Starting phenix.real_space_refine on Wed Jul 30 20:06:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mdl_48173/07_2025/9mdl_48173.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mdl_48173/07_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_48173/07_2025/9mdl_48173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mdl_48173/07_2025/9mdl_48173.map" model { file = "/net/cci-nas-00/data/ceres_data/9mdl_48173/07_2025/9mdl_48173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mdl_48173/07_2025/9mdl_48173.cif" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.35, per 1000 atoms: 0.60 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: 2.31 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.97 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: 4.31 Time building geometry restraints manager: 2.82 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: 0.04 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.940 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.071 0.004 TRP A 245 HIS 0.001 0.000 HIS C 359 PHE 0.016 0.002 PHE A 622 TYR 0.026 0.002 TYR C 628 ARG 0.002 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.14328 ( 320) hydrogen bonds : angle 7.50235 ( 996) covalent geometry : bond 0.00329 (12435) covalent geometry : angle 0.77152 (16878) *********************** 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 : 1.449 Fit side-chains revert: symmetry clash REVERT: B 478 LEU cc_start: 0.8170 (mp) cc_final: 0.7887 (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: 0.7670 (m110) REVERT: C 735 ASN cc_start: 0.8596 (m110) cc_final: 0.8330 (m110) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.2061 time to fit residues: 58.3159 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 : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 0.0050 chunk 91 optimal weight: 0.0770 chunk 141 optimal weight: 8.9990 overall best weight: 0.9754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 397 ASN ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.171032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.147267 restraints weight = 25370.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150606 restraints weight = 16993.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.153113 restraints weight = 12481.257| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12435 Z= 0.115 Angle : 0.558 6.173 16878 Z= 0.296 Chirality : 0.044 0.163 1929 Planarity : 0.004 0.051 2193 Dihedral : 4.886 22.456 1677 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 0.07 % Allowed : 3.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1551 helix: -1.39 (0.40), residues: 147 sheet: 0.75 (0.28), residues: 348 loop : -2.24 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 245 HIS 0.002 0.000 HIS A 359 PHE 0.016 0.002 PHE C 487 TYR 0.016 0.001 TYR B 235 ARG 0.003 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 320) hydrogen bonds : angle 5.37836 ( 996) covalent geometry : bond 0.00263 (12435) covalent geometry : angle 0.55783 (16878) *********************** 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 178 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.459 Fit side-chains REVERT: A 254 TYR cc_start: 0.7482 (m-80) cc_final: 0.7147 (m-10) REVERT: C 634 ASN cc_start: 0.7863 (m110) cc_final: 0.7645 (m110) REVERT: C 735 ASN cc_start: 0.8519 (m110) cc_final: 0.8211 (m110) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1944 time to fit residues: 53.6651 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 : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS A 466 GLN A 735 ASN B 363 ASN B 466 GLN B 501 ASN B 648 ASN ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN C 466 GLN C 523 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.159257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135372 restraints weight = 26455.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138627 restraints weight = 17788.