Starting phenix.real_space_refine on Fri Aug 22 17:23:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d10_30542/08_2025/7d10_30542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d10_30542/08_2025/7d10_30542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d10_30542/08_2025/7d10_30542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d10_30542/08_2025/7d10_30542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d10_30542/08_2025/7d10_30542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d10_30542/08_2025/7d10_30542.map" } resolution = 3.52 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= 0.009 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4294 2.51 5 N 1000 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6424 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3176 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 15, 'TRANS': 430} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 3, 'GLU:plan': 10, 'HIS:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3176 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 15, 'TRANS': 430} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 3, 'GLU:plan': 10, 'HIS:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.77, per 1000 atoms: 0.28 Number of scatterers: 6424 At special positions: 0 Unit cell: (101.463, 79.643, 88.371, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1102 8.00 N 1000 7.00 C 4294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 397.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1636 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 69.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 287 through 290 removed outlier: 3.598A pdb=" N GLY A 290 " --> pdb=" O TRP A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.789A pdb=" N ASN A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 319 through 342 removed outlier: 3.738A pdb=" N THR A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.559A pdb=" N ARG A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 389 removed outlier: 3.909A pdb=" N ALA A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 406 through 426 removed outlier: 4.078A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.948A pdb=" N ILE A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.834A pdb=" N GLY A 504 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.734A pdb=" N ALA A 517 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 518 " --> pdb=" O PRO A 514 " (cutoff:3.500A) Proline residue: A 519 - end of helix removed outlier: 3.671A pdb=" N LEU A 523 " --> pdb=" O PRO A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.606A pdb=" N LEU A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 removed outlier: 3.703A pdb=" N PHE A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 622 through 632 removed outlier: 4.284A pdb=" N ALA A 628 " --> pdb=" O LYS A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.646A pdb=" N GLN A 639 " --> pdb=" O PRO A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 667 removed outlier: 3.639A pdb=" N TYR A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 675 Processing helix chain 'A' and resid 675 through 699 removed outlier: 4.348A pdb=" N PHE A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 730 removed outlier: 3.741A pdb=" N CYS A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 751 removed outlier: 3.735A pdb=" N LEU A 737 " --> pdb=" O TRP A 733 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 290 removed outlier: 3.599A pdb=" N GLY B 290 " --> pdb=" O TRP B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 287 through 290' Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.789A pdb=" N ASN B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 319 through 342 removed outlier: 3.738A pdb=" N THR B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 342 " --> pdb=" O THR B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.558A pdb=" N ARG B 358 " --> pdb=" O TYR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 389 removed outlier: 3.908A pdb=" N ALA B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 380 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 406 through 426 removed outlier: 4.078A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 422 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 436 through 453 removed outlier: 3.948A pdb=" N ILE B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 469 through 476 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 500 through 504 removed outlier: 3.834A pdb=" N GLY B 504 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.734A pdb=" N ALA B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Proline residue: B 519 - end of helix removed outlier: 3.672A pdb=" N LEU B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.607A pdb=" N LEU B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.703A