Starting phenix.real_space_refine on Tue Sep 24 00:56:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/09_2024/7d10_30542.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/09_2024/7d10_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/09_2024/7d10_30542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/09_2024/7d10_30542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/09_2024/7d10_30542.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/09_2024/7d10_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-5461/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: 4.49, per 1000 atoms: 0.70 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: 1.59 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: 0.71 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: 1.73 Time building geometry restraints manager: 1.85 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: 0.00 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.870 Find NCS groups from input model: 0.180 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.580 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.655 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: 0.1689 time to fit residues: 34.1892 Evaluate side-chains 95 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 0.620 Fit side-chains REVERT: A 485 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 506 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8101 (m-40) REVERT: B 485 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 506 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8105 (m-40) outliers start: 28 outliers final: 12 residues processed: 144 average time/residue: 0.1738 time to fit residues: 33.6462 Evaluate side-chains 120 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 44 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 71 optimal weight: 0.0060 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2220 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= 0.144 Angle : 0.548 5.741 8926 Z= 0.287 Chirality : 0.042 0.120 1118 Planarity : 0.004 0.047 1084 Dihedral : 7.079 57.111 974 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % 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 0.019 0.001 PHE B 449 TYR 0.015 0.001 TYR A 748 ARG 0.001 0.000 ARG A 358 *********************** 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 148 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 0.663 Fit side-chains REVERT: A 326 MET cc_start: 0.7955 (ttp) cc_final: 0.7732 (ttp) REVERT: A 485 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 326 MET cc_start: 0.7955 (ttp) cc_final: 0.7737 (ttp) REVERT: B 485 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7475 (mm-30) outliers start: 25 outliers final: 18 residues processed: 142 average time/residue: 0.1640 time to fit residues: 31.3297 Evaluate side-chains 135 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.0050 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 overall best weight: 0.8596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2432 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= 0.185 Angle : 0.542 5.695 8926 Z= 0.285 Chirality : 0.042 0.118 1118 Planarity : 0.004 0.043 1084 Dihedral : 6.831 57.347 974 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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: -3.17 (0.26), residues: 872 helix: -1.33 (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 0.010 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.025 0.001 PHE A 590 TYR 0.012 0.001 TYR A 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 fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.758 Fit side-chains REVERT: A 326 MET cc_start: 0.7980 (ttp) cc_final: 0.7753 (ttp) REVERT: A 485 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 326 MET cc_start: 0.7979 (ttp) cc_final: 0.7756 (ttp) REVERT: B 485 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7481 (mm-30) outliers start: 27 outliers final: 22 residues processed: 131 average time/residue: 0.1752 time to fit residues: 30.5242 Evaluate side-chains 130 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 0.0000 chunk 0 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2637 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= 0.160 Angle : 0.526 5.531 8926 Z= 0.275 Chirality : 0.042 0.116 1118 Planarity : 0.004 0.045 1084 Dihedral : 6.629 58.395 974 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.71 % Allowed : 15.66 % Favored : 79.63 % 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: -2.70 (0.27), residues: 872 helix: -0.98 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -3.57 (0.30), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 714 HIS 0.001 0.000 HIS B 695 PHE 0.021 0.001 PHE B 590 TYR 0.009 0.001 TYR A 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 145 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 0.590 Fit side-chains REVERT: A 288 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.6177 (tt) REVERT: A 485 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 600 THR cc_start: 0.6479 (OUTLIER) cc_final: 0.6137 (p) REVERT: A 670 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7314 (mm-30) REVERT: B 485 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7549 (mm-30) REVERT: B 600 THR cc_start: 0.6483 (OUTLIER) cc_final: 0.6151 (p) REVERT: B 670 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7336 (mm-30) outliers start: 28 outliers final: 21 residues processed: 134 average time/residue: 0.1680 time to fit residues: 30.3159 Evaluate side-chains 138 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 0.0070 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2825 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= 0.147 Angle : 0.535 8.045 8926 Z= 0.274 Chirality : 0.042 0.122 1118 Planarity : 0.004 0.046 1084 Dihedral : 6.458 54.424 974 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.71 % Allowed : 17.68 % 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: -2.32 (0.28), residues: 872 helix: -0.66 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -3.50 (0.31), residues: 268 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 0.019 0.001 PHE A 590 TYR 0.006 0.001 TYR A 353 ARG 0.002 0.000 ARG B 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 140 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.642 Fit side-chains REVERT: A 288 ILE cc_start: 0.6539 (OUTLIER) cc_final: 0.6223 (tt) REVERT: B 288 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6223 (tt) outliers start: 28 outliers final: 22 residues processed: 132 average time/residue: 