Starting phenix.real_space_refine on Fri Jul 3 06:57:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mdl_48173/07_2026/9mdl_48173.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mdl_48173/07_2026/9mdl_48173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mdl_48173/07_2026/9mdl_48173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mdl_48173/07_2026/9mdl_48173.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mdl_48173/07_2026/9mdl_48173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mdl_48173/07_2026/9mdl_48173.map" } resolution = 4.19 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= 0.001 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 9 9.91 5 S 15 5.16 5 C 7635 2.51 5 N 1992 2.21 5 O 2586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12237 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4076 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 20, 'TRANS': 502} Chain breaks: 2 Chain: "B" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4076 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 20, 'TRANS': 502} Chain breaks: 2 Chain: "C" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4076 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 20, 'TRANS': 502} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 3.11, per 1000 atoms: 0.25 Number of scatterers: 12237 At special positions: 0 Unit cell: (98.9, 99.76, 149.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 9 19.99 S 15 16.00 O 2586 8.00 N 1992 7.00 C 7635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 572.9 milliseconds 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2934 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 26 sheets defined 11.2% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.684A pdb=" N ARG A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.719A pdb=" N SER A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 659 through 663 removed outlier: 3.588A pdb=" N GLU A 662 " --> pdb=" O PRO A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 335 through 339 removed outlier: 4.103A pdb=" N GLY B 338 " --> pdb=" O ASN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 473 removed outlier: 3.583A pdb=" N GLY B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 593 removed outlier: 4.131A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 663 removed outlier: 3.732A pdb=" N GLU B 662 " --> pdb=" O PRO B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 272 through 279 removed outlier: 3.772A pdb=" N GLY C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 468 through 473 removed outlier: 4.071A pdb=" N ALA C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 468 through 473' Processing helix chain 'C' and resid 506 through 512 removed outlier: 3.526A pdb=" N SER C 512 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 592 Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 423 removed outlier: 5.111A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 414 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 420 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE A 476 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 365 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 478 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 363 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU A 305 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN A 329 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N GLY A 303 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 447 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 423 removed outlier: 5.111A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 414 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 420 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE A 476 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 365 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 478 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 363 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU A 305 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN A 329 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N GLY A 303 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 460 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 353 removed outlier: 3.512A pdb=" N ASN A 352 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 580 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.625A pdb=" N THR A 489 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 497 " --> pdb=" O THR A 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 560 removed outlier: 3.885A pdb=" N LEU A 564 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 618 through 620 removed outlier: 3.749A pdb=" N LEU A 733 " --> pdb=" O ASN A 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 618 through 620 removed outlier: 5.449A pdb=" N LEU A 733 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS A 676 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN A 735 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 674 " --> pdb=" O