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140983 restraints weight = 13099.606| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 12435 Z= 0.227 Angle : 0.729 8.280 16878 Z= 0.388 Chirality : 0.048 0.167 1929 Planarity : 0.004 0.055 2193 Dihedral : 5.868 23.887 1677 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1551 helix: -1.20 (0.41), residues: 129 sheet: 0.18 (0.26), residues: 381 loop : -2.32 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 245 HIS 0.004 0.001 HIS A 359 PHE 0.031 0.003 PHE B 707 TYR 0.030 0.002 TYR C 235 ARG 0.007 0.001 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 320) hydrogen bonds : angle 5.66700 ( 996) covalent geometry : bond 0.00521 (12435) covalent geometry : angle 0.72867 (16878) *********************** 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 171 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 1.388 Fit side-chains REVERT: A 588 ILE cc_start: 0.7031 (mt) cc_final: 0.6798 (tt) REVERT: B 304 MET cc_start: 0.8376 (mpp) cc_final: 0.8138 (mmt) REVERT: B 363 ASN cc_start: 0.7248 (m-40) cc_final: 0.6907 (m110) REVERT: B 478 LEU cc_start: 0.8383 (mp) cc_final: 0.8123 (mp) REVERT: B 479 GLU cc_start: 0.8276 (pm20) cc_final: 0.7979 (pm20) REVERT: B 660 MET cc_start: 0.7860 (mmm) cc_final: 0.7566 (mmt) REVERT: B 693 GLU cc_start: 0.7659 (pm20) cc_final: 0.6775 (pt0) REVERT: C 262 LEU cc_start: 0.7528 (mp) cc_final: 0.7032 (mm) REVERT: C 607 ARG cc_start: 0.7565 (mpt-90) cc_final: 0.7186 (mmt90) REVERT: C 735 ASN cc_start: 0.8494 (m110) cc_final: 0.8226 (m110) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.1882 time to fit residues: 50.6595 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 : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 74 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 56 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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** B 233 ASN ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.162548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138938 restraints weight = 25874.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.142229 restraints weight = 17262.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144621 restraints weight = 12724.105| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2526 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= 0.148 Angle : 0.611 7.492 16878 Z= 0.325 Chirality : 0.045 0.159 1929 Planarity : 0.004 0.057 2193 Dihedral : 5.412 22.951 1677 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.14 % Allowed : 3.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.20), residues: 1551 helix: -1.22 (0.41), residues: 147 sheet: 0.36 (0.28), residues: 336 loop : -2.28 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 503 HIS 0.003 0.001 HIS C 359 PHE 0.017 0.002 PHE C 566 TYR 0.020 0.002 TYR A 526 ARG 0.004 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 320) hydrogen bonds : angle 5.29124 ( 996) covalent geometry : bond 0.00340 (12435) covalent geometry : angle 0.61112 (16878) *********************** 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 178 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: A 254 TYR cc_start: 0.7799 (m-80) cc_final: 0.7584 (m-10) REVERT: B 660 MET cc_start: 0.7755 (mmm) cc_final: 0.7499 (mmt) REVERT: B 666 TYR cc_start: 0.5880 (m-80) cc_final: 0.5671 (m-80) REVERT: B 693 GLU cc_start: 0.7283 (pm20) cc_final: 0.6541 (pt0) REVERT: C 275 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6248 (tm-30) REVERT: C 422 ILE cc_start: 0.7989 (mm) cc_final: 0.7698 (mm) REVERT: C 582 ASP cc_start: 0.6481 (t0) cc_final: 0.5969 (m-30) REVERT: C 735 ASN cc_start: 0.8603 (m110) cc_final: 0.8340 (m110) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.2168 time to fit residues: 59.6792 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 : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 130 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.0670 chunk 116 optimal weight: 5.9990 chunk 119 optimal weight: 0.0770 chunk 19 optimal weight: 5.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 359 HIS A 482 GLN ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 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 = 0.4139 r_free = 0.4139 target = 0.171655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147957 restraints weight = 25235.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.151681 restraints weight = 16318.