Starting phenix.real_space_refine on Wed Jul 30 00:59:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5is0_8119/07_2025/5is0_8119_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5is0_8119/07_2025/5is0_8119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5is0_8119/07_2025/5is0_8119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5is0_8119/07_2025/5is0_8119.map" model { file = "/net/cci-nas-00/data/ceres_data/5is0_8119/07_2025/5is0_8119_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5is0_8119/07_2025/5is0_8119_trim.cif" } resolution = 3.43 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 76 5.16 5 Cl 4 4.86 5 C 7804 2.51 5 N 1932 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11808 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2927 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 82} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 212 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'6ET': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, E, D Time building chain proxies: 5.81, per 1000 atoms: 0.49 Number of scatterers: 11808 At special positions: 0 Unit cell: (120.344, 120.344, 98.4636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 76 16.00 O 1992 8.00 N 1932 7.00 C 7804 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 67.3% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 353 removed outlier: 3.736A pdb=" N LEU C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.936A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.985A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 500 removed outlier: 4.300A pdb=" N PHE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 513 through 532 removed outlier: 3.555A pdb=" N PHE C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.987A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.800A pdb=" N TYR C 555 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 577 removed outlier: 3.636A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 597 removed outlier: 3.814A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 628 removed outlier: 3.638A pdb=" N ASN C 628 " --> pdb=" O GLY C 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 628' Processing helix chain 'C' and resid 629 through 637 removed outlier: 3.660A pdb=" N THR C 633 " --> pdb=" O SER C 629 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 643 removed outlier: 3.637A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 712 removed outlier: 3.946A pdb=" N ILE C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN C 687 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 709 " --> pdb=" O ILE C 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 345 through 353 removed outlier: 3.735A pdb=" N LEU B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.936A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.985A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 500 removed outlier: 4.301A pdb=" N PHE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 498 " --> pdb=" O GLN B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 513 through 532 removed outlier: 3.555A pdb=" N PHE B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.987A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.799A pdb=" N TYR B 555 " --> pdb=" O MET B 552 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 577 removed outlier: 3.636A pdb=" N ILE B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 597 removed outlier: 3.814A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 628 removed outlier: 3.638A pdb=" N ASN B 628 " --> pdb=" O GLY B 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 602 through 628' Processing helix chain 'B' and resid 629 through 637 removed outlier: 3.659A pdb=" N THR B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.637A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 712 removed outlier: 3.946A pdb=" N ILE B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN B 687 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 345 through 353 removed outlier: 3.736A pdb=" N LEU D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.936A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.984A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 500 removed outlier: 4.300A pdb=" N PHE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 474 " --> pdb=" O GLY D 470 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN D 498 " --> pdb=" O GLN D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 510 Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.556A pdb=" N PHE D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.987A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.800A pdb=" N TYR D 555 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 577 removed outlier: 3.637A pdb=" N ILE D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 597 removed outlier: 3.814A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR D 593 " --> pdb=" O PHE D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 628 removed outlier: 3.638A pdb=" N ASN D 628 " --> pdb=" O GLY D 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 602 through 628' Processing helix chain 'D' and resid 