0.1680 time to fit residues: 29.8136 Evaluate side-chains 137 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 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 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 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2960 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= 0.148 Angle : 0.534 7.459 8926 Z= 0.274 Chirality : 0.042 0.127 1118 Planarity : 0.004 0.049 1084 Dihedral : 6.318 59.172 974 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.21 % Allowed : 17.85 % 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: -2.05 (0.28), residues: 872 helix: -0.45 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.44 (0.32), residues: 266 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 A 590 TYR 0.005 0.001 TYR A 353 ARG 0.002 0.000 ARG B 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 142 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.678 Fit side-chains REVERT: A 288 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6258 (tt) REVERT: A 297 LEU cc_start: 0.9141 (tt) cc_final: 0.8903 (tt) REVERT: B 288 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6259 (tt) outliers start: 25 outliers final: 22 residues processed: 134 average time/residue: 0.1654 time to fit residues: 29.8192 Evaluate side-chains 133 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3051 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= 0.150 Angle : 0.528 7.135 8926 Z= 0.271 Chirality : 0.042 0.135 1118 Planarity : 0.004 0.051 1084 Dihedral : 6.117 52.320 974 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.38 % Allowed : 18.18 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.85 (0.28), residues: 872 helix: -0.27 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.40 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 714 HIS 0.000 0.000 HIS A 695 PHE 0.017 0.001 PHE B 590 TYR 0.004 0.001 TYR B 353 ARG 0.002 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 138 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.785 Fit side-chains REVERT: A 288 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6259 (tt) REVERT: A 297 LEU cc_start: 0.9139 (tt) cc_final: 0.8924 (tt) REVERT: A 326 MET cc_start: 0.7834 (ttp) cc_final: 0.7613 (ttp) REVERT: B 288 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6254 (tt) REVERT: B 326 MET cc_start: 0.7829 (ttp) cc_final: 0.7624 (ttp) outliers start: 26 outliers final: 20 residues processed: 131 average time/residue: 0.1686 time to fit residues: 29.7413 Evaluate side-chains 132 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 83 optimal weight: 0.0470 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3184 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= 0.139 Angle : 0.527 10.956 8926 Z= 0.268 Chirality : 0.041 0.128 1118 Planarity : 0.004 0.053 1084 Dihedral : 5.822 51.645 974 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.70 % Allowed : 19.19 % 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: -1.63 (0.29), residues: 872 helix: -0.09 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.38 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 714 HIS 0.001 0.000 HIS A 695 PHE 0.018 0.001 PHE B 590 TYR 0.005 0.001 TYR A 353 ARG 0.001 0.000 ARG B 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 133 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.705 Fit side-chains REVERT: A 288 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6327 (tt) REVERT: A 297 LEU cc_start: 0.9049 (tt) cc_final: 0.8819 (tt) REVERT: A 473 PHE cc_start: 0.9205 (t80) cc_final: 0.8985 (t80) REVERT: A 619 LEU cc_start: 0.9010 (tp) cc_final: 0.8758 (tt) REVERT: B 288 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6320 (tt) outliers start: 22 outliers final: 19 residues processed: 128 average time/residue: 0.1579 time to fit residues: 27.8510 Evaluate side-chains 131 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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 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 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 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 51 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 0.0030 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3236 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= 0.149 Angle : 0.518 6.244 8926 Z= 0.267 Chirality : 0.041 0.124 1118 Planarity : 0.004 0.054 1084 Dihedral : 5.792 52.146 974 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.37 % Allowed : 19.36 % 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: -1.51 (0.29), residues: 872 helix: 0.01 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.36 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 714 HIS 0.000 0.000 HIS A 695 PHE 0.017 0.001 PHE B 590 TYR 0.005 0.001 TYR B 353 ARG 0.002 0.000 ARG B 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 127 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.669 Fit side-chains REVERT: A 288 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6312 (tt) REVERT: A 619 LEU cc_start: 0.9014 (tp) cc_final: 0.8774 (tt) REVERT: B 288 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.6316 (tt) outliers start: 20 outliers final: 17 residues processed: 123 average time/residue: 0.1556 time to fit residues: 26.3718 Evaluate side-chains 124 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 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 531 LEU 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 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 71 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.135483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109208 restraints weight = 8641.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112200 restraints weight = 4761.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113853 restraints weight = 3426.683| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3291 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= 0.143 Angle : 0.514 5.445 8926 Z= 0.266 Chirality : 0.041 0.140 1118 Planarity : 0.004 0.055 1084 Dihedral : 5.722 51.847 974 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.20 % Allowed : 20.88 % 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: -1.42 (0.29), residues: 872 helix: 0.09 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.34 (0.33), 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 0.017 0.001 PHE B 590 TYR 0.004 0.001 TYR B 353 ARG 0.002 0.000 ARG A 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1429.96 seconds wall clock time: 26 minutes 6.45 seconds (1566.45 seconds total)