Starting phenix.real_space_refine on Thu Sep 18 00:52:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mdl_48173/09_2025/9mdl_48173.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mdl_48173/09_2025/9mdl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mdl_48173/09_2025/9mdl_48173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mdl_48173/09_2025/9mdl_48173.map" model { file = "/net/cci-nas-00/data/ceres_data/9mdl_48173/09_2025/9mdl_48173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mdl_48173/09_2025/9mdl_48173.cif" } 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-2.0-5805/lib/python3.9/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, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.54, per 1000 atoms: 0.29 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: 1.00 Conformation dependent library (CDL) restraints added in 580.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.56 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: 2.22 Time building geometry restraints manager: 1.35 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: 2.970 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 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 aren 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 covalent geometry : bond 0.00329 (12435) covalent geometry : angle 0.77152 (16878) hydrogen bonds : bond 0.14328 ( 320) hydrogen bonds : angle 7.50235 ( 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 : 0.444 Fit side-chains revert: symmetry clash REVERT: B 478 LEU cc_start: 0.8170 (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: 0.0929 time to fit residues: 26.6704 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 : 0.482 ------------------------------------------------------------------------------- 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: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 735 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.166373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142516 restraints weight = 25790.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145864 restraints weight = 17351.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148289 restraints weight = 12721.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149863 restraints weight = 10003.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.151303 restraints weight = 8384.614| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12435 Z= 0.155 Angle : 0.608 6.713 16878 Z= 0.324 Chirality : 0.045 0.166 1929 Planarity : 0.004 0.053 2193 Dihedral : 5.161 22.344 1677 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.14 % Allowed : 4.98 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.20), residues: 1551 helix: -1.05 (0.43), residues: 129 sheet: 0.59 (0.27), residues: 363 loop : -2.18 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 528 TYR 0.023 0.002 TYR C 235 PHE 0.019 0.002 PHE C 487 TRP 0.037 0.002 TRP A 245 HIS 0.003 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00353 (12435) covalent geometry : angle 0.60765 (16878) hydrogen bonds : bond 0.04064 ( 320) hydrogen bonds : angle 5.36077 ( 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 170 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.454 Fit side-chains REVERT: A 254 TYR cc_start: 0.7567 (m-80) cc_final: 0.7232 (m-10) REVERT: A 369 ASP cc_start: 0.7703 (p0) cc_final: 0.7462 (p0) REVERT: B 693 GLU cc_start: 0.7167 (pm20) cc_final: 0.6408 (pt0) REVERT: C 735 ASN cc_start: 0.8493 (m110) cc_final: 0.8194 (m110) outliers start: 2 outliers final: 0 residues processed: 169 average time/residue: 0.0862 time to fit residues: 22.8726 Evaluate side-chains 121 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 8.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 233 ASN B 363 ASN ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 523 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.169278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145717 restraints weight = 25577.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149153 restraints weight = 17018.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151619 restraints weight = 12361.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.153375 restraints weight = 9662.