Starting phenix.real_space_refine on Tue Mar 11 17:21:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d10_30542/03_2025/7d10_30542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d10_30542/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7d10_30542/03_2025/7d10_30542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d10_30542/03_2025/7d10_30542.map" model { file = "/net/cci-nas-00/data/ceres_data/7d10_30542/03_2025/7d10_30542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d10_30542/03_2025/7d10_30542.cif" } resolution = 3.52 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= 0.009 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 3} 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: {'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 3} 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: 4.36, per 1000 atoms: 0.68 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: 1.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.73 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: 1.56 Time building geometry restraints manager: 1.99 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: 0.04 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.020 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- 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= 0.438 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 (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: -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 TRP 0.027 0.003 TRP B 714 HIS 0.005 0.004 HIS A 695 PHE 0.024 0.003 PHE B 494 TYR 0.025 0.002 TYR B 383 ARG 0.007 0.001 ARG B 307 *********************** 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 : 0.685 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: 0.1696 time to fit residues: 34.5693 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 : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 B 506 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.105975 restraints weight = 8826.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108997 restraints weight = 4845.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110762 restraints weight = 3448.318| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6548 Z= 0.180 Angle : 0.590 6.141 8926 Z= 0.313 Chirality : 0.042 0.125 1118 Planarity : 0.005 0.068 1084 Dihedral : 7.765 58.015 974 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.71 % Allowed : 11.11 % 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 (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: -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 TRP 0.012 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.026 0.002 PHE B 590 TYR 0.008 0.001 TYR B 383 ARG 0.001 0.000 ARG B 546 *********************** 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 154 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.688 Fit side-chains REVERT: A 485 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7482 (mm-30) REVERT: A 506 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8060 (m-40) REVERT: B 485 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 506 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8063 (m-40) outliers start: 28 outliers final: 12 residues processed: 144 average time/residue: 0.1689 time to fit residues: 32.7408 Evaluate side-chains 120 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 75 optimal weight: 6.9990 chunk 34 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 61 optimal weight: 0.0370 chunk 85 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106576 restraints weight = 8781.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109564 restraints weight = 4814.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111301 restraints weight = 3420.682| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2200 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= 0.160 Angle : 0.553 5.709 8926 Z= 0.291 Chirality : 0.042 0.135 1118 Planarity : 0.004 0.047 1084 Dihedral : 7.141 56.870 974 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.21 % Allowed : 15.49 % Favored : 80.30 % 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: -3.75 (0.25), residues: 872 helix: -1.78 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -3.90 (0.28), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.018 0.001 PHE B 449 TYR 0.014 0.001 TYR B 748 ARG 0.001 0.000 ARG B 307 *********************** 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 144 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.739 Fit side-chains REVERT: A 326 MET cc_start: 0.8102 (ttp) cc_final: 0.7875 (ttp) REVERT: A 485 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 326 MET cc_start: 0.8098 (ttp) cc_final: 0.7881 (ttp) REVERT: B 485 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7499 (mm-30) outliers start: 25 outliers final: 18 residues processed: 138 average time/residue: 0.1699 time to fit residues: 31.7613 Evaluate side-chains 133 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.0270 chunk 33 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107497 restraints weight = 8871.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110531 restraints weight = 4860.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112414 restraints weight = 3452.253| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2546 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= 0.145 Angle : 0.526 5.613 8926 Z= 0.277 Chirality : 0.041 0.116 1118 Planarity : 0.004 0.042 1084 Dihedral : 6.634 57.272 974 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.55 % Allowed : 16.33 % 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 (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: -3.07 (0.26), residues: 872 helix: -1.27 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.63 (0.30), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 714 HIS 0.001 0.000 HIS B 695 PHE 0.026 0.001 PHE B 590 TYR 0.013 0.001 TYR B 353 ARG 0.001 0.000 ARG B 307 *********************** 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 145 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.626 Fit side-chains REVERT: A 326 MET cc_start: 0.8042 (ttp) cc_final: 0.7828 (ttp) REVERT: A 485 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 600 THR cc_start: 0.6343 (OUTLIER) cc_final: 0.5972 (p) REVERT: A 670 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7284 (mm-30) REVERT: B 326 MET cc_start: 0.8043 (ttp) cc_final: 0.7828 (ttp) REVERT: B 463 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8584 (mttt) REVERT: B 600 THR cc_start: 0.6343 (OUTLIER) cc_final: 0.5963 (p) outliers start: 27 outliers final: 15 residues processed: 139 average time/residue: 0.1729 time to fit residues: 32.2060 Evaluate side-chains 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 421 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 620 VAL 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 35 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 0.3980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.133929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107712 restraints weight = 8779.