C 257 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7384 (mp0) REVERT: C 315 ASP cc_start: 0.7336 (t0) cc_final: 0.6325 (t0) REVERT: C 355 GLU cc_start: 0.8004 (mm-30) cc_final: 0.6800 (mp0) REVERT: C 371 ARG cc_start: 0.7235 (tmm-80) cc_final: 0.6073 (tpt170) REVERT: C 495 MET cc_start: 0.7506 (mtp) cc_final: 0.7251 (mtp) REVERT: C 508 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5728 (mm) REVERT: C 546 GLU cc_start: 0.8056 (mp0) cc_final: 0.7393 (mp0) REVERT: C 580 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7485 (tt0) REVERT: C 716 ARG cc_start: 0.7102 (ptp-110) cc_final: 0.6440 (mmt-90) REVERT: D 257 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7317 (mp0) REVERT: D 315 ASP cc_start: 0.7269 (t0) cc_final: 0.6265 (t0) REVERT: D 332 GLU cc_start: 0.8024 (tt0) cc_final: 0.7476 (pt0) REVERT: D 355 GLU cc_start: 0.7992 (mm-30) cc_final: 0.6750 (mp0) REVERT: D 371 ARG cc_start: 0.7154 (tmm-80) cc_final: 0.6119 (tpt170) REVERT: D 495 MET cc_start: 0.7273 (mtp) cc_final: 0.7054 (mtp) REVERT: D 508 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6114 (mm) REVERT: D 546 GLU cc_start: 0.8075 (mp0) cc_final: 0.7433 (mp0) REVERT: D 627 ASP cc_start: 0.8196 (m-30) cc_final: 0.7844 (m-30) REVERT: D 687 GLU cc_start: 0.8379 (pp20) cc_final: 0.7832 (pp20) REVERT: D 730 LEU cc_start: 0.8281 (mt) cc_final: 0.7887 (tp) REVERT: D 738 LYS cc_start: 0.8840 (tttp) cc_final: 0.8336 (ttmp) outliers start: 71 outliers final: 34 residues processed: 327 average time/residue: 0.5833 time to fit residues: 218.8268 Evaluate side-chains 303 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 223 optimal weight: 0.4980 chunk 211 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.162510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114698 restraints weight = 23796.630| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.22 r_work: 0.3003 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 22440 Z= 0.143 Angle : 0.526 5.412 30040 Z= 0.271 Chirality : 0.039 0.165 3236 Planarity : 0.003 0.038 3608 Dihedral : 21.366 173.940 4092 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 3.47 % Allowed : 9.91 % Favored : 86.62 % 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: -1.42 (0.17), residues: 2484 helix: -0.39 (0.13), residues: 1572 sheet: -0.26 (0.48), residues: 112 loop : -1.97 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 369 TYR 0.015 0.002 TYR A 390 PHE 0.010 0.001 PHE A 449 TRP 0.009 0.001 TRP C 559 HIS 0.007 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (22436) covalent geometry : angle 0.52556 / 0.27 (30032) SS BOND : bond 0.00194 / 0.10 ( 4) SS BOND : angle 0.97797 / 0.58 ( 8) hydrogen bonds : bond 0.03716 / 2.46 ( 920) hydrogen bonds : angle 3.69387 / 2.55 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 279 time to evaluate : 0.830 Fit side-chains REVERT: A 257 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7445 (mp0) REVERT: A 315 ASP cc_start: 0.7281 (t0) cc_final: 0.6431 (t0) REVERT: A 355 GLU cc_start: 0.8074 (mm-30) cc_final: 0.6873 (mp0) REVERT: A 371 ARG cc_start: 0.7348 (tmm-80) cc_final: 0.6240 (tpt170) REVERT: A 488 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.5913 (mmm) REVERT: A 508 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6131 (mm) REVERT: A 546 GLU cc_start: 0.8093 (mp0) cc_final: 0.7479 (mp0) REVERT: A 730 LEU cc_start: 0.8343 (mt) cc_final: 0.7943 (tp) REVERT: A 738 LYS cc_start: 0.8876 (tttp) cc_final: 0.8402 (ttmp) REVERT: B 257 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7389 (mp0) REVERT: B 315 ASP cc_start: 0.7329 (t0) cc_final: 0.6109 (t0) REVERT: B 327 ARG cc_start: 0.7280 (tpt90) cc_final: 0.7056 (mmm-85) REVERT: B 332 GLU cc_start: 0.8075 (tt0) cc_final: 0.7574 (pt0) REVERT: B 355 GLU cc_start: 0.8101 (mm-30) cc_final: 0.6902 (mp0) REVERT: B 371 ARG cc_start: 0.7297 (tmm-80) cc_final: 0.6079 (tpt170) REVERT: B 488 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5928 (mmm) REVERT: B 508 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6155 (mm) REVERT: B 546 GLU cc_start: 0.8169 (mp0) cc_final: 0.7575 (mp0) REVERT: B 688 SER cc_start: 0.7876 (OUTLIER) cc_final: 0.7440 (p) REVERT: B 730 LEU cc_start: 0.8344 (mt) cc_final: 0.7927 (tp) REVERT: B 738 LYS cc_start: 0.8880 (tttp) cc_final: 0.8439 (ttmp) REVERT: C 167 THR cc_start: 0.7716 (p) cc_final: 0.7427 (t) REVERT: C 217 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7823 (p) REVERT: C 257 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7389 (mp0) REVERT: C 315 ASP cc_start: 0.7316 (t0) cc_final: 0.6473 (t0) REVERT: C 355 GLU cc_start: 0.8044 (mm-30) cc_final: 0.6886 (mp0) REVERT: C 371 ARG cc_start: 0.7336 (tmm-80) cc_final: 0.6062 (tpt170) REVERT: C 488 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.5891 (mmm) REVERT: C 495 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7309 (mtp) REVERT: C 508 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5819 (mm) REVERT: C 546 GLU cc_start: 0.8103 (mp0) cc_final: 0.7476 (mp0) REVERT: C 580 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7560 (tt0) REVERT: C 688 SER cc_start: 0.7822 (OUTLIER) cc_final: 0.7412 (p) REVERT: C 716 ARG cc_start: 0.7146 (ptp-110) cc_final: 0.6654 (tpm170) REVERT: D 257 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7432 (mp0) REVERT: D 308 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: D 315 ASP cc_start: 0.7311 (t0) cc_final: 0.6347 (t0) REVERT: D 355 GLU cc_start: 0.8075 (mm-30) cc_final: 0.6879 (mp0) REVERT: D 371 ARG cc_start: 0.7324 (tmm-80) cc_final: 0.6224 (tpt170) REVERT: D 488 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5908 (mmm) REVERT: D 508 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6144 (mm) REVERT: D 546 GLU cc_start: 0.8171 (mp0) cc_final: 0.7577 (mp0) REVERT: D 687 GLU cc_start: 0.8337 (pp20) cc_final: 0.8056 (pp20) REVERT: D 730 LEU cc_start: 0.8332 (mt) cc_final: 0.7931 (tp) REVERT: D 738 LYS cc_start: 0.8886 (tttp) cc_final: 0.8434 (ttmp) outliers start: 77 outliers final: 38 residues processed: 330 average time/residue: 0.6441 time to fit residues: 242.7288 Evaluate side-chains 317 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 266 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 173 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.169839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122918 restraints weight = 23263.146| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.22 r_work: 0.2949 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22440 Z= 0.168 Angle : 0.549 5.913 30040 Z= 0.281 Chirality : 0.040 0.183 3236 Planarity : 0.004 0.040 3608 Dihedral : 20.671 173.892 4092 Min Nonbonded Distance : 1.469 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.75 % Favored : 95.09 % Rotamer: Outliers : 3.11 % Allowed : 11.40 % Favored : 85.50 % 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: -1.05 (0.17), residues: 2484 helix: -0.07 (0.13), residues: 1556 sheet: -0.26 (0.49), residues: 112 loop : -1.85 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 693 TYR 0.014 0.002 TYR B 451 PHE 0.010 0.001 PHE C 316 TRP 0.008 0.001 TRP A 559 HIS 0.008 0.002 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (22436) covalent geometry : angle 0.54904 / 0.28 (30032) SS BOND : bond 0.00265 / 0.13 ( 4) SS BOND : angle 0.98402 / 0.58 ( 8) hydrogen bonds : bond 0.03994 / 2.64 ( 920) hydrogen bonds : angle 3.71163 / 2.57 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 286 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 315 ASP cc_start: 0.7369 (t0) cc_final: 0.6462 (t0) REVERT: A 332 GLU cc_start: 0.8104 (tt0) cc_final: 0.7571 (pt0) REVERT: A 355 GLU cc_start: 0.8015 (mm-30) cc_final: 0.6810 (mp0) REVERT: A 371 ARG cc_start: 0.7313 (tmm-80) cc_final: 0.6015 (tpt170) REVERT: A 488 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5892 (mmm) REVERT: A 508 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6054 (mm) REVERT: A 546 GLU cc_start: 0.8132 (mp0) cc_final: 0.7534 (mp0) REVERT: A 730 LEU cc_start: 0.8325 (mt) cc_final: 0.7906 (tp) REVERT: A 738 LYS cc_start: 0.8867 (tttp) cc_final: 0.8385 (ttmp) REVERT: B 315 ASP cc_start: 0.7312 (t0) cc_final: 0.6123 (t0) REVERT: B 355 GLU cc_start: 0.8033 (mm-30) cc_final: 0.6823 (mp0) REVERT: B 371 ARG cc_start: 0.7301 (tmm-80) cc_final: 0.6013 (tpt170) REVERT: B 508 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6057 (mm) REVERT: B 546 GLU cc_start: 0.8159 (mp0) cc_final: 0.7591 (mp0) REVERT: B 730 LEU cc_start: 0.8316 (mt) cc_final: 0.7898 (tp) REVERT: B 738 LYS cc_start: 0.8868 (tttp) cc_final: 0.8391 (ttmp) REVERT: C 161 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7571 (tppp) REVERT: C 167 THR cc_start: 0.7751 (p) cc_final: 0.7486 (t) REVERT: C 217 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7863 (p) REVERT: C 315 ASP cc_start: 0.7441 (t0) cc_final: 0.6409 (t0) REVERT: C 332 GLU cc_start: 0.8214 (tt0) cc_final: 0.7665 (pt0) REVERT: C 355 GLU cc_start: 0.8028 (mm-30) cc_final: 0.6824 (mp0) REVERT: C 371 ARG cc_start: 0.7350 (tmm-80) cc_final: 0.6133 (tpt170) REVERT: C 488 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5788 (mmm) REVERT: C 495 MET cc_start: 0.7563 (mtp) cc_final: 0.7260 (mtp) REVERT: C 508 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5825 (mm) REVERT: C 546 GLU cc_start: 0.8135 (mp0) cc_final: 0.7516 (mp0) REVERT: C 716 ARG cc_start: 0.7118 (ptp-110) cc_final: 0.6419 (mmt180) REVERT: D 315 ASP cc_start: 0.7391 (t0) cc_final: 0.6368 (t0) REVERT: D 332 GLU cc_start: 0.8117 (tt0) cc_final: 0.7579 (pt0) REVERT: D 355 GLU cc_start: 0.8019 (mm-30) cc_final: 0.6817 (mp0) REVERT: D 371 ARG cc_start: 0.7283 (tmm-80) cc_final: 0.5978 (tpt170) REVERT: D 508 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6045 (mm) REVERT: D 546 GLU cc_start: 0.8167 (mp0) cc_final: 0.7602 (mp0) REVERT: D 687 GLU cc_start: 0.8354 (pp20) cc_final: 0.8029 (pp20) REVERT: D 730 LEU cc_start: 0.8320 (mt) cc_final: 0.7901 (tp) REVERT: D 738 LYS cc_start: 0.8875 (tttp) cc_final: 0.8394 (ttmp) outliers start: 69 outliers final: 53 residues processed: 331 average time/residue: 0.5714 time to fit residues: 217.6913 Evaluate side-chains 321 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 100 optimal weight: 0.9980 chunk 48 optimal weight: 0.0040 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.170189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125082 restraints weight = 23416.778| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.06 r_work: 0.3002 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22440 Z= 0.089 Angle : 0.457 5.624 30040 Z= 0.240 Chirality : 0.037 0.141 3236 Planarity : 0.003 0.038 3608 Dihedral : 19.278 172.055 4092 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 2.03 % Allowed : 12.75 % Favored : 85.23 % 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: -0.49 (0.17), residues: 2484 helix: 0.40 (0.13), residues: 1568 sheet: -0.10 (0.49), residues: 112 loop : -1.72 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 202 TYR 0.010 0.001 TYR D 451 PHE 0.011 0.001 PHE D 316 TRP 0.009 0.001 TRP D 559 HIS 0.007 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (22436) covalent geometry : angle 0.45648 / 0.24 (30032) SS BOND : bond 0.00099 / 0.05 ( 4) SS BOND : angle 0.88194 / 0.53 ( 8) hydrogen bonds : bond 0.02803 / 1.85 ( 920) hydrogen bonds : angle 3.55125 / 2.46 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.859 Fit side-chains REVERT: A 257 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7359 (mp0) REVERT: A 315 ASP cc_start: 0.7433 (t0) cc_final: 0.6582 (t0) REVERT: A 332 GLU cc_start: 0.8213 (tt0) cc_final: 0.7604 (pt0) REVERT: A 335 THR cc_start: 0.8676 (m) cc_final: 0.8411 (p) REVERT: A 355 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7006 (mp0) REVERT: A 371 ARG cc_start: 0.7319 (tmm-80) cc_final: 0.5952 (tpt170) REVERT: A 546 GLU cc_start: 0.8209 (mp0) cc_final: 0.7672 (mp0) REVERT: A 730 LEU cc_start: 0.8381 (mt) cc_final: 0.7965 (tp) REVERT: A 738 LYS cc_start: 0.8923 (tttp) cc_final: 0.8453 (ttmp) REVERT: B 257 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7376 (mp0) REVERT: B 315 ASP cc_start: 0.7404 (t0) cc_final: 0.6542 (t0) REVERT: B 332 GLU cc_start: 0.8210 (tt0) cc_final: 0.7623 (pt0) REVERT: B 335 THR cc_start: 0.8659 (m) cc_final: 0.8421 (p) REVERT: B 355 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7025 (mp0) REVERT: B 371 ARG cc_start: 0.7366 (tmm-80) cc_final: 0.6007 (tpt170) REVERT: B 546 GLU cc_start: 0.8226 (mp0) cc_final: 0.7638 (mp0) REVERT: B 730 LEU cc_start: 0.8390 (mt) cc_final: 0.7980 (tp) REVERT: B 738 LYS cc_start: 0.8933 (tttp) cc_final: 0.8465 (ttmp) REVERT: C 167 THR cc_start: 0.7826 (p) cc_final: 0.7536 (t) REVERT: C 217 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7881 (p) REVERT: C 257 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7412 (mp0) REVERT: C 315 ASP cc_start: 0.7444 (t0) cc_final: 0.6589 (t0) REVERT: C 332 GLU cc_start: 0.8332 (tt0) cc_final: 0.7712 (pt0) REVERT: C 335 THR cc_start: 0.8656 (m) cc_final: 0.8368 (p) REVERT: C 355 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7006 (mp0) REVERT: C 371 ARG cc_start: 0.7402 (tmm-80) cc_final: 0.5932 (tpt170) REVERT: C 495 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7304 (mtp) REVERT: C 519 ASP cc_start: 0.7493 (m-30) cc_final: 0.7254 (m-30) REVERT: C 546 GLU cc_start: 0.8218 (mp0) cc_final: 0.7681 (mp0) REVERT: C 716 ARG cc_start: 0.6982 (ptp-110) cc_final: 0.6445 (tpm170) REVERT: D 257 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7337 (mp0) REVERT: D 315 ASP cc_start: 0.7442 (t0) cc_final: 0.6575 (t0) REVERT: D 332 GLU cc_start: 0.8229 (tt0) cc_final: 0.7601 (pt0) REVERT: D 335 THR cc_start: 0.8666 (m) cc_final: 0.8400 (p) REVERT: D 355 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7012 (mp0) REVERT: D 371 ARG cc_start: 0.7330 (tmm-80) cc_final: 0.5961 (tpt170) REVERT: D 546 GLU cc_start: 0.8259 (mp0) cc_final: 0.7681 (mp0) REVERT: D 687 GLU cc_start: 0.8448 (pp20) cc_final: 0.7790 (pp20) REVERT: D 730 LEU cc_start: 0.8376 (mt) cc_final: 0.7964 (tp) REVERT: D 738 LYS cc_start: 0.8923 (tttp) cc_final: 0.8455 (ttmp) outliers start: 45 outliers final: 22 residues processed: 313 average time/residue: 0.5705 time to fit residues: 204.2662 Evaluate side-chains 290 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 243 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 30.0000 chunk 227 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.165137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119102 restraints weight = 23468.366| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.07 r_work: 0.2930 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 22440 Z= 0.210 Angle : 0.568 6.219 30040 Z= 0.290 Chirality : 0.041 0.177 3236 Planarity : 0.004 0.041 3608 Dihedral : 19.543 173.319 4092 Min Nonbonded Distance : 1.452 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.01 % Rotamer: Outliers : 2.48 % Allowed : 12.70 % Favored : 84.82 % 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: -0.69 (0.17), residues: 2484 helix: 0.22 (0.13), residues: 1580 sheet: -0.08 (0.49), residues: 112 loop : -1.80 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 716 TYR 0.015 0.002 TYR B 451 PHE 0.009 0.001 PHE C 590 TRP 0.007 0.001 TRP C 692 HIS 0.009 0.002 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (22436) covalent geometry : angle 0.56741 / 0.29 (30032) SS BOND : bond 0.00305 / 0.15 ( 4) SS BOND : angle 0.87005 / 0.51 ( 8) hydrogen bonds : bond 0.04181 / 2.77 ( 920) hydrogen bonds : angle 3.70616 / 2.56 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 272 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 257 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7573 (mt-10) REVERT: A 308 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: A 315 ASP cc_start: 0.7619 (t0) cc_final: 0.6769 (t0) REVERT: A 332 GLU cc_start: 0.8216 (tt0) cc_final: 0.7620 (pt0) REVERT: A 355 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7045 (mp0) REVERT: A 371 ARG cc_start: 0.7441 (tmm-80) cc_final: 0.6152 (tpt170) REVERT: A 508 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6067 (mm) REVERT: A 546 GLU cc_start: 0.8265 (mp0) cc_final: 0.7653 (mp0) REVERT: A 688 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7507 (p) REVERT: A 717 MET cc_start: 0.8623 (mmt) cc_final: 0.8017 (mpt) REVERT: A 730 LEU cc_start: 0.8420 (mt) cc_final: 0.7992 (tp) REVERT: A 738 LYS cc_start: 0.8964 (tttp) cc_final: 0.8486 (ttmp) REVERT: B 257 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7342 (mp0) REVERT: B 308 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: B 315 ASP cc_start: 0.7595 (t0) cc_final: 0.6742 (t0) REVERT: B 355 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7061 (mp0) REVERT: B 371 ARG cc_start: 0.7385 (tmm-80) cc_final: 0.6113 (tpt170) REVERT: B 508 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6028 (mm) REVERT: B 546 GLU cc_start: 0.8279 (mp0) cc_final: 0.7706 (mp0) REVERT: B 730 LEU cc_start: 0.8418 (mt) cc_final: 0.7996 (tp) REVERT: B 738 LYS cc_start: 0.8973 (tttp) cc_final: 0.8502 (ttmp) REVERT: C 161 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7581 (tppp) REVERT: C 167 THR cc_start: 0.7802 (p) cc_final: 0.7553 (t) REVERT: C 257 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7601 (mp0) REVERT: C 315 ASP cc_start: 0.7585 (t0) cc_final: 0.6759 (t0) REVERT: C 332 GLU cc_start: 0.8294 (tt0) cc_final: 0.7703 (pt0) REVERT: C 355 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7041 (mp0) REVERT: C 371 ARG cc_start: 0.7432 (tmm-80) cc_final: 0.6122 (tpt170) REVERT: C 508 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5828 (mm) REVERT: C 546 GLU cc_start: 0.8253 (mp0) cc_final: 0.7605 (mp0) REVERT: C 716 ARG cc_start: 0.7100 (ptp-110) cc_final: 0.6518 (tpm170) REVERT: D 257 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7482 (mp0) REVERT: D 315 ASP cc_start: 0.7603 (t0) cc_final: 0.6747 (t0) REVERT: D 332 GLU cc_start: 0.8229 (tt0) cc_final: 0.7629 (pt0) REVERT: D 355 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7050 (mp0) REVERT: D 371 ARG cc_start: 0.7458 (tmm-80) cc_final: 0.6161 (tpt170) REVERT: D 508 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.6066 (mm) REVERT: D 546 GLU cc_start: 0.8303 (mp0) cc_final: 0.7735 (mp0) REVERT: D 687 GLU cc_start: 0.8481 (pp20) cc_final: 0.8072 (pp20) REVERT: D 730 LEU cc_start: 0.8410 (mt) cc_final: 0.7986 (tp) REVERT: D 738 LYS cc_start: 0.8968 (tttp) cc_final: 0.8493 (ttmp) outliers start: 55 outliers final: 37 residues processed: 313 average time/residue: 0.6083 time to fit residues: 218.1943 Evaluate side-chains 298 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 172 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123273 restraints weight = 23354.711| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.83 r_work: 0.3049 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22440 Z= 0.117 Angle : 0.479 5.643 30040 Z= 0.253 Chirality : 0.037 0.123 3236 Planarity : 0.003 0.041 3608 Dihedral : 19.189 172.420 4092 Min Nonbonded Distance : 1.547 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.01 % Rotamer: Outliers : 2.34 % Allowed : 13.11 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2484 helix: 0.47 (0.13), residues: 1572 sheet: 0.02 (0.49), residues: 112 loop : -1.61 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.012 0.001 TYR D 451 PHE 0.012 0.001 PHE A 316 TRP 0.008 0.001 TRP C 559 HIS 0.008 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (22436) covalent geometry : angle 0.47936 / 0.25 (30032) SS BOND : bond 0.00199 / 0.10 ( 4) SS BOND : angle 0.82711 / 0.49 ( 8) hydrogen bonds : bond 0.03264 / 2.16 ( 920) hydrogen bonds : angle 3.62229 / 2.51 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.816 Fit side-chains REVERT: A 202 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6422 (ptm160) REVERT: A 257 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7284 (mp0) REVERT: A 308 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: A 315 ASP cc_start: 0.7412 (t0) cc_final: 0.6531 (t0) REVERT: A 332 GLU cc_start: 0.8161 (tt0) cc_final: 0.7600 (pt0) REVERT: A 355 GLU cc_start: 0.8147 (mm-30) cc_final: 0.6885 (mp0) REVERT: A 371 ARG cc_start: 0.7331 (tmm-80) cc_final: 0.6009 (tpt170) REVERT: A 508 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.5936 (mm) REVERT: A 546 GLU cc_start: 0.8132 (mp0) cc_final: 0.7575 (mp0) REVERT: A 688 SER cc_start: 0.7879 (OUTLIER) cc_final: 0.7421 (p) REVERT: A 717 MET cc_start: 0.8465 (mmt) cc_final: 0.7889 (mpt) REVERT: A 730 LEU cc_start: 0.8327 (mt) cc_final: 0.7927 (tp) REVERT: A 738 LYS cc_start: 0.8919 (tttp) cc_final: 0.8425 (ttmp) REVERT: B 257 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7365 (pm20) REVERT: B 308 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: B 315 ASP cc_start: 0.7388 (t0) cc_final: 0.6512 (t0) REVERT: B 332 GLU cc_start: 0.8183 (tt0) cc_final: 0.7608 (pt0) REVERT: B 355 GLU cc_start: 0.8147 (mm-30) cc_final: 0.6888 (mp0) REVERT: B 371 ARG cc_start: 0.7356 (tmm-80) cc_final: 0.6033 (tpt170) REVERT: B 508 