ASN A 735 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG A 668 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 653 through 658 Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 238 Processing sheet with id=AB2, first strand: chain 'B' and resid 417 through 423 removed outlier: 5.167A pdb=" N THR B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 414 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 420 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE B 476 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 365 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 478 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU B 305 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN B 329 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N GLY B 303 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 447 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 417 through 423 removed outlier: 5.167A pdb=" N THR B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 414 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 420 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE B 476 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 365 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 478 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU B 305 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN B 329 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N GLY B 303 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 389 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 460 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 352 through 353 removed outlier: 3.506A pdb=" N ASN B 352 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 580 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 490 removed outlier: 3.538A pdb=" N THR B 489 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 558 through 560 removed outlier: 3.631A pdb=" N LEU B 564 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 618 through 620 removed outlier: 4.490A pdb=" N LEU B 736 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER B 672 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE B 738 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 670 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU B 740 " --> pdb=" O ARG B 668 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG B 668 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 654 through 658 Processing sheet with id=AB9, first strand: chain 'C' and resid 236 through 238 Processing sheet with id=AC1, first strand: chain 'C' and resid 417 through 423 removed outlier: 6.914A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE C 476 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU C 305 " --> pdb=" O THR C 327 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN C 329 " --> pdb=" O GLY C 303 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLY C 303 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL C 302 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR C 396 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 417 through 423 removed outlier: 6.914A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE C 476 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU C 305 " --> pdb=" O THR C 327 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN C 329 " --> pdb=" O GLY C 303 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLY C 303 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL C 302 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR C 396 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE C 460 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 352 through 353 removed outlier: 6.540A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 489 through 490 removed outlier: 3.846A pdb=" N THR C 489 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 558 through 560 removed outlier: 3.975A pdb=" N LEU C 564 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 618 through 620 removed outlier: 3.827A pdb=" N LEU C 733 " --> pdb=" O ASN C 648 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN C 648 " --> pdb=" O LEU C 733 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 618 through 620 removed outlier: 4.356A pdb=" N LEU C 736 " --> pdb=" O SER C 672 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER C 672 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE C 738 " --> pdb=" O VAL C 670 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 670 " --> pdb=" O ILE C 738 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU C 740 " --> pdb=" O ARG C 668 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ARG C 668 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 653 through 658 398 hydrogen bonds defined for protein. 