629 through 637 removed outlier: 3.660A pdb=" N THR D 633 " --> pdb=" O SER D 629 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 643 removed outlier: 3.637A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 712 removed outlier: 3.946A pdb=" N ILE D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN D 687 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS D 688 " --> pdb=" O GLU D 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 709 " --> pdb=" O ILE D 705 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 344 Processing helix chain 'E' and resid 345 through 353 removed outlier: 3.737A pdb=" N LEU E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 401 Processing helix chain 'E' and resid 411 through 414 Processing helix chain 'E' and resid 415 through 429 removed outlier: 3.937A pdb=" N ARG E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN E 423 " --> pdb=" O ASN E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 454 removed outlier: 3.984A pdb=" N ILE E 433 " --> pdb=" O PHE E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 500 removed outlier: 4.300A pdb=" N PHE E 473 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 474 " --> pdb=" O GLY E 470 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN E 498 " --> pdb=" O GLN E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 510 Processing helix chain 'E' and resid 513 through 532 removed outlier: 3.556A pdb=" N PHE E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 551 removed outlier: 3.987A pdb=" N SER E 540 " --> pdb=" O GLU E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 557 removed outlier: 3.800A pdb=" N TYR E 555 " --> pdb=" O MET E 552 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG E 557 " --> pdb=" O TYR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 577 removed outlier: 3.637A pdb=" N ILE E 564 " --> pdb=" O GLN E 560 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR E 565 " --> pdb=" O GLN E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 597 removed outlier: 3.814A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 593 " --> pdb=" O PHE E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 628 removed outlier: 3.638A pdb=" N ASN E 628 " --> pdb=" O GLY E 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 602 through 628' Processing helix chain 'E' and resid 629 through 637 removed outlier: 3.660A pdb=" N THR E 633 " --> pdb=" O SER E 629 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 636 " --> pdb=" O SER E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 643 removed outlier: 3.638A pdb=" N ILE E 642 " --> pdb=" O PHE E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 671 Processing helix chain 'E' and resid 673 through 712 removed outlier: 3.947A pdb=" N ILE E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN E 687 " --> pdb=" O GLY E 683 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS E 688 " --> pdb=" O GLU E 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN E 691 " --> pdb=" O ASN E 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU E 692 " --> pdb=" O LYS E 688 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS E 694 " --> pdb=" O ALA E 690 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E 709 " --> pdb=" O ILE E 705 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 368 through 372 removed outlier: 3.808A pdb=" N GLU C 371 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 372 removed outlier: 3.807A pdb=" N GLU B 371 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 372 removed outlier: 3.808A pdb=" N GLU D 371 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 368 through 372 removed outlier: 3.808A pdb=" N GLU E 371 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER E 379 " --> pdb=" O GLU E 371 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 2055 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: 3.17 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3514 1.34 - 1.46: 2975 1.46 - 1.57: 5455 1.57 - 1.69: 4 1.69 - 1.81: 128 Bond restraints: 12076 Sorted by residual: bond pdb=" C14 6ET B 801 " pdb=" S15 6ET B 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C14 6ET C 801 " pdb=" S15 6ET C 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C14 6ET D 801 " pdb=" S15 6ET D 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C14 6ET E 801 " pdb=" S15 6ET E 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C14 6ET B 801 " pdb=" N08 6ET B 801 " ideal model delta sigma weight residual 1.348 1.435 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 12071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 15897 3.08 - 6.15: 435 6.15 - 9.23: 52 9.23 - 12.31: 12 12.31 - 15.38: 8 Bond angle restraints: 16404 Sorted by residual: angle pdb=" N GLU B 513 " pdb=" CA GLU B 513 " pdb=" C GLU B 513 " ideal model delta sigma weight residual 114.56 104.09 10.47 1.27e+00 6.20e-01 6.79e+01 angle pdb=" N GLU C 513 " pdb=" CA GLU C 513 " pdb=" C GLU C 513 " ideal model delta sigma weight residual 114.56 104.10 10.46 1.27e+00 6.20e-01 6.78e+01 angle pdb=" N GLU E 513 " pdb=" CA GLU E 513 " pdb=" C GLU E 513 " ideal model delta sigma weight residual 114.56 104.14 10.42 