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.154754 restraints weight = 7992.058| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1593 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= 0.110 Angle : 0.557 6.458 16878 Z= 0.293 Chirality : 0.044 0.162 1929 Planarity : 0.003 0.053 2193 Dihedral : 4.876 21.757 1677 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.14 % Allowed : 3.54 % Favored : 96.32 % 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 aren not related in a simple way. whole: -1.97 (0.20), residues: 1551 helix: -1.06 (0.42), residues: 147 sheet: 0.66 (0.28), residues: 342 loop : -2.19 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 607 TYR 0.015 0.001 TYR C 235 PHE 0.014 0.002 PHE B 281 TRP 0.015 0.001 TRP A 245 HIS 0.001 0.000 HIS C 359 Details of bonding type rmsd covalent geometry : bond 0.00254 (12435) covalent geometry : angle 0.55720 (16878) hydrogen bonds : bond 0.03627 ( 320) hydrogen bonds : angle 5.08830 ( 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 181 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8649 (mt) cc_final: 0.8332 (mt) REVERT: C 582 ASP cc_start: 0.6479 (t0) cc_final: 0.6061 (m-30) REVERT: C 735 ASN cc_start: 0.8494 (m110) cc_final: 0.8181 (m110) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.0967 time to fit residues: 26.5963 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 : 0.475 ------------------------------------------------------------------------------- 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: 4.9990 chunk 150 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 466 GLN B 363 ASN B 466 GLN B 501 ASN B 648 ASN ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.162852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139204 restraints weight = 25972.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142512 restraints weight = 17390.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144907 restraints weight = 12742.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146664 restraints weight = 10034.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147919 restraints weight = 8332.578| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12435 Z= 0.174 Angle : 0.631 7.220 16878 Z= 0.334 Chirality : 0.046 0.161 1929 Planarity : 0.004 0.049 2193 Dihedral : 5.261 22.625 1677 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % 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 aren not related in a simple way. whole: -2.09 (0.20), residues: 1551 helix: -1.09 (0.42), residues: 147 sheet: 0.49 (0.28), residues: 339 loop : -2.25 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 528 TYR 0.023 0.002 TYR A 526 PHE 0.019 0.002 PHE B 707 TRP 0.011 0.002 TRP B 245 HIS 0.002 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00399 (12435) covalent geometry : angle 0.63072 (16878) hydrogen bonds : bond 0.04366 ( 320) hydrogen bonds : angle 5.20737 ( 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 179 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 487 PHE cc_start: 0.7316 (p90) cc_final: 0.6689 (p90) REVERT: B 693 GLU cc_start: 0.7326 (pm20) cc_final: 0.6478 (pt0) REVERT: C 275 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6120 (tm-30) REVERT: C 735 ASN cc_start: 0.8514 (m110) cc_final: 0.8227 (m110) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.0911 time to fit residues: 25.4607 Evaluate side-chains 126 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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: 0.9990 chunk 118 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 0.0370 chunk 115 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4066 r_free = 0.4066 target = 0.164923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.140913 restraints weight = 25899.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144370 restraints weight = 17264.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.146852 restraints weight = 12564.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148701 restraints weight = 9823.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150018 restraints weight = 8112.579| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2297 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= 0.122 Angle : 0.579 6.249 16878 Z= 0.305 Chirality : 0.044 0.161 1929 Planarity : 0.003 0.059 2193 Dihedral : 5.047 25.448 1677 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.76 % 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 aren not related in a simple way. whole: -2.00 (0.21), residues: 1551 helix: -0.92 (0.43), residues: 147 sheet: 0.32 (0.26), residues: 387 loop : -2.21 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 528 TYR 0.018 0.001 TYR C 235 PHE 0.014 0.002 PHE C 487 TRP 0.009 0.001 TRP A 503 HIS 0.001 0.000 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00283 (12435) covalent geometry : angle 0.57945 (16878) hydrogen bonds : bond 0.03791 ( 320) hydrogen bonds : angle 5.03752 ( 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 182 