996 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: 2.09 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4013 1.34 - 1.46: 2565 1.46 - 1.58: 5830 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 12435 Sorted by residual: bond pdb=" CA GLN C 644 " pdb=" CB GLN C 644 " ideal model delta sigma weight residual 1.532 1.575 -0.042 1.62e-02 3.81e+03 6.84e+00 bond pdb=" N ASP C 415 " pdb=" CA ASP C 415 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.40e+00 bond pdb=" CB LYS A 593 " pdb=" CG LYS A 593 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.61e+00 bond pdb=" C TYR C 297 " pdb=" O TYR C 297 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 2.03e+00 bond pdb=" CG LYS A 593 " pdb=" CD LYS A 593 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 12430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 16480 2.14 - 4.29: 325 4.29 - 6.43: 56 6.43 - 8.57: 13 8.57 - 10.71: 4 Bond angle restraints: 16878 Sorted by residual: angle pdb=" C GLU B 246 " pdb=" N ASP B 247 " pdb=" CA ASP B 247 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.19e+01 angle pdb=" CB LYS A 593 " pdb=" CG LYS A 593 " pdb=" CD LYS A 593 " ideal model delta sigma weight residual 111.30 122.01 -10.71 2.30e+00 1.89e-01 2.17e+01 angle pdb=" C LEU C 414 " pdb=" N ASP C 415 " pdb=" CA ASP C 415 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C LEU B 414 " pdb=" N ASP B 415 " pdb=" CA ASP B 415 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C ARG B 232 " pdb=" N ASN B 233 " pdb=" CA ASN B 233 " ideal model delta sigma weight residual 122.08 127.21 -5.13 1.47e+00 4.63e-01 1.22e+01 ... (remaining 16873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6787 17.91 - 35.82: 633 35.82 - 53.73: 87 53.73 - 71.64: 18 71.64 - 89.55: 17 Dihedral angle restraints: 7542 sinusoidal: 2958 harmonic: 4584 Sorted by residual: dihedral pdb=" CA LYS A 691 " pdb=" C LYS A 691 " pdb=" N GLU A 692 " pdb=" CA GLU A 692 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA LYS C 383 " pdb=" C LYS C 383 " pdb=" N GLY C 384 " pdb=" CA GLY C 384 " ideal model delta harmonic sigma weight residual 180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA MET C 660 " pdb=" C MET C 660 " pdb=" N SER C 661 " pdb=" CA SER C 661 " ideal model delta harmonic sigma weight residual 180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 7539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1297 0.041 - 0.083: 432 0.083 - 0.124: 150 0.124 - 0.165: 38 0.165 - 0.207: 12 Chirality restraints: 1929 Sorted by residual: chirality pdb=" CB ILE B 726 " pdb=" CA ILE B 726 " pdb=" CG1 ILE B 726 " pdb=" CG2 ILE B 726 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE C 658 " pdb=" CA ILE C 658 " pdb=" CG1 ILE C 658 " pdb=" CG2 ILE C 658 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE C 688 " pdb=" N ILE C 688 " pdb=" C ILE C 688 " pdb=" CB ILE C 688 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1926 not shown) Planarity restraints: 2193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 245 " -0.024 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP A 245 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP A 245 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP A 245 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 245 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 245 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 245 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 245 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 245 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 245 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 269 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO A 270 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 245 " 0.011 2.00e-02 2.50e+03 1.49e-02 5.54e+00 pdb=" CG TRP C 245 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 245 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 245 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 245 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 245 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 245 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 245 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 245 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 245 " -0.001 2.00e-02 2.50e+03 ... (remaining 2190 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2220 2.77 - 3.31: 10857 3.31 - 3.84: 19134 3.84 - 4.37: 20494 4.37 - 4.90: 36887 Nonbonded interactions: 89592 Sorted by model distance: nonbonded pdb=" OD1 ASN C 260 " pdb=" OG1 THR C 266 " model vdw 2.243 3.040 nonbonded pdb=" OG SER B 259 " pdb=" OG1 THR B 266 " model vdw 2.277 3.040 nonbonded pdb=" OG SER B 310 " pdb=" OD1 ASN B 312 " model vdw 2.284 3.040 nonbonded pdb=" O TYR C 274 " pdb=" OG SER C 278 " model vdw 2.299 3.040 nonbonded pdb=" OG SER C 374 " pdb=" OG1 THR C 377 " model vdw 2.304 3.040 ... (remaining 89587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.690 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 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 : 0.003 0.048 12435 Z= 0.158 Angle : 0.772 10.715 16878 Z= 0.410 Chirality : 0.050 0.207 1929 Planarity : 0.005 0.063 2193 Dihedral : 14.398 89.545 4608 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % 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: -2.10 (0.20), residues: 1551 helix: -1.69 (0.40), residues: 129 sheet: 0.76 (0.27), residues: 354 loop : -2.31 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 528 TYR 0.026 0.002 TYR C 628 PHE 0.016 0.002 PHE A 622 TRP 0.071 0.004 TRP A 245 HIS 0.001 0.000 HIS C 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (12435) covalent geometry : angle 0.77152 / 0.41 (16878) hydrogen bonds : bond 0.14328 / 9.07 ( 320) hydrogen bonds : angle 7.50235 / 5.23 ( 996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: B 478 LEU cc_start: 0.8171 (mp) cc_final: 0.7888 (mp) REVERT: B 693 GLU cc_start: 0.7177 (pm20) cc_final: 0.6335 (pt0) REVERT: C 634 ASN cc_start: 0.7881 (m110) cc_final: 0.7671 (m110) REVERT: C 735 ASN cc_start: 0.8596 (m110) cc_final: 0.8340 (m110) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.0907 time to fit residues: 26.4018 Evaluate side-chains 125 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN C 376 ASN C 523 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.166832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143058 restraints weight = 25844.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146419 restraints weight = 17328.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148845 restraints weight = 12714.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150629 restraints weight = 9991.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151899 restraints weight = 8269.914| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12435 Z= 0.149 Angle : 0.603 6.721 16878 Z= 0.321 Chirality : 0.045 0.164 1929 Planarity : 0.004 0.052 2193 Dihedral : 5.136 22.491 1677 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.22 % Allowed : 4.83 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.20), residues: 1551 helix: -1.03 (0.43), residues: 129 sheet: 0.60 (0.27), residues: 363 loop : -2.20 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 528 TYR 0.022 0.002 TYR A 526 PHE 0.018 0.002 PHE C 487 TRP 0.035 0.002 TRP A 245 HIS 0.002 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (12435) covalent geometry : angle 0.60277 / 0.32 (16878) hydrogen bonds : bond 0.04081 / 2.69 ( 320) hydrogen bonds : angle 5.35936 / 3.73 ( 996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.457 Fit side-chains REVERT: A 254 TYR cc_start: 0.7565 (m-80) cc_final: 0.7216 (m-10) REVERT: A 369 ASP cc_start: 0.7693 (p0) cc_final: 0.7449 (p0) REVERT: B 693 GLU cc_start: 0.7157 (pm20) cc_final: 0.6406 (pt0) REVERT: C 735 ASN cc_start: 0.8487 (m110) cc_final: 0.8177 (m110) outliers start: 3 outliers final: 0 residues processed: 171 average time/residue: 0.0884 time to fit residues: 23.7388 Evaluate side-chains 123 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 10.0000 chunk 28 optimal weight: 0.0070 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN B 233 ASN B 363 ASN C 523 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.167930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144413 restraints weight = 25751.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.147778 restraints weight = 17191.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150288 restraints weight = 12596.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152114 restraints weight = 9821.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.153365 restraints weight = 8096.799| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12435 Z= 0.118 Angle : 0.564 6.582 16878 Z= 0.297 Chirality : 0.044 0.163 1929 Planarity : 0.003 0.053 2193 Dihedral : 4.923 21.893 1677 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 0.14 % Allowed : 3.68 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.20), residues: 1551 helix: -0.74 (0.44), residues: 129 sheet: 0.63 (0.28), residues: 342 loop : -2.16 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 607 TYR 0.018 0.001 TYR C 235 PHE 0.017 0.002 PHE B 281 TRP 0.013 0.001 TRP A 245 HIS 0.002 0.001 HIS C 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12435) covalent geometry : angle 0.56407 / 0.30 (16878) hydrogen bonds : bond 0.03742 / 2.44 ( 320) hydrogen bonds : angle 5.11671 / 3.57 ( 996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8686 (mt) cc_final: 0.8372 (mt) REVERT: A 588 ILE cc_start: 0.6897 (mt) cc_final: 0.6692 (tt) REVERT: C 735 ASN cc_start: 0.8454 (m110) cc_final: 0.8133 (m110) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.0939 time to fit residues: 25.8844 Evaluate side-chains 123 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 135 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN C 523 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.167483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144097 restraints weight = 25725.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147497 restraints weight = 17160.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.149936 restraints weight = 12545.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151756 restraints weight = 9828.