1.27e+00 6.20e-01 6.73e+01 angle pdb=" N GLU D 513 " pdb=" CA GLU D 513 " pdb=" C GLU D 513 " ideal model delta sigma weight residual 114.56 104.17 10.39 1.27e+00 6.20e-01 6.69e+01 angle pdb=" C07 6ET B 801 " pdb=" N08 6ET B 801 " pdb=" C09 6ET B 801 " ideal model delta sigma weight residual 115.16 130.54 -15.38 3.00e+00 1.11e-01 2.63e+01 ... (remaining 16399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 6828 24.69 - 49.38: 132 49.38 - 74.07: 8 74.07 - 98.76: 4 98.76 - 123.45: 16 Dihedral angle restraints: 6988 sinusoidal: 2376 harmonic: 4612 Sorted by residual: dihedral pdb=" CA GLY C 375 " pdb=" C GLY C 375 " pdb=" N PRO C 376 " pdb=" CA PRO C 376 " ideal model delta harmonic sigma weight residual -180.00 -141.79 -38.21 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA GLY E 375 " pdb=" C GLY E 375 " pdb=" N PRO E 376 " pdb=" CA PRO E 376 " ideal model delta harmonic sigma weight residual -180.00 -141.80 -38.20 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA GLY B 375 " pdb=" C GLY B 375 " pdb=" N PRO B 376 " pdb=" CA PRO B 376 " ideal model delta harmonic sigma weight residual -180.00 -141.83 -38.17 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 6985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1058 0.051 - 0.103: 667 0.103 - 0.154: 139 0.154 - 0.206: 19 0.206 - 0.257: 13 Chirality restraints: 1896 Sorted by residual: chirality pdb=" CB VAL B 595 " pdb=" CA VAL B 595 " pdb=" CG1 VAL B 595 " pdb=" CG2 VAL B 595 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL D 595 " pdb=" CA VAL D 595 " pdb=" CG1 VAL D 595 " pdb=" CG2 VAL D 595 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL E 595 " pdb=" CA VAL E 595 " pdb=" CG1 VAL E 595 " pdb=" CG2 VAL E 595 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1893 not shown) Planarity restraints: 2024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 375 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C GLY D 375 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY D 375 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO D 376 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 375 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C GLY E 375 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY E 375 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO E 376 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 375 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C GLY B 375 " -0.045 2.00e-02 2.50e+03 pdb=" O GLY B 375 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO B 376 " 0.015 2.00e-02 2.50e+03 ... (remaining 2021 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 4 2.01 - 2.73: 1440 2.73 - 3.45: 16758 3.45 - 4.18: 27400 4.18 - 4.90: 48173 Nonbonded interactions: 93775 Sorted by model distance: nonbonded pdb=" OG SER B 512 " pdb=" O13 6ET B 801 " model vdw 1.283 3.040 nonbonded pdb=" OG SER C 512 " pdb=" O13 6ET C 801 " model vdw 1.302 3.040 nonbonded pdb=" OG SER E 512 " pdb=" O13 6ET E 801 " model vdw 1.314 3.040 nonbonded pdb=" OG SER D 512 " pdb=" O13 6ET D 801 " model vdw 1.330 3.040 nonbonded pdb=" CB SER B 512 " pdb=" O13 6ET B 801 " model vdw 2.094 3.440 ... (remaining 93770 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: 0.09 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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 individual isotropic 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: 0.350 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 26.220 Find NCS groups from input model: 0.230 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.020 0.745 12080 Z= 1.478 Angle : 1.237 15.382 16404 Z= 0.646 Chirality : 0.064 0.257 1896 Planarity : 0.006 0.043 2024 Dihedral : 12.935 123.449 4044 Min Nonbonded Distance : 1.283 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.08 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.26 % 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: -5.27 (0.15), residues: 1568 helix: -3.51 (0.09), residues: 932 sheet: -3.99 (0.60), residues: 64 loop : -3.04 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP E 697 HIS 0.001 0.001 HIS C 410 PHE 0.035 0.004 PHE D 448 TYR 0.016 0.003 TYR D 653 ARG 0.012 0.002 ARG C 743 Details of bonding type rmsd hydrogen bonds : bond 0.28308 ( 697) hydrogen bonds : angle 9.92700 ( 2055) covalent geometry : bond 0.01454 (12076) covalent geometry : angle 1.23704 (16404) Misc. bond : bond 0.72678 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 656 LYS cc_start: 0.8352 (tttt) cc_final: 0.8086 (tttm) REVERT: D 656 LYS cc_start: 0.8399 (tttt) cc_final: 0.8143 (tttm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2696 time to fit residues: 111.2084 Evaluate side-chains 167 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 HIS C 423 GLN C 700 GLN B 410 HIS B 423 GLN B 700 GLN D 410 HIS D 700 GLN E 410 HIS E 700 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.113012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.080976 restraints weight = 28088.750| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.99 r_work: 0.2967 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12080 Z= 0.156 Angle : 0.655 9.723 16404 Z= 0.344 Chirality : 0.043 0.168 