pdb=" N PHE B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 617 Processing helix chain 'B' and resid 622 through 632 removed outlier: 4.284A pdb=" N ALA B 628 " --> pdb=" O LYS B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.646A pdb=" N GLN B 639 " --> pdb=" O PRO B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 667 removed outlier: 3.639A pdb=" N TYR B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 675 through 699 removed outlier: 4.349A pdb=" N PHE B 681 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 688 " --> pdb=" O ALA B 684 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 694 " --> pdb=" O ASN B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 730 removed outlier: 3.741A pdb=" N CYS B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET B 727 " --> pdb=" O CYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 751 removed outlier: 3.735A pdb=" N LEU B 737 " --> pdb=" O TRP B 733 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B 746 " --> pdb=" O VAL B 742 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 912 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: 0.65 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1592 1.33 - 1.45: 1190 1.45 - 1.57: 3718 1.57 - 1.68: 2 1.68 - 1.80: 46 Bond restraints: 6548 Sorted by residual: bond pdb=" C ALA A 622 " pdb=" N PRO A 623 " ideal model delta sigma weight residual 1.337 1.373 -0.036 1.24e-02 6.50e+03 8.22e+00 bond pdb=" C ALA B 622 " pdb=" N PRO B 623 " ideal model delta sigma weight residual 1.337 1.373 -0.036 1.24e-02 6.50e+03 8.22e+00 bond pdb=" C PHE A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.337 1.359 -0.023 9.80e-03 1.04e+04 5.32e+00 bond pdb=" C PHE B 495 " pdb=" N PRO B 496 " ideal model delta sigma weight residual 1.337 1.359 -0.022 9.80e-03 1.04e+04 5.18e+00 bond pdb=" C ILE B 518 " pdb=" O ILE B 518 " ideal model delta sigma weight residual 1.240 1.216 0.024 1.22e-02 6.72e+03 3.88e+00 ... (remaining 6543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 8543 2.16 - 4.32: 298 4.32 - 6.48: 55 6.48 - 8.64: 26 8.64 - 10.80: 4 Bond angle restraints: 8926 Sorted by residual: angle pdb=" N PRO B 581 " pdb=" CA PRO B 581 " pdb=" CB PRO B 581 " ideal model delta sigma weight residual 103.25 111.00 -7.75 1.05e+00 9.07e-01 5.45e+01 angle pdb=" N PRO A 581 " pdb=" CA PRO A 581 " pdb=" CB PRO A 581 " ideal model delta sigma weight residual 103.25 111.00 -7.75 1.05e+00 9.07e-01 5.44e+01 angle pdb=" N ALA B 517 " pdb=" CA ALA B 517 " pdb=" C ALA B 517 " ideal model delta sigma weight residual 111.36 119.01 -7.65 1.09e+00 8.42e-01 4.93e+01 angle pdb=" N ALA A 517 " pdb=" CA ALA A 517 " pdb=" C ALA A 517 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N PRO A 754 " pdb=" CA PRO A 754 " pdb=" CB PRO A 754 " ideal model delta sigma weight residual 103.00 110.65 -7.65 1.10e+00 8.26e-01 4.84e+01 ... (remaining 8921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 3363 11.91 - 23.82: 278 23.82 - 35.73: 79 35.73 - 47.64: 25 47.64 - 59.55: 5 Dihedral angle restraints: 3750 sinusoidal: 1208 harmonic: 2542 Sorted by residual: dihedral pdb=" CA ALA B 707 " pdb=" C ALA B 707 " pdb=" N PHE B 708 " pdb=" CA PHE B 708 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ALA A 707 " pdb=" C ALA A 707 " pdb=" N PHE A 708 " pdb=" CA PHE A 708 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS A 398 " pdb=" C HIS A 398 " pdb=" N SER A 399 " pdb=" CA SER A 399 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 3747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 777 0.058 - 0.116: 275 0.116 - 0.174: 52 0.174 - 0.232: 10 0.232 - 0.289: 4 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CA LYS B 520 " pdb=" N LYS B 520 " pdb=" C LYS B 520 " pdb=" CB LYS B 520 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LYS A 520 " pdb=" N LYS A 520 " pdb=" C LYS A 520 " pdb=" CB LYS A 520 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ALA B 517 " pdb=" N ALA B 517 " pdb=" C ALA B 517 " pdb=" CB ALA B 517 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1115 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 518 " 0.076 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO B 519 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO B 519 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 519 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 518 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 519 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 519 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 519 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 515 " 0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C GLN B 515 " -0.072 2.00e-02 2.50e+03 pdb=" O GLN B 515 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 516 " 0.024 2.00e-02 2.50e+03 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1602 2.78 - 3.31: 5814 3.31 - 3.84: 10053 3.84 - 4.37: 11862 