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110731 restraints weight = 4878.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112592 restraints weight = 3504.944| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2721 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= 0.160 Angle : 0.536 7.372 8926 Z= 0.277 Chirality : 0.042 0.118 1118 Planarity : 0.004 0.044 1084 Dihedral : 6.541 57.625 974 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.55 % Allowed : 15.99 % 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 (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: -2.62 (0.27), residues: 872 helix: -0.92 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.52 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.019 0.001 PHE A 590 TYR 0.008 0.001 TYR A 353 ARG 0.001 0.000 ARG B 307 *********************** 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 144 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.707 Fit side-chains REVERT: A 325 MET cc_start: 0.8162 (mmm) cc_final: 0.7957 (mmp) REVERT: A 326 MET cc_start: 0.8052 (ttp) cc_final: 0.7841 (ttp) REVERT: A 485 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 600 THR cc_start: 0.6364 (OUTLIER) cc_final: 0.6059 (p) REVERT: A 670 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7421 (mm-30) REVERT: B 325 MET cc_start: 0.8167 (mmm) cc_final: 0.7966 (mmp) REVERT: B 463 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8571 (mttt) REVERT: B 485 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 600 THR cc_start: 0.6362 (OUTLIER) cc_final: 0.6074 (p) outliers start: 27 outliers final: 22 residues processed: 135 average time/residue: 0.1634 time to fit residues: 29.8787 Evaluate side-chains 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 461 LYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 593 MET 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 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 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 616 LEU Chi-restraints excluded: chain B residue 620 VAL 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 10 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.129131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103039 restraints weight = 8787.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105940 restraints weight = 4878.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107683 restraints weight = 3511.459| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6548 Z= 0.232 Angle : 0.570 9.138 8926 Z= 0.293 Chirality : 0.044 0.123 1118 Planarity : 0.004 0.047 1084 Dihedral : 6.748 53.899 974 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.71 % Allowed : 18.18 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.35 (0.28), residues: 872 helix: -0.65 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.50 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 714 HIS 0.001 0.001 HIS B 695 PHE 0.019 0.001 PHE A 590 TYR 0.006 0.001 TYR A 353 ARG 0.002 0.000 ARG B 307 *********************** 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 136 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.631 Fit side-chains REVERT: A 485 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7623 (mm-30) REVERT: A 670 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7455 (mm-30) outliers start: 28 outliers final: 25 residues processed: 127 average time/residue: 0.1667 time to fit residues: 28.4227 Evaluate side-chains 136 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 461 LYS Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 593 MET 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 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 421 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 486 THR 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 616 LEU Chi-restraints excluded: chain B residue 620 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 19 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.131762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105663 restraints weight = 8706.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108578 restraints weight = 4878.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110349 restraints weight = 3536.370| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2897 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= 0.176 Angle : 0.531 7.117 8926 Z= 0.277 Chirality : 0.042 0.117 1118 Planarity : 0.004 0.049 1084 Dihedral : 6.627 59.808 974 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.55 % Allowed : 18.18 % Favored : 77.27 % 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: -2.04 (0.28), residues: 872 helix: -0.38 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.48 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 714 HIS 0.001 0.001 HIS B 695 PHE 0.018 0.001 PHE A 590 TYR 0.004 0.001 TYR A 353 ARG 0.001 0.000 ARG B 307 *********************** 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 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.632 Fit side-chains REVERT: A 297 LEU cc_start: 0.9183 (tt) cc_final: 0.8939 (tt) REVERT: A 485 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 619 LEU cc_start: 0.9050 (tp) cc_final: 0.8840 (tt) REVERT: A 670 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7472 (mm-30) REVERT: B 473 PHE cc_start: 0.9266 (t80) cc_final: 0.9019 (t80) outliers start: 27 outliers final: 26 residues processed: 129 average time/residue: 0.1528 time to fit residues: 27.3374 Evaluate side-chains 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 461 LYS Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 593 MET 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 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 421 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 486 THR 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 616 LEU Chi-restraints excluded: chain B residue 620 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 0.0670 chunk 38 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.134038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107967 restraints weight = 8698.