1896 Planarity : 0.004 0.027 2024 Dihedral : 13.737 117.218 1788 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.25 % Favored : 93.49 % Rotamer: Outliers : 1.12 % Allowed : 9.55 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.44 (0.19), residues: 1568 helix: -0.88 (0.14), residues: 1000 sheet: -2.64 (0.79), residues: 56 loop : -2.83 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 697 HIS 0.001 0.000 HIS C 410 PHE 0.018 0.002 PHE E 489 TYR 0.014 0.001 TYR B 565 ARG 0.004 0.000 ARG B 474 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 697) hydrogen bonds : angle 4.55965 ( 2055) covalent geometry : bond 0.00342 (12076) covalent geometry : angle 0.65514 (16404) Misc. bond : bond 0.00341 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: C 339 LEU cc_start: 0.9051 (mm) cc_final: 0.8529 (tt) REVERT: C 581 MET cc_start: 0.8312 (mmm) cc_final: 0.8100 (mmm) REVERT: C 682 MET cc_start: 0.8749 (mtt) cc_final: 0.8467 (mtt) REVERT: B 511 TYR cc_start: 0.7947 (t80) cc_final: 0.7746 (t80) REVERT: B 513 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8427 (tm-30) REVERT: B 571 LYS cc_start: 0.9163 (mmtm) cc_final: 0.8799 (mmmm) REVERT: B 673 LEU cc_start: 0.9170 (tt) cc_final: 0.8660 (mt) REVERT: B 677 MET cc_start: 0.8604 (tpp) cc_final: 0.8388 (tpp) REVERT: B 682 MET cc_start: 0.8693 (mtt) cc_final: 0.8259 (mtt) REVERT: D 339 LEU cc_start: 0.8997 (mm) cc_final: 0.8614 (tt) REVERT: E 571 LYS cc_start: 0.9122 (mmtm) cc_final: 0.8771 (mmmm) outliers start: 12 outliers final: 7 residues processed: 291 average time/residue: 0.2059 time to fit residues: 89.4252 Evaluate side-chains 211 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 204 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 155 optimal weight: 50.0000 chunk 87 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 76 optimal weight: 0.0870 chunk 94 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 HIS C 423 GLN C 700 GLN B 410 HIS B 423 GLN B 676 ASN D 410 HIS D 423 GLN D 700 GLN E 410 HIS E 423 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.112194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.080098 restraints weight = 28220.863| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.01 r_work: 0.2945 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12080 Z= 0.144 Angle : 0.578 6.744 16404 Z= 0.307 Chirality : 0.042 0.155 1896 Planarity : 0.003 0.018 2024 Dihedral : 13.074 113.019 1788 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.50 % Allowed : 12.27 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.84 (0.22), residues: 1568 helix: 0.53 (0.17), residues: 972 sheet: -2.79 (0.73), residues: 56 loop : -2.33 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 697 HIS 0.002 0.001 HIS C 410 PHE 0.011 0.001 PHE E 489 TYR 0.014 0.001 TYR C 511 ARG 0.004 0.000 ARG C 474 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 697) hydrogen bonds : angle 4.15142 ( 2055) covalent geometry : bond 0.00320 (12076) covalent geometry : angle 0.57780 (16404) Misc. bond : bond 0.00157 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 252 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8968 (mm) cc_final: 0.8495 (tt) REVERT: C 401 TYR cc_start: 0.8090 (m-10) cc_final: 0.7423 (m-80) REVERT: C 419 ASN cc_start: 0.9091 (m-40) cc_final: 0.8762 (m-40) REVERT: C 511 TYR cc_start: 0.8269 (t80) cc_final: 0.7944 (t80) REVERT: C 572 MET cc_start: 0.8846 (ttm) cc_final: 0.8605 (mtm) REVERT: C 646 ASP cc_start: 0.9063 (t0) cc_final: 0.8838 (t0) REVERT: C 682 MET cc_start: 0.8792 (mtt) cc_final: 0.8142 (mtp) REVERT: C 706 LEU cc_start: 0.9507 (mp) cc_final: 0.9300 (mt) REVERT: B 359 GLU cc_start: 0.6928 (tt0) cc_final: 0.6511 (mp0) REVERT: B 419 ASN cc_start: 0.9053 (m-40) cc_final: 0.8813 (m-40) REVERT: B 571 LYS cc_start: 0.9079 (mmtm) cc_final: 0.8789 (mmmm) REVERT: B 572 MET cc_start: 0.8577 (ttm) cc_final: 0.8333 (ttm) REVERT: B 646 ASP cc_start: 0.9082 (t0) cc_final: 0.8838 (t0) REVERT: B 677 MET cc_start: 0.8659 (tpp) cc_final: 0.8425 (tpp) REVERT: B 682 MET cc_start: 0.8626 (mtt) cc_final: 0.8416 (mtt) REVERT: B 706 LEU cc_start: 0.9495 (mp) cc_final: 0.9290 (mt) REVERT: D 339 LEU cc_start: 0.8941 (mm) cc_final: 0.8460 (tt) REVERT: D 359 GLU cc_start: 0.6925 (tt0) cc_final: 0.6549 (mp0) REVERT: D 401 TYR cc_start: 0.8112 (m-10) cc_final: 0.7897 (m-80) REVERT: D 419 ASN cc_start: 0.9039 (m-40) cc_final: 0.8717 (m-40) REVERT: D 511 TYR cc_start: 0.8260 (t80) cc_final: 0.7962 (t80) REVERT: D 581 MET cc_start: 0.8303 (mmm) cc_final: 0.8102 (ptt) REVERT: D 600 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8050 (mt-10) REVERT: D 636 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8929 (mm-30) REVERT: D 646 ASP cc_start: 0.9083 (t0) cc_final: 0.8856 (t0) REVERT: E 359 GLU cc_start: 0.6906 (tt0) cc_final: 0.6527 (mp0) REVERT: E 401 TYR cc_start: 0.8100 (m-10) cc_final: 0.7880 (m-80) REVERT: E 419 ASN cc_start: 0.9075 (m-40) cc_final: 0.8862 (m-40) REVERT: E 511 TYR cc_start: 0.8268 (t80) cc_final: 0.7848 (t80) REVERT: E 571 LYS cc_start: 0.9021 (mmtm) cc_final: 0.8710 (mmmm) REVERT: E 646 ASP cc_start: 0.9081 (t0) cc_final: 0.8865 (t0) outliers start: 16 outliers final: 12 residues