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154341 restraints weight = 11609.185| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12435 Z= 0.097 Angle : 0.549 6.982 16878 Z= 0.288 Chirality : 0.043 0.165 1929 Planarity : 0.003 0.055 2193 Dihedral : 4.848 26.653 1677 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.14 % Allowed : 1.66 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.21), residues: 1551 helix: -0.90 (0.43), residues: 147 sheet: 0.30 (0.27), residues: 390 loop : -2.15 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 503 HIS 0.002 0.001 HIS C 359 PHE 0.010 0.001 PHE B 487 TYR 0.016 0.001 TYR B 235 ARG 0.002 0.000 ARG B 528 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 320) hydrogen bonds : angle 4.87620 ( 996) covalent geometry : bond 0.00222 (12435) covalent geometry : angle 0.54911 (16878) *********************** 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 186 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 265 ASN cc_start: 0.8858 (m-40) cc_final: 0.8577 (m-40) REVERT: B 478 LEU cc_start: 0.8361 (mp) cc_final: 0.8059 (mp) REVERT: B 689 LYS cc_start: 0.7068 (tptt) cc_final: 0.6809 (tptt) REVERT: B 693 GLU cc_start: 0.6794 (pm20) cc_final: 0.6234 (pt0) REVERT: C 275 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6298 (tm-30) REVERT: C 422 ILE cc_start: 0.7769 (mm) cc_final: 0.7512 (mm) REVERT: C 582 ASP cc_start: 0.6530 (t0) cc_final: 0.6037 (m-30) REVERT: C 735 ASN cc_start: 0.8538 (m110) cc_final: 0.8215 (m110) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.2112 time to fit residues: 58.7281 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 : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 33 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** B 651 ASN ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4067 r_free = 0.4067 target = 0.165460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.141448 restraints weight = 26009.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144929 restraints weight = 17267.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.147427 restraints weight = 12556.543| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2599 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= 0.123 Angle : 0.569 6.221 16878 Z= 0.300 Chirality : 0.044 0.167 1929 Planarity : 0.003 0.058 2193 Dihedral : 4.940 26.815 1677 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.21), residues: 1551 helix: -0.81 (0.44), residues: 147 sheet: 0.40 (0.27), residues: 384 loop : -2.15 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 245 HIS 0.002 0.001 HIS A 359 PHE 0.013 0.002 PHE C 487 TYR 0.020 0.001 TYR C 235 ARG 0.006 0.000 ARG A 529 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 320) hydrogen bonds : angle 4.90786 ( 996) covalent geometry : bond 0.00286 (12435) covalent geometry : angle 0.56927 (16878) *********************** 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 173 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8702 (pt) cc_final: 0.8280 (pt) REVERT: A 604 LYS cc_start: 0.7170 (mptt) cc_final: 0.6868 (tppt) REVERT: B 230 TYR cc_start: 0.6234 (m-10) cc_final: 0.5843 (m-10) REVERT: B 689 LYS cc_start: 0.7110 (tptt) cc_final: 0.6879 (tptt) REVERT: B 693 GLU cc_start: 0.7123 (pm20) cc_final: 0.6533 (pt0) REVERT: C 275 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6241 (tm-30) REVERT: C 422 ILE cc_start: 0.7871 (mm) cc_final: 0.7642 (mm) REVERT: C 582 ASP cc_start: 0.6571 (t0) cc_final: 0.6011 (m-30) REVERT: C 735 ASN cc_start: 0.8545 (m110) cc_final: 0.8230 (m110) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1968 time to fit residues: 52.4736 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 : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 28 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** 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 = 0.4144 r_free = 0.4144 target = 0.172940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.152711 restraints weight = 23830.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.155710 restraints weight = 16373.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.157919 restraints weight = 12085.830| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2708 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= 0.119 Angle : 0.568 6.346 16878 Z= 0.301 Chirality : 0.044 0.167 1929 Planarity : 0.003 0.060 2193 Dihedral : 4.918 27.204 1677 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.07 % Allowed : 1.73 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.21), residues: 1551 helix: -0.75 (0.44), residues: 147 sheet: 0.35 (0.27), residues: 387 loop : -2.15 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 503 HIS 0.001 0.000 HIS A 359 PHE 0.020 0.002 PHE C 487 TYR 0.019 0.001 TYR A 271 ARG 0.005 0.000 ARG A 529 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 320) hydrogen bonds : angle 4.89645 ( 