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8531 (mt) cc_final: 0.8156 (mt) REVERT: B 666 TYR cc_start: 0.6093 (m-80) cc_final: 0.5806 (m-80) REVERT: B 693 GLU cc_start: 0.7151 (pm20) cc_final: 0.6468 (pt0) REVERT: B 717 ASP cc_start: 0.8060 (t70) cc_final: 0.7762 (t70) REVERT: C 275 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6141 (tm-30) REVERT: C 735 ASN cc_start: 0.8520 (m110) cc_final: 0.8237 (m110) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.0991 time to fit residues: 27.3954 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 : 0.507 ------------------------------------------------------------------------------- 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: 7.9990 chunk 43 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.168185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.144161 restraints weight = 25482.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147862 restraints weight = 16563.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150461 restraints weight = 11853.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152419 restraints weight = 9146.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153798 restraints weight = 7449.350| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2419 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= 0.110 Angle : 0.565 6.321 16878 Z= 0.297 Chirality : 0.044 0.169 1929 Planarity : 0.004 0.074 2193 Dihedral : 4.892 24.190 1677 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.07 % Allowed : 2.45 % Favored : 97.47 % 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 aren not related in a simple way. whole: -1.92 (0.21), residues: 1551 helix: -0.82 (0.43), residues: 147 sheet: 0.36 (0.27), residues: 387 loop : -2.16 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 607 TYR 0.017 0.001 TYR C 235 PHE 0.012 0.002 PHE C 487 TRP 0.008 0.001 TRP A 503 HIS 0.001 0.000 HIS C 359 Details of bonding type rmsd covalent geometry : bond 0.00257 (12435) covalent geometry : angle 0.56545 (16878) hydrogen bonds : bond 0.03565 ( 320) hydrogen bonds : angle 4.92050 ( 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 179 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8535 (pt) cc_final: 0.8053 (pt) REVERT: A 604 LYS cc_start: 0.7254 (mptt) cc_final: 0.6929 (tppt) REVERT: B 230 TYR cc_start: 0.6267 (m-10) cc_final: 0.5727 (m-10) REVERT: B 666 TYR cc_start: 0.6128 (m-80) cc_final: 0.5826 (m-80) REVERT: B 693 GLU cc_start: 0.7078 (pm20) cc_final: 0.6434 (pt0) REVERT: C 275 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6123 (tm-30) REVERT: C 335 ASN cc_start: 0.7147 (t0) cc_final: 0.6936 (m-40) REVERT: C 582 ASP cc_start: 0.6550 (t0) cc_final: 0.6035 (m-30) REVERT: C 735 ASN cc_start: 0.8534 (m110) cc_final: 0.8217 (m110) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1013 time to fit residues: 27.4231 Evaluate side-chains 134 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 7.9990 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.167990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144286 restraints weight = 25193.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147910 restraints weight = 16500.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150459 restraints weight = 11840.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.152397 restraints weight = 9171.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153763 restraints weight = 7478.296| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2527 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= 0.115 Angle : 0.573 6.268 16878 Z= 0.300 Chirality : 0.044 0.198 1929 Planarity : 0.003 0.062 2193 Dihedral : 4.892 23.124 1677 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.07 % Allowed : 1.37 % Favored : 98.56 % 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 aren not related in a simple way. whole: -2.00 (0.21), residues: 1551 helix: -1.11 (0.40), residues: 165 sheet: 0.36 (0.26), residues: 387 loop : -2.22 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 528 TYR 0.014 0.001 TYR A 526 PHE 0.020 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 covalent geometry : bond 0.00267 (12435) covalent geometry : angle 0.57331 (16878) hydrogen bonds : bond 0.03617 ( 320) hydrogen bonds : angle 4.91494 ( 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 179 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8597 (pt) cc_final: 0.8132 (pt) REVERT: B 230 TYR cc_start: 0.6189 (m-10) cc_final: 0.5759 (m-10) REVERT: B 666 TYR cc_start: 0.6116 (m-80) cc_final: 0.5836 (m-80) REVERT: B 693 GLU cc_start: 0.7023 (pm20) cc_final: 0.6391 (pt0) REVERT: B 717 ASP