processed: 265 average time/residue: 0.2218 time to fit residues: 86.0898 Evaluate side-chains 238 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 226 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 142 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 0.0870 chunk 125 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 676 ASN C 700 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.114670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082294 restraints weight = 27846.642| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.05 r_work: 0.3001 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12080 Z= 0.108 Angle : 0.526 5.424 16404 Z= 0.283 Chirality : 0.041 0.155 1896 Planarity : 0.003 0.018 2024 Dihedral : 12.449 109.319 1788 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.78 % Allowed : 13.01 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.46 (0.22), residues: 1568 helix: 0.85 (0.17), residues: 1008 sheet: -2.73 (0.64), residues: 56 loop : -2.40 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 697 HIS 0.001 0.000 HIS E 410 PHE 0.010 0.001 PHE E 489 TYR 0.013 0.001 TYR D 511 ARG 0.004 0.000 ARG C 499 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 697) hydrogen bonds : angle 3.90592 ( 2055) covalent geometry : bond 0.00227 (12076) covalent geometry : angle 0.52646 (16404) Misc. bond : bond 0.00101 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8261 (tt) REVERT: C 359 GLU cc_start: 0.7070 (tt0) cc_final: 0.6634 (mp0) REVERT: C 401 TYR cc_start: 0.7900 (m-10) cc_final: 0.7632 (m-80) REVERT: C 419 ASN cc_start: 0.9101 (m-40) cc_final: 0.8759 (m-40) REVERT: C 572 MET cc_start: 0.8909 (ttm) cc_final: 0.8672 (ttm) REVERT: C 646 ASP cc_start: 0.9031 (t0) cc_final: 0.8793 (t0) REVERT: C 682 MET cc_start: 0.8837 (mtt) cc_final: 0.8358 (mtp) REVERT: B 359 GLU cc_start: 0.6962 (tt0) cc_final: 0.6509 (mp0) REVERT: B 419 ASN cc_start: 0.9077 (m-40) cc_final: 0.8735 (m-40) REVERT: B 571 LYS cc_start: 0.9059 (mmtm) cc_final: 0.8783 (mmmm) REVERT: B 646 ASP cc_start: 0.9029 (t0) cc_final: 0.8786 (t0) REVERT: B 673 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8822 (mt) REVERT: B 691 GLN cc_start: 0.8548 (pm20) cc_final: 0.8240 (mp10) REVERT: D 339 LEU cc_start: 0.8665 (mm) cc_final: 0.8194 (tt) REVERT: D 359 GLU cc_start: 0.6844 (tt0) cc_final: 0.6478 (mp0) REVERT: D 419 ASN cc_start: 0.9046 (m-40) cc_final: 0.8738 (m-40) REVERT: D 513 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8521 (tm-30) REVERT: D 636 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8854 (mm-30) REVERT: D 646 ASP cc_start: 0.9043 (t0) cc_final: 0.8792 (t0) REVERT: E 359 GLU cc_start: 0.6876 (tt0) cc_final: 0.6548 (mp0) REVERT: E 419 ASN cc_start: 0.9102 (m-40) cc_final: 0.8815 (m-40) REVERT: E 564 ILE cc_start: 0.9051 (mt) cc_final: 0.8727 (mm) REVERT: E 571 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8586 (mmmm) REVERT: E 581 MET cc_start: 0.8468 (mmm) cc_final: 0.8188 (ptt) REVERT: E 646 ASP cc_start: 0.9070 (t0) cc_final: 0.8849 (t0) outliers start: 19 outliers final: 9 residues processed: 262 average time/residue: 0.2176 time to fit residues: 83.5479 Evaluate side-chains 233 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 222 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 16 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 chunk 30 optimal weight: 0.0980 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 676 ASN E 533 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.111397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.077949 restraints weight = 28030.729| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.94 r_work: 0.2917 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12080 Z= 0.216 Angle : 0.635 10.945 16404 Z= 0.324 Chirality : 0.043 0.156 1896 Planarity : 0.003 0.020 2024 Dihedral : 12.600 109.757 1788 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.09 % Allowed : 15.17 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.22 (0.23), residues: 1568 helix: 1.02 (0.17), residues: 1008 sheet: -2.85 (0.60), residues: 56 loop : -2.26 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 697 HIS 0.001 0.001 HIS C 410 PHE 0.015 0.002 PHE E 438 TYR 0.017 0.002 TYR E 511 ARG 0.003 0.000 ARG C 743 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 697) hydrogen bonds : angle 3.91623 ( 2055) covalent geometry : bond 0.00491 (12076) covalent geometry : angle 0.63535 (16404) Misc. bond : bond 0.00150 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8552 (tt) REVERT: C 359 GLU cc_start: 0.7040 (tt0) cc_final: 0.6598 (mp0) REVERT: C 419 ASN cc_start: 0.9079 (m-40) cc_final: 0.8776 (m-40) REVERT: C 423 GLN cc_start: 0.9086 (tp40) cc_final: 0.8868 (tp-100) REVERT: C 646 ASP cc_start: 0.9106 (t0) cc_final: 0.8869 (t0) REVERT: B 359 GLU cc_start: 0.6859 (tt0) cc_final: 0.6400 (mp0) REVERT: B 419 ASN cc_start: 0.9169 (m-40) cc_final: 0.8842 (m-40) REVERT: B 423 GLN cc_start: 0.9078 (tp40) cc_final: 0.8849 (tp-100) REVERT: B 571 LYS cc_start: 0.9059 (mmtm) cc_final: 0.8746 (mmmm) REVERT: B 581 MET cc_start: 0.8540 (mmm) cc_final: 0.8242 (ptt) REVERT: B 646 ASP cc_start: 0.9131 (t0) cc_final: 0.8861 (t0) REVERT: B 691 GLN cc_start: 0.8575 (pm20) cc_final: 0.8257 (mp10) REVERT: D 339 LEU cc_start: 0.8857 (mm) cc_final: 0.8456 (tt) REVERT: D 359 GLU cc_start: 0.6873 (tt0) cc_final: 0.6472 (mp0) REVERT: D 419 ASN cc_start: 0.9134 (m-40) cc_final: 0.8820 (m-40) REVERT: D 423 GLN cc_start: 0.9100 (tp40) cc_final: 0.8869 (tp-100) REVERT: D 564 ILE cc_start: 0.9106 (mt) cc_final: 0.8842 (mm) REVERT: D 581 MET cc_start: 0.8612 (mmm) cc_final: 0.8291 (ptt) REVERT: D 636 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8937 (mm-30) REVERT: D 646 ASP cc_start: 0.9119 (t0) cc_final: 0.8885 (t0) REVERT: E 359 GLU cc_start: 0.6882 (tt0) cc_final: 0.6454 (mp0) REVERT: E 419 ASN cc_start: 0.9181 (m-40) cc_final: 0.8862 (m-40) REVERT: E 423 GLN cc_start: 0.9105 (tp40) cc_final: 0.8874 (tp-100) REVERT: E 564 ILE cc_start: 0.9122 (mt) cc_final: 0.8862 (mm) REVERT: E 571 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8533 (mmmm) REVERT: E 581 MET cc_start: 0.8512 (mmm) cc_final: 0.8247 (ptt) REVERT: E 646 ASP cc_start: 0.9131 (t0) cc_final: 0.8912 (t0) REVERT: E 682 MET cc_start: 0.8468 (mtt) cc_final: 0.8000 (mtt) outliers start: 33 outliers final: 27 residues processed: 253 average time/residue: 0.2063 time to fit residues: 79.7475 Evaluate side-chains 254 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 137 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 130 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 0.4980 chunk 135 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.114101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081089 restraints weight = 27725.278| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.99 r_work: 0.2978 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12080 Z= 0.118 Angle : 0.552 11.261 16404 Z= 0.290 Chirality : 0.040 0.166 1896 Planarity : 0.002 0.018 2024 Dihedral : 12.251 107.384 1788 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.25 % Allowed : 15.07 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.08 (0.23), residues: 1568 helix: 1.12 (0.17), residues: 1008 sheet: -2.86 (0.57), residues: 56 loop : -2.16 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 697 HIS 0.001 0.000 HIS D 410 PHE 0.011 0.001 PHE B 496 TYR 0.010 0.001 TYR D 511 ARG 0.003 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 697) hydrogen bonds : angle 3.79911 ( 2055) covalent geometry : bond 0.00262 (12076) covalent geometry : angle 0.55183 (16404) Misc. bond : bond 0.00090 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8400 (tt) REVERT: C 359 GLU cc_start: 0.6989 (tt0) cc_final: 0.6564 (mp0) REVERT: C 401 TYR cc_start: 0.8251 (m-80) cc_final: 0.7912 (m-80) REVERT: C 419 ASN cc_start: 0.9106 (m-40) cc_final: 0.8867 (m-40) REVERT: C 423 GLN cc_start: 0.9122 (tp40) cc_final: 0.8840 (tp-100) REVERT: C 564 ILE cc_start: 0.9035 (mt) cc_final: 0.8715 (mm) REVERT: C 646 ASP cc_start: 0.9056 (t0) cc_final: 0.8812 (t0) REVERT: C 682 MET cc_start: 0.8631 (mtt) cc_final: 0.8395 (mtt) REVERT: B 359 GLU cc_start: 0.6899 (tt0) cc_final: 0.6463 (mp0) REVERT: B 419 ASN cc_start: 0.9128 (m-40) cc_final: 0.8868 (m-40) REVERT: B 571 LYS cc_start: 0.8945 (mmtm) cc_final: 0.8624 (mmmm) REVERT: B 581 MET cc_start: 0.8497 (mmm) cc_final: 0.8166 (ptt) REVERT: B 646 ASP cc_start: 0.9041 (t0) cc_final: 0.8790 (t0) REVERT: B 691 GLN cc_start: 0.8576 (pm20) cc_final: 0.8301 (mp10) REVERT: D 359 GLU cc_start: 0.6882 (tt0) cc_final: 0.6523 (mp0) REVERT: D 419 ASN cc_start: 0.9121 (m-40) cc_final: 0.8894 (m-40) REVERT: D 564 ILE cc_start: 0.9072 (mt) cc_final: 0.8759 (mm) REVERT: D 581 MET cc_start: 0.8604 (mmm) cc_final: 0.8295 (ptt) REVERT: D 636 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8921 (mm-30) REVERT: D 646 ASP cc_start: 0.9048 (t0) cc_final: 0.8815 (t0) REVERT: E 359 GLU cc_start: 0.6789 (tt0) cc_final: 0.6412 (mp0) REVERT: E 419 ASN cc_start: 0.9152 (m-40) cc_final: 0.8922 (m-40) REVERT: E 493 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9114 (pt) REVERT: E 564 ILE cc_start: 0.9065 (mt) cc_final: 0.8801 (mm) REVERT: E 571 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8526 (mmmm) REVERT: E 581 MET cc_start: 0.8486 (mmm) cc_final: 0.8194 (ptt) REVERT: E 646 ASP cc_start: 0.9022 (t0) cc_final: 0.8776 (t0) REVERT: E 709 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8698 (tm-30) outliers start: 24 outliers final: 19 residues processed: 262 average time/residue: 0.1823 time to fit residues: 73.6501 Evaluate side-chains 248 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 686 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 38 optimal weight: 50.0000 chunk 93 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 676 ASN E 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.114868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082205 restraints weight = 27981.812| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.03 r_work: 0.2965 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12080 Z= 0.124 Angle : 0.597 13.919 16404 Z= 0.301 Chirality : 0.041 0.176 1896 Planarity : 0.002 0.020 2024 Dihedral : 11.970 105.111 1788 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.25 % Allowed : 16.20 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.02 (0.23), residues: 1568 helix: 1.16 (0.17), residues: 1008 sheet: -2.76 (0.56), residues: 56 loop : -2.13 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 697 HIS 0.001 0.000 HIS C 410 PHE 0.011 0.001 PHE C 496 TYR 0.018 0.001 TYR D 511 ARG 0.002 0.000 ARG D 743 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 697) hydrogen bonds : angle 3.74954 ( 2055) covalent geometry : bond 0.00281 (12076) covalent geometry : angle 0.59741 (16404) Misc. bond : bond 0.00075 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 359 GLU cc_start: 0.6846 (tt0) cc_final: 0.6581 (mp0) REVERT: C 401 TYR cc_start: 0.8227 (m-80) cc_final: 0.8008 (m-80) REVERT: C 419 ASN cc_start: 0.9107 (m-40) cc_final: 0.8869 (m-40) REVERT: C 423 GLN cc_start: 0.9123 (tp40) cc_final: 0.8857 (tp-100) REVERT: C 564 ILE cc_start: 0.9030 (mt) cc_final: 0.8781 (mm) REVERT: C 646 ASP cc_start: 0.9054 (t0) cc_final: 0.8843 (t0) REVERT: B 359 GLU cc_start: 0.6732 (tt0) cc_final: 0.6475 (mp0) REVERT: B 419 ASN cc_start: 0.9146 (m-40) cc_final: 0.8895 (m-40) REVERT: B 423 GLN cc_start: 0.9096 (tp40) cc_final: 0.8877 (tp-100) REVERT: B 571 LYS cc_start: 0.8870 (mmtm) cc_final: 0.8612 (mmmm) REVERT: B 581 MET cc_start: 0.8504 (mmm) cc_final: 0.8238 (ptt) REVERT: B 646 ASP cc_start: 0.9019 (t0) cc_final: 0.8816 (t0) REVERT: B 691 GLN cc_start: 0.8579 (pm20) cc_final: 0.8283 (mp10) REVERT: D 339 LEU cc_start: 0.8870 (mm) cc_final: 0.8433 (tt) REVERT: D 359 GLU cc_start: 0.6724 (tt0) cc_final: 0.6523 (mp0) REVERT: D 419 ASN cc_start: 0.9116 (m-40) cc_final: 0.8900 (m-40) REVERT: D 423 GLN cc_start: 0.9084 (tp40) cc_final: 0.8847 (tp-100) REVERT: D 564 ILE cc_start: 0.9049 (mt) cc_final: 0.8782 (mm) REVERT: D 581 MET cc_start: 0.8593 (mmm) cc_final: 0.8292 (ptt) REVERT: D 636 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8882 (mm-30) REVERT: E 419 ASN cc_start: 0.9153 (m-40) cc_final: 0.8919 (m-40) REVERT: E 493 ILE cc_start: 0.9532 (OUTLIER) cc_final: 0.9141 (pt) REVERT: E 564 ILE cc_start: 0.9080 (mt) cc_final: 0.8780 (mm) REVERT: E 571 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8558 (mmmm) REVERT: E 581 MET cc_start: 0.8490 (mmm) cc_final: 0.8250 (ptt) outliers start: 24 outliers final: 22 residues processed: 253 average time/residue: 0.2644 time to fit residues: 104.7016 Evaluate side-chains 250 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 686 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 39 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 chunk 4 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.115964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083131 restraints weight = 27862.846| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.03 r_work: 0.2995 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12080 Z= 0.115 Angle : 0.612 15.045 16404 Z= 0.306 Chirality : 0.040 0.136 1896 Planarity : 0.002 0.024 2024 Dihedral : 11.661 102.098 1788 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.72 % Allowed : 16.01 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.06 (0.23), residues: 1568 helix: 1.21 (0.17), residues: 1008 sheet: -2.74 (0.53), residues: 56 loop : -2.07 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 697 HIS 0.000 0.000 HIS D 410 PHE 0.011 0.001 PHE B 496 TYR 0.012 0.001 TYR E 511 ARG 0.003 0.000 ARG C 575 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 697) hydrogen bonds : angle 3.69845 ( 2055) covalent geometry : bond 0.00257 (12076) covalent geometry : angle 0.61153 (16404) Misc. bond : bond 0.00053 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8962 (mm) cc_final: 0.8537 (tt) REVERT: C 359 GLU cc_start: 0.6780 (tt0) cc_final: 0.6577 (mp0) REVERT: C 401 TYR cc_start: 0.8252 (m-80) cc_final: 0.7984 (m-80) REVERT: C 419 ASN cc_start: 0.9094 (m-40) cc_final: 0.8875 (m-40) REVERT: C 423 GLN cc_start: 0.9117 (tp40) cc_final: 0.8832 (tp-100) REVERT: C 493 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9146 (pt) REVERT: C 564 ILE cc_start: 0.9049 (mt) cc_final: 0.8792 (mm) REVERT: B 359 GLU cc_start: 0.6690 (tt0) cc_final: 0.6302 (mp0) REVERT: B 419 ASN cc_start: 0.9114 (m-40) cc_final: 0.8852 (m-40) REVERT: B 571 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8479 (mmmm) REVERT: B 581 MET cc_start: 0.8477 (mmm) cc_final: 0.8250 (ptt) REVERT: B 646 ASP cc_start: 0.8961 (t0) cc_final: 0.8737 (t0) REVERT: B 691 GLN cc_start: 0.8541 (pm20) cc_final: 0.8267 (mp10) REVERT: D 339 LEU cc_start: 0.8806 (mm) cc_final: 0.8347 (tt) REVERT: D 359 GLU cc_start: 0.6749 (tt0) cc_final: 0.6399 (mp0) REVERT: D 419 ASN cc_start: 0.9107 (m-40) cc_final: 0.8876 (m-40) REVERT: D 423 GLN cc_start: 0.9073 (tp40) cc_final: 0.8800 (tp-100) REVERT: D 564 ILE cc_start: 0.9038 (mt) cc_final: 0.8786 (mm) REVERT: D 581 MET cc_start: 0.8583 (mmm) cc_final: 0.8302 (ptt) REVERT: D 636 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8804 (mm-30) REVERT: D 673 LEU cc_start: 0.9192 (mt) cc_final: 0.8881 (tt) REVERT: E 419 ASN cc_start: 0.9130 (m-40) cc_final: 0.8882 (m-40) REVERT: E 423 GLN cc_start: 0.9080 (tp40) cc_final: 0.8811 (tp-100) REVERT: E 493 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9131 (pt) REVERT: E 564 ILE cc_start: 