4.37 - 4.90: 20179 Nonbonded interactions: 49510 Sorted by model distance: nonbonded pdb=" O LEU B 438 " pdb=" OG SER B 609 " model vdw 2.249 3.040 nonbonded pdb=" O LEU A 438 " pdb=" OG SER A 609 " model vdw 2.249 3.040 nonbonded pdb=" O SER A 339 " pdb=" OG1 THR A 343 " model vdw 2.295 3.040 nonbonded pdb=" O SER B 339 " pdb=" OG1 THR B 343 " model vdw 2.295 3.040 nonbonded pdb=" O THR A 499 " pdb=" OH TYR A 686 " model vdw 2.341 3.040 ... (remaining 49505 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.510 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.480 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.007 0.063 6548 Z= 0.295 Angle : 1.055 10.800 8926 Z= 0.592 Chirality : 0.063 0.289 1118 Planarity : 0.009 0.116 1084 Dihedral : 10.873 59.548 2114 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.94 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % 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: -6.70 (0.15), residues: 872 helix: -4.28 (0.10), residues: 594 sheet: None (None), residues: 0 loop : -4.33 (0.25), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 307 TYR 0.025 0.002 TYR B 383 PHE 0.024 0.003 PHE B 494 TRP 0.027 0.003 TRP B 714 HIS 0.005 0.004 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 6548) covalent geometry : angle 1.05460 ( 8926) hydrogen bonds : bond 0.19228 ( 312) hydrogen bonds : angle 7.48523 ( 912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.205 Fit side-chains REVERT: A 382 MET cc_start: 0.8932 (ttp) cc_final: 0.8508 (ttt) REVERT: A 415 ILE cc_start: 0.9100 (pp) cc_final: 0.8565 (mm) REVERT: A 601 PRO cc_start: 0.6176 (Cg_endo) cc_final: 0.5972 (Cg_exo) REVERT: B 382 MET cc_start: 0.8931 (ttp) cc_final: 0.8565 (ttt) REVERT: B 415 ILE cc_start: 0.9108 (pp) cc_final: 0.8558 (mm) REVERT: B 469 LYS cc_start: 0.6858 (mmpt) cc_final: 0.6636 (mmtt) REVERT: B 601 PRO cc_start: 0.6195 (Cg_endo) cc_final: 0.5992 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0690 time to fit residues: 13.9797 Evaluate side-chains 95 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 476 ASN A 506 ASN B 298 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106147 restraints weight = 8936.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109187 restraints weight = 4882.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110862 restraints weight = 3460.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112066 restraints weight = 2882.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112066 restraints weight = 2564.873| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6548 Z= 0.123 Angle : 0.589 6.093 8926 Z= 0.312 Chirality : 0.042 0.121 1118 Planarity : 0.005 0.067 1084 Dihedral : 7.741 58.025 974 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.55 % Allowed : 11.28 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.81 (0.21), residues: 872 helix: -2.68 (0.16), residues: 600 sheet: None (None), residues: 0 loop : -4.06 (0.27), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.008 0.001 TYR B 383 PHE 0.027 0.002 PHE A 590 TRP 0.012 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6548) covalent geometry : angle 0.58905 ( 8926) hydrogen bonds : bond 0.04489 ( 312) hydrogen bonds : angle 4.49138 ( 912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.232 Fit side-chains REVERT: A 485 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 506 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8051 (m-40) REVERT: B 485 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7480 (mm-30) REVERT: B 506 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8058 (m-40) outliers start: 27 outliers final: 12 residues processed: 146 average time/residue: 0.0667 time to fit residues: 13.2622 Evaluate side-chains 123 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105154 restraints weight = 8803.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108133 restraints weight = 4861.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109828 restraints weight = 3468.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111029 restraints weight = 2894.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111168 restraints weight = 2578.775| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6548 Z= 0.123 Angle : 0.562 5.873 8926 Z= 0.297 Chirality : 0.043 0.132 1118 Planarity : 0.004 0.047 1084 Dihedral : 7.246 56.658 974 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.38 % Allowed : 15.66 % Favored : 79.97 % 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: -3.73 (0.25), residues: 872 helix: -1.76 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -3.90 (0.28), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 358 TYR 0.015 0.001 TYR B 748 PHE 0.025 0.001 PHE B 590 TRP 0.010 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6548) covalent geometry : angle 0.56233 ( 8926) hydrogen bonds : bond 0.03944 ( 312) hydrogen bonds : angle 4.13301 ( 912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.204 Fit side-chains REVERT: A 485 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 326 MET cc_start: 0.8087 (ttp) cc_final: 0.7867 (ttp) REVERT: B 485 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7512 (mm-30) outliers start: 26 outliers final: 18 residues processed: 133 average time/residue: 0.0702 time to fit residues: 12.7993 Evaluate side-chains 128 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.0000 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN B 515 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107397 restraints weight = 8865.