cc_start: 0.8062 (t70) cc_final: 0.7655 (t70) REVERT: C 275 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6102 (tm-30) REVERT: C 422 ILE cc_start: 0.7980 (mm) cc_final: 0.7717 (mm) REVERT: C 582 ASP cc_start: 0.6602 (t0) cc_final: 0.6024 (m-30) REVERT: C 735 ASN cc_start: 0.8592 (m110) cc_final: 0.8275 (m110) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.0960 time to fit residues: 26.3705 Evaluate side-chains 136 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 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: 2.9990 chunk 130 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 141 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 347 ASN A 482 GLN B 651 ASN C 335 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 = 0.4107 r_free = 0.4107 target = 0.169567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145874 restraints weight = 25235.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149560 restraints weight = 16400.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.152185 restraints weight = 11720.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.154099 restraints weight = 9027.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.155264 restraints weight = 7341.704| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2645 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= 0.105 Angle : 0.562 6.537 16878 Z= 0.295 Chirality : 0.044 0.186 1929 Planarity : 0.003 0.064 2193 Dihedral : 4.792 25.550 1677 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 0.14 % Allowed : 0.65 % Favored : 99.21 % 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 aren not related in a simple way. whole: -1.95 (0.21), residues: 1551 helix: -1.07 (0.41), residues: 165 sheet: 0.45 (0.27), residues: 387 loop : -2.21 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 528 TYR 0.016 0.001 TYR C 464 PHE 0.014 0.002 PHE C 487 TRP 0.007 0.001 TRP A 503 HIS 0.002 0.000 HIS C 359 Details of bonding type rmsd covalent geometry : bond 0.00247 (12435) covalent geometry : angle 0.56193 (16878) hydrogen bonds : bond 0.03449 ( 320) hydrogen bonds : angle 4.83284 ( 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 180 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8473 (pt) cc_final: 0.8014 (pt) REVERT: B 230 TYR cc_start: 0.6133 (m-10) cc_final: 0.5766 (m-10) REVERT: B 304 MET cc_start: 0.8344 (mpp) cc_final: 0.8101 (mpp) REVERT: B 666 TYR cc_start: 0.6182 (m-80) cc_final: 0.5934 (m-80) REVERT: B 693 GLU cc_start: 0.6924 (pm20) cc_final: 0.6356 (pt0) REVERT: C 422 ILE cc_start: 0.7942 (mm) cc_final: 0.7700 (mm) REVERT: C 582 ASP cc_start: 0.6577 (t0) cc_final: 0.6003 (m-30) REVERT: C 735 ASN cc_start: 0.8534 (m110) cc_final: 0.8202 (m110) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.0971 time to fit residues: 27.0680 Evaluate side-chains 135 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 5.9990 chunk 66 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 140 optimal weight: 0.0570 chunk 58 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 586 ASN C 335 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 = 0.4166 r_free = 0.4166 target = 0.174744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.155054 restraints weight = 23903.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.158024 restraints weight = 16458.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.160161 restraints weight = 12192.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.161759 restraints weight = 9548.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162803 restraints weight = 7847.739| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2738 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= 0.105 Angle : 0.565 6.914 16878 Z= 0.297 Chirality : 0.044 0.180 1929 Planarity : 0.003 0.065 2193 Dihedral : 4.758 26.873 1677 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.07 % Allowed : 0.72 % Favored : 99.21 % 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 aren not related in a simple way. whole: -1.95 (0.21), residues: 1551 helix: -0.97 (0.41), residues: 165 sheet: 0.42 (0.27), residues: 390 loop : -2.22 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 528 TYR 0.016 0.001 TYR C 464 PHE 0.011 0.002 PHE A 281 TRP 0.007 0.001 TRP A 503 HIS 0.001 0.001 HIS C 359 Details of bonding type rmsd covalent geometry : bond 0.00247 (12435) covalent geometry : angle 0.56489 (16878) hydrogen bonds : bond 0.03386 ( 320) hydrogen bonds : angle 4.76310 ( 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 178 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8552 (pt) cc_final: 0.8111 (pt) REVERT: B 230 TYR cc_start: 0.6025 (m-10) cc_final: 0.5685 (m-10) REVERT: B 666 TYR cc_start: 0.5934 (m-80) cc_final: 0.5728 (m-80) REVERT: B 693 GLU cc_start: 0.6864 (pm20) cc_final: 0.6346 (pt0) REVERT: B 717 ASP cc_start: 0.7763 (t70) cc_final: 0.7391 (t70) REVERT: C 422 ILE cc_start: 0.7962 (mm) cc_final: 0.7728 (mm) REVERT: C 569 ILE cc_start: 0.7188 (mm) cc_final: 0.6983 (mm) REVERT: C 582 ASP cc_start: 0.6576 (t0) cc_final: 0.6061 (m-30) REVERT: C 735 ASN cc_start: 0.8537 (m110) cc_final: 0.8221 (m110) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.1012 time to fit residues: 27.0575 Evaluate side-chains 135 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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: 0.0770 chunk 109 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 132 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 586 ASN C 523 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.175859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.156233 restraints weight = 24006.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.159211 restraints weight = 16364.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.161343 restraints weight = 12053.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.162955 restraints weight = 9437.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.164138 restraints weight = 7736.511| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2821 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 : 0.552 7.254 16878 Z= 0.290 Chirality : 0.044 0.177 1929 Planarity : 0.003 0.066 2193 Dihedral : 4.613 26.833 1677 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.78 % 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 aren not related in a simple way. whole: -1.90 (0.21), residues: 1551 helix: -0.94 (0.42), residues: 165 sheet: 0.46 (0.27), residues: 390 loop : -2.19 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 232 TYR 0.015 0.001 TYR C 464 PHE 0.010 0.001 PHE B 487 TRP 0.008 0.001 TRP A 503 HIS 0.001 0.000 HIS C 359 Details of bonding type rmsd covalent geometry : bond 0.00233 (12435) covalent geometry : angle 0.55218 (16878) hydrogen bonds : bond 0.03172 ( 320) hydrogen bonds : angle 4.66827 ( 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 175 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8412 (pt) cc_final: 0.7928 (pt) REVERT: B 230 TYR cc_start: 0.5851 (m-10) cc_final: 0.5625 (m-10) REVERT: B 609 MET cc_start: 0.7900 (ptt) cc_final: 0.7285 (ptt) REVERT: B 666 TYR cc_start: 0.5886 (m-80) cc_final: 0.5581 (m-80) REVERT: B 693 GLU cc_start: 0.6776 (pm20) cc_final: 0.6335 (pt0) REVERT: C 422 ILE cc_start: 0.7929 (mm) cc_final: 0.7685 (mm) REVERT: C 582 ASP cc_start: 0.6653 (t0) cc_final: 0.6165 (m-30) REVERT: C 660 MET cc_start: 0.7328 (tmm) cc_final: 0.6873 (tmm) REVERT: C 735 ASN cc_start: 0.8524 (m110) cc_final: 0.8198 (m110) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.0938 time to fit residues: 25.7221 Evaluate side-chains 137 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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: 0.1980 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 0.0870 chunk 132 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 586 ASN C 523 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.176786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.156963 restraints weight = 23756.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.160027 restraints weight = 16137.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162215 restraints weight = 11845.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163853 restraints weight = 9243.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.165017 restraints weight = 7571.050| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2899 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= 0.097 Angle : 0.547 7.306 16878 Z= 0.286 Chirality : 0.043 0.176 1929 Planarity : 0.003 0.067 2193 Dihedral : 4.507 26.996 1677 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.07 % Allowed : 0.58 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.21), residues: 1551 helix: -0.97 (0.41), residues: 168 sheet: 0.49 (0.27), residues: 390 loop : -2.18 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 528 TYR 0.015 0.001 TYR C 464 PHE 0.010 0.001 PHE C 566 TRP 0.008 0.001 TRP B 503 HIS 0.001 0.000 HIS C 359 Details of bonding type rmsd covalent geometry : bond 0.00229 (12435) covalent geometry : angle 0.54709 (16878) hydrogen bonds : bond 0.03125 ( 320) hydrogen bonds : angle 4.58466 ( 996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.74 seconds wall clock time: 33 minutes 42.63 seconds (2022.63 seconds total)