996) covalent geometry : bond 0.00280 (12435) covalent geometry : angle 0.56832 (16878) *********************** 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 180 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8746 (pt) cc_final: 0.8309 (pt) REVERT: B 230 TYR cc_start: 0.6112 (m-10) cc_final: 0.5777 (m-10) REVERT: B 265 ASN cc_start: 0.8913 (m-40) cc_final: 0.8665 (m-40) REVERT: B 689 LYS cc_start: 0.6971 (tptt) cc_final: 0.6744 (tptt) REVERT: B 693 GLU cc_start: 0.7057 (pm20) cc_final: 0.6473 (pt0) REVERT: C 275 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6244 (tm-30) REVERT: C 422 ILE cc_start: 0.7864 (mm) cc_final: 0.7625 (mm) REVERT: C 582 ASP cc_start: 0.6547 (t0) cc_final: 0.5997 (m-30) REVERT: C 735 ASN cc_start: 0.8556 (m110) cc_final: 0.8237 (m110) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1961 time to fit residues: 54.6194 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 : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 90 optimal weight: 3.9990 chunk 131 optimal weight: 0.0370 chunk 132 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 128 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.0670 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 overall best weight: 0.2774 ------------------------------------------------------------------------------- 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 B 363 ASN C 466 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.176897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.157326 restraints weight = 23844.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.160369 restraints weight = 16129.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.162588 restraints weight = 11768.157| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2743 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= 0.096 Angle : 0.548 6.750 16878 Z= 0.289 Chirality : 0.044 0.209 1929 Planarity : 0.003 0.062 2193 Dihedral : 4.666 26.848 1677 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.21), residues: 1551 helix: -1.06 (0.41), residues: 165 sheet: 0.37 (0.27), residues: 396 loop : -2.18 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 503 HIS 0.000 0.000 HIS A 359 PHE 0.011 0.002 PHE C 487 TYR 0.017 0.001 TYR A 271 ARG 0.005 0.000 ARG A 529 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 320) hydrogen bonds : angle 4.74749 ( 996) covalent geometry : bond 0.00226 (12435) covalent geometry : angle 0.54838 (16878) *********************** 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 186 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8534 (pt) cc_final: 0.8050 (pt) REVERT: B 230 TYR cc_start: 0.5789 (m-10) cc_final: 0.5466 (m-10) REVERT: B 265 ASN cc_start: 0.8711 (m-40) cc_final: 0.8455 (m-40) REVERT: B 689 LYS cc_start: 0.6928 (tptt) cc_final: 0.6682 (tptt) REVERT: B 693 GLU cc_start: 0.6687 (pm20) cc_final: 0.6270 (pt0) REVERT: C 422 ILE cc_start: 0.7710 (mm) cc_final: 0.7455 (mm) REVERT: C 502 SER cc_start: 0.7942 (p) cc_final: 0.7717 (p) REVERT: C 582 ASP cc_start: 0.6582 (t0) cc_final: 0.6110 (m-30) REVERT: C 735 ASN cc_start: 0.8513 (m110) cc_final: 0.8181 (m110) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2466 time to fit residues: 70.9365 Evaluate side-chains 143 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 107 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 B 363 ASN B 651 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 = 0.4086 r_free = 0.4086 target = 0.167546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143883 restraints weight = 24863.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.147493 restraints weight = 16099.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.150112 restraints weight = 11513.172| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2953 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= 0.137 Angle : 0.591 6.518 16878 Z= 0.313 Chirality : 0.045 0.190 1929 Planarity : 0.003 0.065 2193 Dihedral : 4.936 26.807 1677 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 0.07 % Allowed : 0.51 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.21), residues: 1551 helix: -0.66 (0.44), residues: 147 sheet: 0.31 (0.27), residues: 393 loop : -2.14 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 245 HIS 0.002 0.001 HIS A 359 PHE 0.014 0.002 PHE B 707 TYR 0.019 0.001 TYR C 235 ARG 0.004 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 320) hydrogen