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5915 (mm) REVERT: B 546 GLU cc_start: 0.8145 (mp0) cc_final: 0.7572 (mp0) REVERT: B 688 SER cc_start: 0.7860 (OUTLIER) cc_final: 0.7409 (p) REVERT: B 717 MET cc_start: 0.8462 (mmt) cc_final: 0.7891 (mpt) REVERT: B 730 LEU cc_start: 0.8339 (mt) cc_final: 0.7941 (tp) REVERT: B 738 LYS cc_start: 0.8929 (tttp) cc_final: 0.8450 (ttmp) REVERT: C 161 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7540 (tppp) REVERT: C 167 THR cc_start: 0.7705 (p) cc_final: 0.7455 (t) REVERT: C 257 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7549 (mp0) REVERT: C 294 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7976 (p) REVERT: C 315 ASP cc_start: 0.7415 (t0) cc_final: 0.6555 (t0) REVERT: C 332 GLU cc_start: 0.8310 (tt0) cc_final: 0.7688 (tm-30) REVERT: C 355 GLU cc_start: 0.8102 (mm-30) cc_final: 0.6849 (mp0) REVERT: C 371 ARG cc_start: 0.7326 (tmm-80) cc_final: 0.5997 (tpt170) REVERT: C 495 MET cc_start: 0.7582 (mtm) cc_final: 0.7274 (mtp) REVERT: C 508 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5777 (mm) REVERT: C 546 GLU cc_start: 0.8172 (mp0) cc_final: 0.7581 (mp0) REVERT: C 688 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7313 (p) REVERT: C 716 ARG cc_start: 0.7034 (ptp-110) cc_final: 0.6521 (tpm170) REVERT: D 202 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6397 (ptm160) REVERT: D 257 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7354 (mp0) REVERT: D 315 ASP cc_start: 0.7422 (t0) cc_final: 0.6556 (t0) REVERT: D 332 GLU cc_start: 0.8191 (tt0) cc_final: 0.7623 (pt0) REVERT: D 355 GLU cc_start: 0.8139 (mm-30) cc_final: 0.6875 (mp0) REVERT: D 371 ARG cc_start: 0.7311 (tmm-80) cc_final: 0.6007 (tpt170) REVERT: D 508 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5912 (mm) REVERT: D 546 GLU cc_start: 0.8172 (mp0) cc_final: 0.7602 (mp0) REVERT: D 687 GLU cc_start: 0.8402 (pp20) cc_final: 0.7746 (pp20) REVERT: D 730 LEU cc_start: 0.8345 (mt) cc_final: 0.7948 (tp) REVERT: D 738 LYS cc_start: 0.8914 (tttp) cc_final: 0.8424 (ttmp) outliers start: 52 outliers final: 33 residues processed: 309 average time/residue: 0.6166 time to fit residues: 218.1274 Evaluate side-chains 304 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 14 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 149 optimal weight: 0.0060 chunk 176 optimal weight: 3.9990 chunk 49 optimal weight: 0.0020 chunk 102 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.170766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128021 restraints weight = 23389.382| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.82 r_work: 0.3063 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22440 Z= 0.078 Angle : 0.432 5.695 30040 Z= 0.229 Chirality : 0.035 0.122 3236 Planarity : 0.003 0.041 3608 Dihedral : 18.577 170.044 4092 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.51 % Favored : 95.33 % Rotamer: Outliers : 1.76 % Allowed : 14.14 % Favored : 84.10 % 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: 0.04 (0.18), residues: 2484 helix: 0.82 (0.13), residues: 1572 sheet: 0.12 (0.49), residues: 112 loop : -1.55 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.009 0.001 TYR C 451 PHE 0.014 0.001 PHE A 316 TRP 0.008 0.001 TRP C 559 HIS 0.008 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00164 / 0.08 (22436) covalent geometry : angle 0.43170 / 0.23 (30032) SS BOND : bond 0.00046 / 0.02 ( 4) SS BOND : angle 0.80595 / 0.49 ( 8) hydrogen bonds : bond 0.02503 / 1.66 ( 920) hydrogen bonds : angle 3.45628 / 2.40 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6192 (ptm160) REVERT: A 257 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7448 (pm20) REVERT: A 315 ASP cc_start: 0.7210 (t0) cc_final: 0.6375 (t0) REVERT: A 332 GLU cc_start: 0.8213 (tt0) cc_final: 0.7547 (pt0) REVERT: A 335 THR cc_start: 0.8650 (m) cc_final: 0.8389 (p) REVERT: A 355 GLU cc_start: 0.8127 (mm-30) cc_final: 0.6918 (mp0) REVERT: A 371 ARG cc_start: 0.7279 (tmm-80) cc_final: 0.5839 (tpt170) REVERT: A 546 GLU cc_start: 0.8088 (mp0) cc_final: 0.7539 (mp0) REVERT: A 717 MET cc_start: 0.8413 (mmt) cc_final: 0.7874 (mpt) REVERT: A 730 LEU cc_start: 0.8329 (mt) cc_final: 0.7918 (tp) REVERT: A 738 LYS cc_start: 0.8862 (tttp) cc_final: 