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110423 restraints weight = 4882.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112141 restraints weight = 3479.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113175 restraints weight = 2899.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114011 restraints weight = 2605.853| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6548 Z= 0.101 Angle : 0.525 5.587 8926 Z= 0.277 Chirality : 0.041 0.113 1118 Planarity : 0.004 0.041 1084 Dihedral : 6.678 57.455 974 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.21 % Allowed : 16.33 % Favored : 79.46 % 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: -3.08 (0.26), residues: 872 helix: -1.28 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.63 (0.30), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.012 0.001 TYR B 353 PHE 0.025 0.001 PHE A 590 TRP 0.009 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 6548) covalent geometry : angle 0.52515 ( 8926) hydrogen bonds : bond 0.03417 ( 312) hydrogen bonds : angle 3.73831 ( 912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.163 Fit side-chains REVERT: A 485 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 600 THR cc_start: 0.6385 (OUTLIER) cc_final: 0.5996 (p) REVERT: B 326 MET cc_start: 0.8038 (ttp) cc_final: 0.7826 (ttp) REVERT: B 485 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 600 THR cc_start: 0.6392 (OUTLIER) cc_final: 0.5999 (p) outliers start: 25 outliers final: 16 residues processed: 145 average time/residue: 0.0772 time to fit residues: 15.1310 Evaluate side-chains 134 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107458 restraints weight = 8913.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110506 restraints weight = 4896.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112324 restraints weight = 3497.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113348 restraints weight = 2899.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114101 restraints weight = 2621.241| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6548 Z= 0.106 Angle : 0.532 7.207 8926 Z= 0.276 Chirality : 0.042 0.117 1118 Planarity : 0.004 0.044 1084 Dihedral : 6.562 57.384 974 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.71 % Allowed : 16.16 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.27), residues: 872 helix: -0.94 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -3.52 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.008 0.001 TYR A 353 PHE 0.020 0.001 PHE A 590 TRP 0.009 0.001 TRP B 714 HIS 0.001 0.000 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6548) covalent geometry : angle 0.53233 ( 8926) hydrogen bonds : bond 0.03366 ( 312) hydrogen bonds : angle 3.67258 ( 912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.243 Fit side-chains REVERT: A 326 MET cc_start: 0.7944 (ttp) cc_final: 0.7734 (ttp) REVERT: A 485 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7605 (mm-30) REVERT: A 600 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.6070 (p) REVERT: A 670 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7397 (mm-30) REVERT: B 485 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 593 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.7027 (ptm) REVERT: B 600 THR cc_start: 0.6417 (OUTLIER) cc_final: 0.6075 (p) REVERT: B 670 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7401 (mm-30) outliers start: 28 outliers final: 18 residues processed: 133 average time/residue: 0.0719 time to fit residues: 12.9574 Evaluate side-chains 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 0.0670 chunk 8 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 chunk 57 optimal weight: 0.0870 chunk 33 optimal weight: 0.0170 chunk 72 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 overall best weight: 0.1272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113282 restraints weight = 8768.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116430 restraints weight = 4794.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118360 restraints weight = 3416.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119533 restraints weight = 2825.