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153012 restraints weight = 8098.671| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12435 Z= 0.123 Angle : 0.568 7.125 16878 Z= 0.300 Chirality : 0.044 0.162 1929 Planarity : 0.003 0.047 2193 Dihedral : 4.909 21.909 1677 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.40 % 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: -1.92 (0.20), residues: 1551 helix: -0.67 (0.44), residues: 129 sheet: 0.62 (0.28), residues: 339 loop : -2.16 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 528 TYR 0.019 0.001 TYR A 271 PHE 0.014 0.002 PHE C 487 TRP 0.007 0.001 TRP A 503 HIS 0.001 0.000 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (12435) covalent geometry : angle 0.56836 / 0.30 (16878) hydrogen bonds : bond 0.03754 / 2.44 ( 320) hydrogen bonds : angle 5.00190 / 3.49 ( 996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8604 (mt) cc_final: 0.8253 (mt) REVERT: A 588 ILE cc_start: 0.6904 (mt) cc_final: 0.6652 (tt) REVERT: B 478 LEU cc_start: 0.8624 (mp) cc_final: 0.8344 (mp) REVERT: B 693 GLU cc_start: 0.7069 (pm20) cc_final: 0.6335 (pt0) REVERT: C 582 ASP cc_start: 0.6502 (t0) cc_final: 0.6028 (m-30) REVERT: C 735 ASN cc_start: 0.8492 (m110) cc_final: 0.8176 (m110) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.0879 time to fit residues: 24.5098 Evaluate side-chains 124 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 43 optimal weight: 0.0870 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN A 466 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN B 363 ASN B 648 ASN C 523 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.165182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141436 restraints weight = 26102.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144834 restraints weight = 17447.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147285 restraints weight = 12772.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.149112 restraints weight = 10001.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150460 restraints weight = 8250.499| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12435 Z= 0.130 Angle : 0.582 6.878 16878 Z= 0.306 Chirality : 0.044 0.167 1929 Planarity : 0.003 0.059 2193 Dihedral : 4.990 26.036 1677 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 0.07 % Allowed : 2.02 % Favored : 97.91 % 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: -1.91 (0.21), residues: 1551 helix: -0.55 (0.45), residues: 129 sheet: 0.35 (0.26), residues: 387 loop : -2.17 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 528 TYR 0.019 0.001 TYR C 235 PHE 0.014 0.002 PHE C 487 TRP 0.008 0.001 TRP B 245 HIS 0.001 0.000 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (12435) covalent geometry : angle 0.58169 / 0.31 (16878) hydrogen bonds : bond 0.03854 / 2.53 ( 320) hydrogen bonds : angle 5.00919 / 3.48 ( 996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 653 GLU cc_start: 0.6743 (pm20) cc_final: 0.6152 (mm-30) REVERT: B 478 LEU cc_start: 0.8606 (mp) cc_final: 0.8214 (mp) REVERT: B 693 GLU cc_start: 0.7159 (pm20) cc_final: 0.6525 (pt0) REVERT: B 717 ASP cc_start: 0.8087 (t70) cc_final: 0.7789 (t70) REVERT: C 275 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6160 (tm-30) REVERT: C 735 ASN cc_start: 0.8579 (m110) cc_final: 0.8278 (m110) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.0871 time to fit residues: 23.8615 Evaluate side-chains 127 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 36 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 117 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 155 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN A 586 ASN B 466 GLN C 523 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.168829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145449 restraints weight = 26555.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148744 restraints weight = 17770.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151181 restraints weight = 13049.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.152993 restraints weight = 10252.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.154175 restraints weight = 8476.772| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12435 Z= 0.098 Angle : 0.545 6.415 16878 Z= 0.286 Chirality : 0.044 0.169 1929 Planarity : 0.003 0.061 2193 Dihedral : 4.740 25.639 1677 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.07 % Allowed : 2.31 % Favored : 97.62 % 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: -1.80 (0.21), residues: 1551 helix: -0.39 (0.46), residues: 129 sheet: 0.47 (0.27), residues: 387 loop : -2.12 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 528 TYR 0.014 0.001 TYR B 235 PHE 0.011 0.001 PHE C 487 TRP 0.008 0.001 TRP A 503 HIS 0.001 0.000 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (12435) covalent geometry : angle 0.54539 / 0.29 (16878) hydrogen bonds : bond 0.03322 / 2.16 ( 320) hydrogen bonds : angle 4.80391 / 3.34 ( 996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8502 (mt) cc_final: 0.8132 (mt) REVERT: A 496 ILE cc_start: 