bonds : angle 4.89208 ( 996) covalent geometry : bond 0.00319 (12435) covalent geometry : angle 0.59112 (16878) *********************** 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 179 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8521 (pt) cc_final: 0.8064 (pt) REVERT: B 230 TYR cc_start: 0.6168 (m-10) cc_final: 0.5903 (m-10) REVERT: B 265 ASN cc_start: 0.9072 (m-40) cc_final: 0.8847 (m-40) REVERT: B 363 ASN cc_start: 0.7076 (m-40) cc_final: 0.6806 (m110) REVERT: B 689 LYS cc_start: 0.7062 (tptt) cc_final: 0.6862 (tptt) REVERT: B 693 GLU cc_start: 0.7110 (pm20) cc_final: 0.6599 (pt0) REVERT: C 422 ILE cc_start: 0.7887 (mm) cc_final: 0.7656 (mm) REVERT: C 582 ASP cc_start: 0.6603 (t0) cc_final: 0.5974 (m-30) REVERT: C 735 ASN cc_start: 0.8553 (m110) cc_final: 0.8229 (m110) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2013 time to fit residues: 55.2760 Evaluate side-chains 133 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 chunk 126 optimal weight: 0.0030 chunk 132 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.4568 ------------------------------------------------------------------------------- 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 B 363 ASN ** B 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.175919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.155950 restraints weight = 23902.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.159030 restraints weight = 16270.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.161237 restraints weight = 11902.602| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2950 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= 0.096 Angle : 0.552 6.852 16878 Z= 0.290 Chirality : 0.044 0.189 1929 Planarity : 0.004 0.073 2193 Dihedral : 4.664 26.612 1677 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.21), residues: 1551 helix: -0.94 (0.42), residues: 165 sheet: 0.34 (0.27), residues: 396 loop : -2.19 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 503 HIS 0.001 0.000 HIS A 314 PHE 0.010 0.001 PHE B 487 TYR 0.013 0.001 TYR C 235 ARG 0.002 0.000 ARG B 668 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 320) hydrogen bonds : angle 4.72572 ( 996) covalent geometry : bond 0.00225 (12435) covalent geometry : angle 0.55155 (16878) ********************** 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: 0 poor density : 175 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8493 (pt) cc_final: 0.8061 (pt) REVERT: B 230 TYR cc_start: 0.5863 (m-10) cc_final: 0.5652 (m-10) REVERT: B 363 ASN cc_start: 0.7199 (m110) cc_final: 0.6740 (m110) REVERT: B 666 TYR cc_start: 0.5821 (m-80) cc_final: 0.5545 (m-80) REVERT: B 689 LYS cc_start: 0.6977 (tptt) cc_final: 0.6735 (tptt) REVERT: B 693 GLU cc_start: 0.6693 (pm20) cc_final: 0.6270 (pt0) REVERT: C 422 ILE cc_start: 0.7678 (mm) cc_final: 0.7446 (mm) REVERT: C 499 GLU cc_start: 0.7059 (tp30) cc_final: 0.6767 (tp30) REVERT: C 582 ASP cc_start: 0.6605 (t0) cc_final: 0.6134 (m-30) REVERT: C 735 ASN cc_start: 0.8537 (m110) cc_final: 0.8203 (m110) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2025 time to fit residues: 54.8008 Evaluate side-chains 138 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 30 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 B 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.173041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.153004 restraints weight = 23968.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.156005 restraints weight = 16359.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.158207 restraints weight = 12020.535| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3068 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 : 0.565 6.328 16878 Z= 0.299 Chirality : 0.044 0.187 1929 Planarity : 0.004 0.067 2193 Dihedral : 4.758 26.422 1677 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.21), residues: 1551 helix: -0.52 (0.45), residues: 147 sheet: 0.29 (0.27), residues: 396 loop : -2.15 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 245 HIS 0.001 0.000 HIS A 359 PHE 0.011 0.002 PHE B 566 TYR 0.017 0.001 TYR A 271 ARG 0.003 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 320) hydrogen bonds : angle 4.76620 ( 996) covalent geometry : bond 0.00267 (12435) covalent geometry : angle 0.56519 (16878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.41 seconds wall clock time: 65 minutes 39.86 seconds (3939.86 seconds total)