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120120 restraints weight = 2521.987| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6548 Z= 0.089 Angle : 0.522 9.607 8926 Z= 0.265 Chirality : 0.041 0.130 1118 Planarity : 0.004 0.047 1084 Dihedral : 6.100 54.857 974 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.70 % Allowed : 18.86 % Favored : 77.44 % 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: -2.17 (0.28), residues: 872 helix: -0.54 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -3.48 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 294 TYR 0.007 0.001 TYR B 353 PHE 0.017 0.001 PHE A 590 TRP 0.009 0.001 TRP B 733 HIS 0.000 0.000 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 6548) covalent geometry : angle 0.52164 ( 8926) hydrogen bonds : bond 0.02843 ( 312) hydrogen bonds : angle 3.44614 ( 912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.240 Fit side-chains REVERT: A 297 LEU cc_start: 0.9082 (tt) cc_final: 0.8828 (tt) REVERT: A 670 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7423 (mm-30) REVERT: A 751 TYR cc_start: 0.8585 (m-80) cc_final: 0.8279 (m-10) REVERT: B 297 LEU cc_start: 0.9050 (tt) cc_final: 0.8786 (tt) REVERT: B 593 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6663 (ptm) REVERT: B 670 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7424 (mm-30) REVERT: B 751 TYR cc_start: 0.8563 (m-80) cc_final: 0.8283 (m-10) outliers start: 22 outliers final: 13 residues processed: 145 average time/residue: 0.0694 time to fit residues: 13.8718 Evaluate side-chains 133 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 0.0040 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN B 515 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108618 restraints weight = 8744.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111604 restraints weight = 4816.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113466 restraints weight = 3473.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114225 restraints weight = 2890.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115062 restraints weight = 2646.734| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6548 Z= 0.107 Angle : 0.517 5.236 8926 Z= 0.271 Chirality : 0.042 0.125 1118 Planarity : 0.004 0.046 1084 Dihedral : 6.072 57.652 974 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.86 % Allowed : 20.37 % Favored : 76.77 % 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: -1.91 (0.28), residues: 872 helix: -0.31 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -3.45 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.005 0.001 TYR A 353 PHE 0.017 0.001 PHE A 590 TRP 0.007 0.001 TRP A 714 HIS 0.000 0.000 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6548) covalent geometry : angle 0.51705 ( 8926) hydrogen bonds : bond 0.03293 ( 312) hydrogen bonds : angle 3.54179 ( 912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.152 Fit side-chains REVERT: A 297 LEU cc_start: 0.9115 (tt) cc_final: 0.8870 (tt) REVERT: A 751 TYR cc_start: 0.8673 (m-80) cc_final: 0.8410 (m-10) REVERT: B 297 LEU cc_start: 0.9076 (tt) cc_final: 0.8852 (tt) REVERT: B 595 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7355 (mtm) REVERT: B 751 TYR cc_start: 0.8685 (m-80) cc_final: 0.8459 (m-10) outliers start: 17 outliers final: 14 residues processed: 133 average time/residue: 0.0610 time to fit residues: 11.0222 Evaluate side-chains 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 0.0570 chunk 58 optimal weight: 0.0980 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN B 515 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108913 restraints weight = 8627.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111876 restraints weight = 4800.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113765 restraints weight = 3468.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114466 restraints weight = 2885.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115279 restraints weight = 2657.624| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6548 Z= 0.099 Angle : 0.497 5.241 8926 Z= 0.261 Chirality : 0.042 0.126 1118 Planarity : 0.004 0.048 1084 Dihedral : 5.803 51.560 974 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.03 % Allowed : 20.03 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.29), residues: 872 helix: -0.05 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -3.01 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.004 0.001 TYR B 353 PHE 0.016 0.001 PHE B 590 TRP 0.009 0.001 TRP B 714 HIS 0.000 0.000 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6548) covalent geometry : angle 0.49653 ( 8926) hydrogen bonds : bond 0.03165 ( 312) hydrogen bonds : angle 3.47280 ( 912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.213 Fit side-chains REVERT: A 297 LEU cc_start: 0.9072 (tt) cc_final: 0.8831 (tt) REVERT: B 297 LEU cc_start: 0.9039 (tt) cc_final: 0.8823 (tt) REVERT: B 751 TYR cc_start: 0.8711 (m-80) cc_final: 0.8467 (m-10) outliers start: 18 outliers final: 17 residues processed: 128 average time/residue: 0.0615 time to fit residues: 10.9205 Evaluate side-chains 129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN B 515 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107739 restraints weight = 8861.