0.8391 (ttmp) REVERT: B 174 LYS cc_start: 0.7582 (tptt) cc_final: 0.6934 (tptp) REVERT: B 315 ASP cc_start: 0.7211 (t0) cc_final: 0.6333 (t0) REVERT: B 332 GLU cc_start: 0.8184 (tt0) cc_final: 0.7532 (pt0) REVERT: B 335 THR cc_start: 0.8643 (m) cc_final: 0.8398 (p) REVERT: B 355 GLU cc_start: 0.8128 (mm-30) cc_final: 0.6918 (mp0) REVERT: B 371 ARG cc_start: 0.7363 (tmm-80) cc_final: 0.5909 (tpt170) REVERT: B 546 GLU cc_start: 0.8149 (mp0) cc_final: 0.7576 (mp0) REVERT: B 717 MET cc_start: 0.8439 (mmt) cc_final: 0.7918 (mpt) REVERT: B 730 LEU cc_start: 0.8342 (mt) cc_final: 0.7923 (tp) REVERT: B 738 LYS cc_start: 0.8878 (tttp) cc_final: 0.8408 (ttmp) REVERT: C 161 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7497 (tppp) REVERT: C 167 THR cc_start: 0.7767 (p) cc_final: 0.7542 (t) REVERT: C 210 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7151 (tt0) REVERT: C 257 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7389 (pm20) REVERT: C 294 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.8051 (p) REVERT: C 315 ASP cc_start: 0.7211 (t0) cc_final: 0.6380 (t0) REVERT: C 332 GLU cc_start: 0.8289 (tt0) cc_final: 0.7601 (tm-30) REVERT: C 335 THR cc_start: 0.8651 (m) cc_final: 0.8376 (p) REVERT: C 355 GLU cc_start: 0.8125 (mm-30) cc_final: 0.6925 (mp0) REVERT: C 371 ARG cc_start: 0.7330 (tmm-80) cc_final: 0.6029 (tpt170) REVERT: C 495 MET cc_start: 0.7622 (mtm) cc_final: 0.7276 (mtp) REVERT: C 546 GLU cc_start: 0.8090 (mp0) cc_final: 0.7551 (mp0) REVERT: C 688 SER cc_start: 0.7632 (OUTLIER) cc_final: 0.7351 (p) REVERT: C 716 ARG cc_start: 0.6938 (ptp-110) cc_final: 0.6553 (tpm170) REVERT: D 174 LYS cc_start: 0.7688 (tptt) cc_final: 0.6951 (tptp) REVERT: D 257 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7344 (pm20) REVERT: D 315 ASP cc_start: 0.7211 (t0) cc_final: 0.6362 (t0) REVERT: D 332 GLU cc_start: 0.8246 (tt0) cc_final: 0.7621 (pt0) REVERT: D 335 THR cc_start: 0.8660 (m) cc_final: 0.8393 (p) REVERT: D 355 GLU cc_start: 0.8122 (mm-30) cc_final: 0.6914 (mp0) REVERT: D 371 ARG cc_start: 0.7307 (tmm-80) cc_final: 0.5854 (tpt170) REVERT: D 546 GLU cc_start: 0.8170 (mp0) cc_final: 0.7612 (mp0) REVERT: D 687 GLU cc_start: 0.8381 (pp20) cc_final: 0.7926 (pp20) REVERT: D 730 LEU cc_start: 0.8345 (mt) cc_final: 0.7940 (tp) REVERT: D 738 LYS cc_start: 0.8860 (tttp) cc_final: 0.8388 (ttmp) outliers start: 39 outliers final: 28 residues processed: 313 average time/residue: 0.6409 time to fit residues: 229.2179 Evaluate side-chains 301 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 204 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.172081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128402 restraints weight = 23263.932| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.87 r_work: 0.3054 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (29 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22440 Z= 0.097 Angle : 0.456 5.589 30040 Z= 0.241 Chirality : 0.037 0.125 3236 Planarity : 0.003 0.041 3608 Dihedral : 18.484 170.279 4092 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.51 % Favored : 95.33 % Rotamer: Outliers : 1.80 % Allowed : 14.64 % Favored : 83.56 % 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: 0.15 (0.18), residues: 2484 helix: 0.91 (0.13), residues: 1584 sheet: 0.09 (0.49), residues: 112 loop : -1.53 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 188 TYR 0.012 0.001 TYR C 451 PHE 0.013 0.001 PHE C 316 TRP 0.011 0.001 TRP C 739 HIS 0.008 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (22436) covalent geometry : angle 0.45586 / 0.24 (30032) SS BOND : bond 0.00123 / 0.06 ( 4) SS BOND : angle 0.77229 / 0.47 ( 8) hydrogen bonds : bond 0.02864 / 1.90 ( 920) hydrogen bonds : angle 3.56457 / 2.47 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 273 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ASP cc_start: 0.7281 (t0) cc_final: 0.6431 (t0) REVERT: A 330 ASN cc_start: 0.8272 (p0) cc_final: 0.7789 (p0) REVERT: A 332 GLU cc_start: 0.8096 (tt0) cc_final: 0.7176 (pt0) REVERT: A 335 THR cc_start: 0.8641 (m) cc_final: 0.8352 (p) REVERT: A 355 GLU cc_start: 0.8092 (mm-30) cc_final: 0.6844 (mp0) REVERT: A 371 ARG cc_start: 0.7275 (tmm-80) cc_final: 0.5844 (tpt170) REVERT: A 546 