Starting phenix.real_space_refine on Tue Feb 11 17:51:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d10_30542/02_2025/7d10_30542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d10_30542/02_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_30542/02_2025/7d10_30542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d10_30542/02_2025/7d10_30542.map" model { file = "/net/cci-nas-00/data/ceres_data/7d10_30542/02_2025/7d10_30542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d10_30542/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.19, per 1000 atoms: 0.65 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: 1.48 Conformation dependent library (CDL) restraints added in 894.1 milliseconds 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: 0.62 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: 1.55 Time building geometry restraints manager: 1.78 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: 0.03 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.640 Find NCS groups from input model: 0.120 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.320 ------------------------------------------------------------------------------- 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 : 0.647 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: 0.1713 time to fit residues: 34.5832 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 : 0.688 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.105976 restraints weight = 8826.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109013 restraints weight = 4845.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110836 restraints weight = 3442.885| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.698 Fit side-chains REVERT: A 485 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7479 (mm-30) REVERT: A 506 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8063 (m-40) REVERT: B 485 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7483 (mm-30) REVERT: B 506 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8066 (m-40) outliers start: 28 outliers final: 12 residues processed: 144 average time/residue: 0.1699 time to fit residues: 32.9017 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 : 0.674 ------------------------------------------------------------------------------- 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: 0.0170 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 61 optimal weight: 0.0170 chunk 85 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.132383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106780 restraints weight = 8771.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109775 restraints weight = 4793.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111576 restraints weight = 3415.796| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2206 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= 0.154 Angle : 0.551 5.676 8926 Z= 0.290 Chirality : 0.042 0.132 1118 Planarity : 0.004 0.047 1084 Dihedral : 7.119 56.904 974 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 0.010 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.019 0.001 PHE B 590 TYR 0.015 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 145 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.658 Fit side-chains REVERT: A 326 MET cc_start: 0.8098 (ttp) cc_final: 0.7879 (ttp) REVERT: A 485 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7502 (mm-30) REVERT: B 326 MET cc_start: 0.8096 (ttp) cc_final: 0.7881 (ttp) REVERT: B 485 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7496 (mm-30) outliers start: 25 outliers final: 18 residues processed: 139 average time/residue: 0.1684 time to fit residues: 31.5609 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 : 0.707 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.130942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104959 restraints weight = 8969.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107994 restraints weight = 4914.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109666 restraints weight = 3483.009| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2415 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= 0.193 Angle : 0.548 5.654 8926 Z= 0.289 Chirality : 0.042 0.117 1118 Planarity : 0.004 0.042 1084 Dihedral : 6.894 58.387 974 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.71 % Allowed : 16.33 % Favored : 78.96 % 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: -3.16 (0.26), residues: 872 helix: -1.32 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.72 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.027 0.002 PHE A 590 TYR 0.013 0.001 TYR B 353 ARG 0.004 0.000 ARG A 294 *********************** 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 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.646 Fit side-chains REVERT: A 485 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 485 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7546 (mm-30) outliers start: 28 outliers final: 23 residues processed: 130 average time/residue: 0.1741 time to fit residues: 30.3431 Evaluate side-chains 131 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 436 ILE 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 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 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 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: 3.9990 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.132013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106012 restraints weight = 8765.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108981 restraints weight = 4827.