0.8470 (pt) cc_final: 0.7953 (pt) REVERT: A 653 GLU cc_start: 0.6676 (pm20) cc_final: 0.6132 (mm-30) REVERT: B 609 MET cc_start: 0.7749 (ptt) cc_final: 0.7517 (ptt) REVERT: B 693 GLU cc_start: 0.6918 (pm20) cc_final: 0.6339 (pt0) REVERT: C 275 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6250 (tm-30) REVERT: C 582 ASP cc_start: 0.6642 (t0) cc_final: 0.6093 (m-30) REVERT: C 735 ASN cc_start: 0.8505 (m110) cc_final: 0.8176 (m110) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.0952 time to fit residues: 25.6400 Evaluate side-chains 127 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 154 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B 501 ASN C 523 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.164167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140755 restraints weight = 25646.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144227 restraints weight = 16915.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.146703 restraints weight = 12240.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148517 restraints weight = 9507.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.149857 restraints weight = 7804.596| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12435 Z= 0.183 Angle : 0.654 7.806 16878 Z= 0.346 Chirality : 0.046 0.168 1929 Planarity : 0.004 0.080 2193 Dihedral : 5.323 26.713 1677 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.07 % Allowed : 2.02 % Favored : 97.91 % 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: -2.06 (0.20), residues: 1551 helix: -0.57 (0.44), residues: 132 sheet: 0.15 (0.27), residues: 351 loop : -2.16 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 607 TYR 0.023 0.002 TYR A 526 PHE 0.026 0.003 PHE C 487 TRP 0.012 0.002 TRP B 245 HIS 0.002 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (12435) covalent geometry : angle 0.65427 / 0.35 (16878) hydrogen bonds : bond 0.04410 / 2.92 ( 320) hydrogen bonds : angle 5.16381 / 3.60 ( 996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 487 PHE cc_start: 0.7388 (p90) cc_final: 0.6724 (p90) REVERT: B 230 TYR cc_start: 0.6565 (m-10) cc_final: 0.6110 (m-10) REVERT: B 363 ASN cc_start: 0.7191 (m-40) cc_final: 0.6817 (m110) REVERT: B 478 LEU cc_start: 0.8798 (mp) cc_final: 0.8524 (mp) REVERT: C 422 ILE cc_start: 0.8011 (mm) cc_final: 0.7763 (mm) REVERT: C 735 ASN cc_start: 0.8584 (m110) cc_final: 0.8282 (m110) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.0917 time to fit residues: 25.0158 Evaluate side-chains 127 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 85 optimal weight: 0.0370 chunk 138 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN B 466 GLN B 651 ASN ** B 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.165586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141837 restraints weight = 25919.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145255 restraints weight = 17253.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147754 restraints weight = 12532.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.149547 restraints weight = 9795.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150930 restraints weight = 8083.705| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12435 Z= 0.114 Angle : 0.586 7.158 16878 Z= 0.309 Chirality : 0.045 0.168 1929 Planarity : 0.003 0.064 2193 Dihedral : 5.025 26.724 1677 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -1.99 (0.21), residues: 1551 helix: -0.73 (0.43), residues: 147 sheet: 0.30 (0.27), residues: 372 loop : -2.20 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 528 TYR 0.014 0.001 TYR C 235 PHE 0.015 0.002 PHE C 487 TRP 0.007 0.001 TRP A 503 HIS 0.001 0.000 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (12435) covalent geometry : angle 0.58566 / 0.31 (16878) hydrogen bonds : bond 0.03680 / 2.41 ( 320) hydrogen bonds : angle 4.94762 / 3.45 ( 996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8723 (pt) cc_final: 0.8290 (pt) REVERT: A 604 LYS cc_start: 0.7211 (mptt) cc_final: 0.6925 (tppt) REVERT: B 230 TYR cc_start: 0.6394 (m-10) cc_final: 0.5975 (m-10) REVERT: B 693 GLU cc_start: 0.7320 (pm20) cc_final: 0.6485 (pt0) REVERT: C 422 ILE cc_start: 0.7938 (mm) cc_final: 0.7673 (mm) REVERT: C 582 ASP cc_start: 0.6542 (t0) cc_final: 0.6055 (m-30) REVERT: C 735 ASN cc_start: 0.8551 (m110) cc_final: 0.8237 (m110) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0925 time to fit residues: 25.6575 Evaluate side-chains 130 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 chunk 132 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 147 optimal weight: 7.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN A 586 ASN B 466 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.172085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153204 restraints weight = 24209.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.155884 restraints weight = 16872.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157824 restraints weight = 12596.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.159274 restraints weight = 10021.