GLU cc_start: 0.8104 (mp0) cc_final: 0.7529 (mp0) REVERT: A 688 SER cc_start: 0.7776 (OUTLIER) cc_final: 0.7421 (p) REVERT: A 717 MET cc_start: 0.8391 (mmt) cc_final: 0.7832 (mpt) REVERT: A 730 LEU cc_start: 0.8317 (mt) cc_final: 0.7900 (tp) REVERT: A 738 LYS cc_start: 0.8832 (tttp) cc_final: 0.8351 (ttmp) REVERT: B 174 LYS cc_start: 0.7409 (tptt) cc_final: 0.6714 (tptp) REVERT: B 213 TYR cc_start: 0.8116 (m-80) cc_final: 0.7910 (m-80) REVERT: B 315 ASP cc_start: 0.7243 (t0) cc_final: 0.6350 (t0) REVERT: B 330 ASN cc_start: 0.8274 (p0) cc_final: 0.7833 (p0) REVERT: B 332 GLU cc_start: 0.8133 (tt0) cc_final: 0.7244 (pt0) REVERT: B 335 THR cc_start: 0.8639 (m) cc_final: 0.8368 (p) REVERT: B 355 GLU cc_start: 0.8104 (mm-30) cc_final: 0.6855 (mp0) REVERT: B 371 ARG cc_start: 0.7292 (tmm-80) cc_final: 0.5829 (tpt170) REVERT: B 508 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5844 (mm) REVERT: B 546 GLU cc_start: 0.8148 (mp0) cc_final: 0.7578 (mp0) REVERT: B 688 SER cc_start: 0.7842 (OUTLIER) cc_final: 0.7471 (p) REVERT: B 717 MET cc_start: 0.8407 (mmt) cc_final: 0.7814 (mpt) REVERT: B 730 LEU cc_start: 0.8342 (mt) cc_final: 0.7924 (tp) REVERT: B 738 LYS cc_start: 0.8872 (tttp) cc_final: 0.8397 (ttmp) REVERT: C 161 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7392 (tppp) REVERT: C 167 THR cc_start: 0.7735 (p) cc_final: 0.7524 (t) REVERT: C 294 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8020 (p) REVERT: C 315 ASP cc_start: 0.7262 (t0) cc_final: 0.6419 (t0) REVERT: C 332 GLU cc_start: 0.8273 (tt0) cc_final: 0.7444 (tm-30) REVERT: C 335 THR cc_start: 0.8653 (m) cc_final: 0.8348 (p) REVERT: C 355 GLU cc_start: 0.8098 (mm-30) cc_final: 0.6857 (mp0) REVERT: C 371 ARG cc_start: 0.7333 (tmm-80) cc_final: 0.5833 (tpt170) REVERT: C 495 MET cc_start: 0.7551 (mtm) cc_final: 0.7248 (mtp) REVERT: C 508 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5741 (mm) REVERT: C 546 GLU cc_start: 0.8072 (mp0) cc_final: 0.7519 (mp0) REVERT: C 688 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.7324 (p) REVERT: C 716 ARG cc_start: 0.6894 (ptp-110) cc_final: 0.6518 (tpm170) REVERT: D 174 LYS cc_start: 0.7552 (tptt) cc_final: 0.6851 (tptp) REVERT: D 309 ASP cc_start: 0.7706 (p0) cc_final: 0.7496 (p0) REVERT: D 315 ASP cc_start: 0.7243 (t0) cc_final: 0.6390 (t0) REVERT: D 332 GLU cc_start: 0.8118 (tt0) cc_final: 0.7433 (pt0) REVERT: D 335 THR cc_start: 0.8643 (m) cc_final: 0.8355 (p) REVERT: D 355 GLU cc_start: 0.8095 (mm-30) cc_final: 0.6850 (mp0) REVERT: D 371 ARG cc_start: 0.7273 (tmm-80) cc_final: 0.5842 (tpt170) REVERT: D 546 GLU cc_start: 0.8171 (mp0) cc_final: 0.7603 (mp0) REVERT: D 687 GLU cc_start: 0.8390 (pp20) cc_final: 0.7899 (pp20) REVERT: D 730 LEU cc_start: 0.8327 (mt) cc_final: 0.7918 (tp) REVERT: D 738 LYS cc_start: 0.8875 (tttp) cc_final: 0.8402 (ttmp) outliers start: 40 outliers final: 29 residues processed: 304 average time/residue: 0.6478 time to fit residues: 225.4070 Evaluate side-chains 305 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 142 optimal weight: 0.6980 chunk 214 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127915 restraints weight = 23215.066| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.90 r_work: 0.3114 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 22440 Z= 0.077 Angle : 0.428 5.607 30040 Z= 0.228 Chirality : 0.036 0.122 3236 Planarity : 0.003 0.041 3608 Dihedral : 18.094 169.349 4092 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 1.53 % Allowed : 15.18 % Favored : 83.29 % 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: 0.47 (0.18), residues: 2484 helix: 1.21 (0.13), residues: 1572 sheet: 0.13 (0.49), residues: 112 loop : -1.46 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.009 0.001 TYR B 208 PHE 0.013 0.001 PHE C 316 TRP 0.008 0.001 TRP B 559 HIS 0.008 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00168 / 0.08 (22436) covalent geometry : angle 0.42831 / 0.23 (30032) SS BOND : bond 0.00024 / 0.01 ( 4) SS BOND : angle 0.68665 / 0.42 ( 8) hydrogen bonds : bond 0.02383 / 1.59 ( 920) hydrogen bonds : angle 3.47822 / 2.42 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8317.18 seconds wall clock time: 142 minutes 1.49 seconds (8521.49 seconds total)