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110782 restraints weight = 3456.826| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2610 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= 0.163 Angle : 0.531 5.465 8926 Z= 0.278 Chirality : 0.042 0.119 1118 Planarity : 0.004 0.044 1084 Dihedral : 6.671 56.789 974 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.71 % Allowed : 15.82 % 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: -2.72 (0.27), residues: 872 helix: -1.00 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -3.56 (0.30), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.021 0.001 PHE A 590 TYR 0.009 0.001 TYR B 353 ARG 0.003 0.000 ARG A 294 *********************** 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 146 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.726 Fit side-chains REVERT: A 288 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6061 (tt) REVERT: A 485 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 670 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 288 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.6100 (tt) REVERT: B 485 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7581 (mm-30) REVERT: B 670 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7396 (mm-30) outliers start: 28 outliers final: 23 residues processed: 136 average time/residue: 0.1757 time to fit residues: 32.1384 Evaluate side-chains 138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE 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 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 660 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 288 ILE 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 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: 3.9990 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 0.0060 chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 27 optimal weight: 0.0970 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.134037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107917 restraints weight = 8682.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110911 restraints weight = 4772.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112621 restraints weight = 3422.506| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2863 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= 0.139 Angle : 0.534 8.915 8926 Z= 0.273 Chirality : 0.041 0.133 1118 Planarity : 0.004 0.046 1084 Dihedral : 6.390 53.599 974 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.38 % Allowed : 17.68 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.27 (0.28), residues: 872 helix: -0.63 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -3.48 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 714 HIS 0.000 0.000 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 A 294 *********************** 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 146 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.729 Fit side-chains REVERT: A 288 ILE cc_start: 0.6461 (OUTLIER) cc_final: 0.6164 (tt) REVERT: A 297 LEU cc_start: 0.9195 (tt) cc_final: 0.8942 (tt) REVERT: A 485 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 670 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7480 (mm-30) REVERT: B 288 ILE cc_start: 0.6481 (OUTLIER) cc_final: 0.6171 (tt) REVERT: B 670 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7447 (mm-30) outliers start: 26 outliers final: 20 residues processed: 139 average time/residue: 0.1545 time to fit residues: 29.3086 Evaluate side-chains 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE 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 288 ILE 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 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 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: 4.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 0.0000 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.128149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102033 restraints weight = 8792.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104883 restraints weight = 4856.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106664 restraints weight = 3500.214| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6548 Z= 0.266 Angle : 0.583 6.894 8926 Z= 0.303 Chirality : 0.044 0.142 1118 Planarity : 0.004 0.049 1084 Dihedral : 6.971 59.186 974 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.88 % Allowed : 17.51 % Favored : 77.61 % 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: -2.22 (0.28), residues: 872 helix: -0.57 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.50 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 714 HIS 0.002 0.001 HIS B 695 PHE 0.019 0.002 PHE A 590 TYR 0.006 0.001 TYR B 468 ARG 0.002 0.000 ARG A 294 *********************** 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 134 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.651 Fit side-chains REVERT: A 326 MET cc_start: 0.8069 (ttp) cc_final: 0.7833 (ttp) REVERT: A 485 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 619 LEU cc_start: 0.9112 (tp) cc_final: 0.8891 (tt) REVERT: A 670 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7514 (mm-30) REVERT: B 288 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.6016 (tt) REVERT: B 326 MET cc_start: 0.8071 (ttp) cc_final: 0.7851 (ttp) REVERT: B 670 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7493 (mm-30) outliers start: 29 outliers final: 25 residues processed: 128 average time/residue: 0.1733 time to fit residues: 29.8016 Evaluate side-chains 126 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 660 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 461 LYS 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 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: 4.9990 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.129650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103563 restraints weight = 8801.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106480 restraints weight = 4859.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108097 restraints weight = 3494.397| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6548 Z= 0.200 Angle : 0.558 9.862 8926 Z= 0.289 Chirality : 0.043 0.117 1118 Planarity : 0.004 0.051 1084 Dihedral : 6.555 53.650 974 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.55 % Allowed : 18.