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110964 restraints weight = 4857.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112792 restraints weight = 3503.566| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3047 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= 0.141 Angle : 0.532 10.330 8926 Z= 0.273 Chirality : 0.042 0.136 1118 Planarity : 0.004 0.051 1084 Dihedral : 6.323 56.880 974 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.55 % Allowed : 19.19 % Favored : 76.26 % 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: -1.82 (0.29), residues: 872 helix: -0.19 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.43 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 714 HIS 0.000 0.000 HIS B 695 PHE 0.018 0.001 PHE B 590 TYR 0.004 0.001 TYR B 353 ARG 0.001 0.000 ARG B 294 *********************** 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 141 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.719 Fit side-chains REVERT: A 297 LEU cc_start: 0.9123 (tt) cc_final: 0.8875 (tt) REVERT: A 326 MET cc_start: 0.7946 (ttp) cc_final: 0.7726 (ttp) REVERT: A 619 LEU cc_start: 0.9013 (tp) cc_final: 0.8798 (tt) REVERT: A 670 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 326 MET cc_start: 0.7935 (ttp) cc_final: 0.7731 (ttp) REVERT: B 356 ILE cc_start: 0.8531 (pt) cc_final: 0.8327 (mt) outliers start: 27 outliers final: 26 residues processed: 134 average time/residue: 0.1528 time to fit residues: 28.4809 Evaluate side-chains 134 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 461 LYS Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 593 MET 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 385 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 592 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.0970 chunk 43 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.134202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107994 restraints weight = 8756.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111000 restraints weight = 4869.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112842 restraints weight = 3508.573| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6548 Z= 0.149 Angle : 0.525 6.240 8926 Z= 0.273 Chirality : 0.042 0.123 1118 Planarity : 0.004 0.052 1084 Dihedral : 6.079 52.252 974 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.55 % Allowed : 19.53 % Favored : 75.93 % 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: -1.63 (0.29), residues: 872 helix: -0.03 (0.23), residues: 592 sheet: None (None), residues: 0 loop : -3.40 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 714 HIS 0.000 0.000 HIS A 695 PHE 0.016 0.001 PHE A 590 TYR 0.004 0.001 TYR B 353 ARG 0.001 0.000 ARG A 546 *********************** 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 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.681 Fit side-chains REVERT: A 297 LEU cc_start: 0.9099 (tt) cc_final: 0.8889 (tt) REVERT: A 326 MET cc_start: 0.7953 (ttp) cc_final: 0.7731 (ttp) REVERT: A 619 LEU cc_start: 0.9000 (tp) cc_final: 0.8772 (tt) REVERT: A 670 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7498 (mm-30) REVERT: B 326 MET cc_start: 0.7946 (ttp) cc_final: 0.7731 (ttp) REVERT: B 356 ILE cc_start: 0.8526 (pt) cc_final: 0.8320 (mt) REVERT: B 619 LEU cc_start: 0.8949 (tp) cc_final: 0.8712 (tt) outliers start: 27 outliers final: 26 residues processed: 127 average time/residue: 0.1507 time to fit residues: 26.7925 Evaluate side-chains 132 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 461 LYS Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 593 MET 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 382 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 592 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 19 optimal weight: 0.0050 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.136154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110317 restraints weight = 8714.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113208 restraints weight = 4926.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114987 restraints weight = 3586.985| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3303 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= 0.134 Angle : 0.511 6.428 8926 Z= 0.264 Chirality : 0.041 0.131 1118 Planarity : 0.004 0.055 1084 Dihedral : 5.596 51.460 974 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.55 % Allowed : 19.70 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.29), residues: 872 helix: 0.01 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.27 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.000 0.000 HIS A 695 PHE 0.016 0.001 PHE B 590 TYR 0.004 0.001 TYR B 353 ARG 0.001 0.000 ARG A 546 ********************** 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 138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.648 Fit side-chains REVERT: A 619 LEU cc_start: 0.8970 (tp) cc_final: 0.8754 (tt) REVERT: B 356 ILE cc_start: 0.8467 (pt) cc_final: 0.8258 (mt) REVERT: B 619 LEU cc_start: 0.8935 (tp) cc_final: 0.8693 (tt) outliers start: 27 outliers final: 22 residues processed: 129 average time/residue: 0.1480 time to fit residues: 26.9362 Evaluate side-chains 128 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 461 LYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 593 MET 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 385 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 593 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 23 optimal weight: 0.0570 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.135903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109759 restraints weight = 8788.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112882 restraints weight = 4775.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114759 restraints weight = 3391.034| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6548 Z= 0.134 Angle : 0.530 6.888 8926 Z= 0.270 Chirality : 0.041 0.134 1118 Planarity : 0.004 0.051 1084 Dihedral : 5.499 51.533 974 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.55 % Allowed : 19.70 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.29), residues: 872 helix: 0.10 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.25 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 733 HIS 0.001 0.000 HIS A 695 PHE 0.016 0.001 PHE B 590 TYR 0.004 0.000 TYR B 353 ARG 0.001 0.000 ARG A 546 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2004.88 seconds wall clock time: 35 minutes 20.91 seconds (2120.91 seconds total)