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110752 restraints weight = 4850.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112614 restraints weight = 3465.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113648 restraints weight = 2879.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114313 restraints weight = 2594.460| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6548 Z= 0.107 Angle : 0.519 9.785 8926 Z= 0.267 Chirality : 0.042 0.124 1118 Planarity : 0.004 0.049 1084 Dihedral : 5.764 51.738 974 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.20 % Allowed : 19.87 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.29), residues: 872 helix: 0.02 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -2.99 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.003 0.001 TYR A 746 PHE 0.016 0.001 PHE A 590 TRP 0.010 0.001 TRP A 714 HIS 0.001 0.000 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6548) covalent geometry : angle 0.51889 ( 8926) hydrogen bonds : bond 0.03280 ( 312) hydrogen bonds : angle 3.52963 ( 912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.179 Fit side-chains REVERT: A 297 LEU cc_start: 0.9060 (tt) cc_final: 0.8833 (tt) REVERT: B 297 LEU cc_start: 0.9036 (tt) cc_final: 0.8822 (tt) REVERT: B 751 TYR cc_start: 0.8753 (m-80) cc_final: 0.8523 (m-10) outliers start: 19 outliers final: 19 residues processed: 126 average time/residue: 0.0578 time to fit residues: 10.1345 Evaluate side-chains 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 0.0870 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108744 restraints weight = 8677.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111760 restraints weight = 4777.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113485 restraints weight = 3435.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114464 restraints weight = 2886.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115262 restraints weight = 2609.346| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6548 Z= 0.100 Angle : 0.500 5.325 8926 Z= 0.261 Chirality : 0.042 0.123 1118 Planarity : 0.004 0.051 1084 Dihedral : 5.667 51.878 974 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.03 % Allowed : 20.37 % Favored : 76.60 % 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: -1.27 (0.29), residues: 872 helix: 0.13 (0.23), residues: 590 sheet: None (None), residues: 0 loop : -2.94 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 294 TYR 0.004 0.001 TYR B 353 PHE 0.017 0.001 PHE A 590 TRP 0.010 0.001 TRP B 714 HIS 0.000 0.000 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6548) covalent geometry : angle 0.49969 ( 8926) hydrogen bonds : bond 0.03170 ( 312) hydrogen bonds : angle 3.49363 ( 912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.232 Fit side-chains REVERT: A 297 LEU cc_start: 0.9041 (tt) cc_final: 0.8835 (tt) REVERT: A 751 TYR cc_start: 0.8685 (m-80) cc_final: 0.8432 (m-10) REVERT: B 619 LEU cc_start: 0.8982 (tp) cc_final: 0.8724 (tt) REVERT: B 751 TYR cc_start: 0.8722 (m-80) cc_final: 0.8506 (m-10) outliers start: 18 outliers final: 18 residues processed: 129 average time/residue: 0.0633 time to fit residues: 11.4007 Evaluate side-chains 131 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 0.0000 chunk 80 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109373 restraints weight = 8708.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112255 restraints weight = 4986.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114023 restraints weight = 3647.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114703 restraints weight = 3061.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115454 restraints weight = 2827.173| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6548 Z= 0.100 Angle : 0.506 5.291 8926 Z= 0.264 Chirality : 0.042 0.139 1118 Planarity : 0.004 0.051 1084 Dihedral : 5.610 51.648 974 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.20 % Allowed : 21.21 % Favored : 75.59 % 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: -1.18 (0.30), residues: 872 helix: 0.20 (0.23), residues: 590 sheet: None (None), residues: 0 loop : -2.92 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 294 TYR 0.003 0.001 TYR B 353 PHE 0.017 0.001 PHE A 590 TRP 0.010 0.001 TRP A 714 HIS 0.000 0.000 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6548) covalent geometry : angle 0.50571 ( 8926) hydrogen bonds : bond 0.03137 ( 312) hydrogen bonds : angle 3.47461 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1014.94 seconds wall clock time: 18 minutes 7.28 seconds (1087.28 seconds total)