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.29), residues: 872 helix: -0.35 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.17 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.019 0.001 PHE B 590 TYR 0.004 0.001 TYR B 748 ARG 0.002 0.000 ARG A 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 132 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.550 Fit side-chains REVERT: A 326 MET cc_start: 0.8016 (ttp) cc_final: 0.7782 (ttp) REVERT: A 485 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 619 LEU cc_start: 0.9091 (tp) cc_final: 0.8854 (tt) REVERT: A 670 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 288 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6146 (tt) REVERT: B 326 MET cc_start: 0.8023 (ttp) cc_final: 0.7800 (ttp) REVERT: B 670 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7469 (mm-30) outliers start: 27 outliers final: 21 residues processed: 128 average time/residue: 0.1688 time to fit residues: 29.5265 Evaluate side-chains 126 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 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 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 288 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.130261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104105 restraints weight = 8842.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107034 restraints weight = 4879.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108647 restraints weight = 3512.508| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2980 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= 0.186 Angle : 0.536 6.696 8926 Z= 0.280 Chirality : 0.042 0.125 1118 Planarity : 0.004 0.052 1084 Dihedral : 6.250 53.497 974 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % 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: -1.91 (0.29), residues: 872 helix: -0.32 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.43 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 714 HIS 0.000 0.000 HIS A 695 PHE 0.019 0.001 PHE A 590 TYR 0.003 0.001 TYR B 383 ARG 0.002 0.000 ARG A 294 *********************** 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 136 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.742 Fit side-chains REVERT: A 297 LEU cc_start: 0.9212 (tt) cc_final: 0.8973 (tt) REVERT: A 326 MET cc_start: 0.8024 (ttp) cc_final: 0.7795 (ttp) REVERT: A 485 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7632 (mm-30) REVERT: A 619 LEU cc_start: 0.9071 (tp) cc_final: 0.8840 (tt) REVERT: A 670 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 288 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.6209 (tt) REVERT: B 326 MET cc_start: 0.8008 (ttp) cc_final: 0.7789 (ttp) REVERT: B 670 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7488 (mm-30) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.1627 time to fit residues: 29.5439 Evaluate side-chains 127 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 288 ILE 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 592 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.129001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102980 restraints weight = 8888.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105846 restraints weight = 4942.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107622 restraints weight = 3570.051| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6548 Z= 0.217 Angle : 0.558 6.527 8926 Z= 0.291 Chirality : 0.043 0.121 1118 Planarity : 0.004 0.054 1084 Dihedral : 6.293 53.477 974 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.21 % Allowed : 20.54 % Favored : 75.25 % 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: -1.75 (0.29), residues: 872 helix: -0.24 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.13 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.019 0.001 PHE A 590 TYR 0.003 0.001 TYR B 751 ARG 0.004 0.000 ARG A 294 ********************** 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 129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.707 Fit side-chains REVERT: A 297 LEU cc_start: 0.9248 (tt) cc_final: 0.9003 (tt) REVERT: A 326 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7790 (ttp) REVERT: A 485 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 619 LEU cc_start: 0.9083 (tp) cc_final: 0.8858 (tt) REVERT: A 670 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7481 (mm-30) REVERT: B 288 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.6214 (tt) REVERT: B 326 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7812 (ttp) REVERT: B 670 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7438 (mm-30) outliers start: 25 outliers final: 21 residues processed: 124 average time/residue: 0.1916 time to fit residues: 32.5476 Evaluate side-chains 125 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 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 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 288 ILE Chi-restraints excluded: chain B residue 326 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 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 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: 0.9990 chunk 71 optimal weight: 0.0000 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.0470 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 overall best weight: 0.6088 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.132132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105751 restraints weight = 8910.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108755 restraints weight = 4887.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110580 restraints weight = 3511.359| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3110 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= 0.155 Angle : 0.534 6.715 8926 Z= 0.278 Chirality : 0.042 0.119 1118 Planarity : 0.004 0.054 1084 Dihedral : 6.051 53.017 974 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.04 % Allowed : 21.04 % Favored : 74.92 % 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: -1.59 (0.29), residues: 872 helix: -0.12 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.07 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.004 0.000 ARG A 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.05 seconds wall clock time: 35 minutes 15.71 seconds (2115.71 seconds total)