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.160219 restraints weight = 8352.767| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12435 Z= 0.132 Angle : 0.605 6.876 16878 Z= 0.320 Chirality : 0.045 0.217 1929 Planarity : 0.003 0.067 2193 Dihedral : 5.086 27.132 1677 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.21), residues: 1551 helix: -0.78 (0.43), residues: 150 sheet: 0.29 (0.27), residues: 372 loop : -2.21 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 528 TYR 0.017 0.001 TYR A 526 PHE 0.015 0.002 PHE C 487 TRP 0.008 0.001 TRP B 245 HIS 0.002 0.000 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (12435) covalent geometry : angle 0.60523 / 0.32 (16878) hydrogen bonds : bond 0.03850 / 2.51 ( 320) hydrogen bonds : angle 5.00526 / 3.49 ( 996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: B 230 TYR cc_start: 0.6312 (m-10) cc_final: 0.6023 (m-10) REVERT: B 693 GLU cc_start: 0.7294 (pm20) cc_final: 0.6514 (pt0) REVERT: B 717 ASP cc_start: 0.7773 (t70) cc_final: 0.7408 (t70) REVERT: C 422 ILE cc_start: 0.7993 (mm) cc_final: 0.7726 (mm) REVERT: C 582 ASP cc_start: 0.6577 (t0) cc_final: 0.6077 (m-30) REVERT: C 735 ASN cc_start: 0.8594 (m110) cc_final: 0.8292 (m110) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0938 time to fit residues: 25.2951 Evaluate side-chains 128 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 86 optimal weight: 0.0970 chunk 109 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN A 586 ASN B 363 ASN B 466 GLN C 335 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.173932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.154051 restraints weight = 24238.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.157032 restraints weight = 16410.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.159192 restraints weight = 12044.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.160813 restraints weight = 9443.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.161998 restraints weight = 7760.919| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12435 Z= 0.106 Angle : 0.576 7.320 16878 Z= 0.303 Chirality : 0.044 0.200 1929 Planarity : 0.003 0.066 2193 Dihedral : 4.870 26.864 1677 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.21), residues: 1551 helix: -1.00 (0.41), residues: 165 sheet: 0.35 (0.27), residues: 387 loop : -2.27 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 528 TYR 0.017 0.001 TYR C 464 PHE 0.013 0.002 PHE A 622 TRP 0.008 0.001 TRP B 503 HIS 0.004 0.001 HIS C 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (12435) covalent geometry : angle 0.57609 / 0.30 (16878) hydrogen bonds : bond 0.03419 / 2.22 ( 320) hydrogen bonds : angle 4.84731 / 3.38 ( 996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.483 Fit side-chains REVERT: A 496 ILE cc_start: 0.8650 (pt) cc_final: 0.8211 (pt) REVERT: B 230 TYR cc_start: 0.6244 (m-10) cc_final: 0.5978 (m-10) REVERT: B 331 LYS cc_start: 0.9010 (mmtm) cc_final: 0.7730 (mmtm) REVERT: B 693 GLU cc_start: 0.7093 (pm20) cc_final: 0.6258 (tt0) REVERT: C 422 ILE cc_start: 0.7906 (mm) cc_final: 0.7650 (mm) REVERT: C 582 ASP cc_start: 0.6617 (t0) cc_final: 0.6108 (m-30) REVERT: C 688 ILE cc_start: 0.8859 (mm) cc_final: 0.8454 (mt) REVERT: C 735 ASN cc_start: 0.8519 (m110) cc_final: 0.8196 (m110) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0891 time to fit residues: 24.0277 Evaluate side-chains 131 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 93 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 86 optimal weight: 0.0030 chunk 71 optimal weight: 4.9990 chunk 116 optimal weight: 0.0170 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN A 586 ASN B 466 GLN C 335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.170176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.151058 restraints weight = 24137.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.153774 restraints weight = 16781.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.155681 restraints weight = 12535.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.157166 restraints weight = 9986.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.158251 restraints weight = 8323.473| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12435 Z= 0.140 Angle : 0.615 7.355 16878 Z= 0.325 Chirality : 0.045 0.198 1929 Planarity : 0.004 0.069 2193 Dihedral : 5.071 26.858 1677 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.21), residues: 1551 helix: -0.32 (0.46), residues: 132 sheet: 0.17 (0.27), residues: 366 loop : -2.14 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 528 TYR 0.019 0.001 TYR C 235 PHE 0.014 0.002 PHE B 580 TRP 0.009 0.001 TRP B 245 HIS 0.004 0.001 HIS C 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (12435) covalent geometry : angle 0.61518 / 0.33 (16878) hydrogen bonds : bond 0.03921 / 2.57 ( 320) hydrogen bonds : angle 5.02259 / 3.50 ( 996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1814.98 seconds wall clock time: 32 minutes 31.27 seconds (1951.27 seconds total)