0.9031 (mt) cc_final: 0.8681 (mm) REVERT: E 567 VAL cc_start: 0.9516 (t) cc_final: 0.9162 (p) REVERT: E 571 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8435 (mmmm) REVERT: E 581 MET cc_start: 0.8498 (mmm) cc_final: 0.8245 (ptt) outliers start: 29 outliers final: 24 residues processed: 266 average time/residue: 0.2862 time to fit residues: 116.2332 Evaluate side-chains 252 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 483 SER Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.111959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.078710 restraints weight = 28529.995| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.95 r_work: 0.2923 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12080 Z= 0.204 Angle : 0.692 13.870 16404 Z= 0.343 Chirality : 0.043 0.138 1896 Planarity : 0.003 0.026 2024 Dihedral : 11.890 104.946 1788 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.28 % Allowed : 16.29 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.04 (0.22), residues: 1568 helix: 1.11 (0.17), residues: 1008 sheet: -2.81 (0.51), residues: 56 loop : -2.05 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 697 HIS 0.002 0.001 HIS C 410 PHE 0.013 0.001 PHE E 438 TYR 0.021 0.001 TYR D 511 ARG 0.003 0.000 ARG E 420 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 697) hydrogen bonds : angle 3.87336 ( 2055) covalent geometry : bond 0.00466 (12076) covalent geometry : angle 0.69245 (16404) Misc. bond : bond 0.00103 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: C 359 GLU cc_start: 0.6711 (tt0) cc_final: 0.6439 (mp0) REVERT: C 419 ASN cc_start: 0.9159 (m-40) cc_final: 0.8878 (m-40) REVERT: C 423 GLN cc_start: 0.9111 (tp40) cc_final: 0.8873 (tp-100) REVERT: C 561 GLN cc_start: 0.7294 (pm20) cc_final: 0.6661 (pt0) REVERT: B 359 GLU cc_start: 0.6660 (tt0) cc_final: 0.6292 (mp0) REVERT: B 419 ASN cc_start: 0.9164 (m-40) cc_final: 0.8902 (m-40) REVERT: B 493 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9172 (pt) REVERT: B 511 TYR cc_start: 0.8273 (t80) cc_final: 0.8027 (t80) REVERT: B 571 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8656 (mmmm) REVERT: B 581 MET cc_start: 0.8516 (mmm) cc_final: 0.8222 (ptt) REVERT: B 646 ASP cc_start: 0.9065 (t0) cc_final: 0.8826 (t0) REVERT: D 359 GLU cc_start: 0.6708 (tt0) cc_final: 0.6349 (mp0) REVERT: D 419 ASN cc_start: 0.9162 (m-40) cc_final: 0.8863 (m-40) REVERT: D 423 GLN cc_start: 0.9090 (tp40) cc_final: 0.8875 (tp-100) REVERT: D 493 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9159 (pt) REVERT: D 561 GLN cc_start: 0.7608 (pm20) cc_final: 0.6915 (pt0) REVERT: D 564 ILE cc_start: 0.9069 (mt) cc_final: 0.8554 (mm) REVERT: D 581 MET cc_start: 0.8662 (mmm) cc_final: 0.8289 (ptt) REVERT: D 636 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8903 (mm-30) REVERT: E 419 ASN cc_start: 0.9165 (m-40) cc_final: 0.8905 (m-40) REVERT: E 423 GLN cc_start: 0.9070 (tp40) cc_final: 0.8835 (tp-100) REVERT: E 511 TYR cc_start: 0.8201 (t80) cc_final: 0.7934 (t80) REVERT: E 523 MET cc_start: 0.9078 (mmm) cc_final: 0.8641 (ttt) REVERT: E 561 GLN cc_start: 0.7491 (pm20) cc_final: 0.6885 (pt0) REVERT: E 564 ILE cc_start: 0.9074 (mt) cc_final: 0.8828 (mm) REVERT: E 571 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8492 (mmmm) REVERT: E 581 MET cc_start: 0.8534 (mmm) cc_final: 0.8237 (ptt) outliers start: 35 outliers final: 32 residues processed: 259 average time/residue: 0.1818 time to fit residues: 72.8651 Evaluate side-chains 264 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 483 SER Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 114 optimal weight: 40.0000 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 50.0000 chunk 100 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076868 restraints weight = 28212.027| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.92 r_work: 0.2893 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12080 Z= 0.279 Angle : 0.746 14.708 16404 Z= 0.374 Chirality : 0.045 0.131 1896 Planarity : 0.003 0.034 2024 Dihedral : 12.337 107.605 1788 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.56 % Allowed : 16.10 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.13 (0.22), residues: 1568 helix: 1.03 (0.17), residues: 1000 sheet: -2.75 (0.53), residues: 56 loop : -2.01 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 697 HIS 0.002 0.001 HIS C 410 PHE 0.018 0.002 PHE D 448 TYR 0.018 0.002 TYR D 584 ARG 0.003 0.001 ARG B 499 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 697) hydrogen bonds : angle 4.02773 ( 2055) covalent geometry : bond 0.00634 (12076) covalent geometry : angle 0.74623 (16404) Misc. bond : bond 0.00180 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: C 359 GLU cc_start: 0.6818 (tt0) cc_final: 0.6461 (mp0) REVERT: C 564 ILE cc_start: 0.9042 (mp) cc_final: 0.8793 (mm) REVERT: B 359 GLU cc_start: 0.6658 (tt0) cc_final: 0.6168 (mp0) REVERT: B 419 ASN cc_start: 0.9214 (m-40) cc_final: 0.8990 (m-40) REVERT: B 571 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8669 (mmmm) REVERT: B 581 MET cc_start: 0.8584 (mmm) cc_final: 0.8254 (ptt) REVERT: B 600 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7788 (mt-10) REVERT: B 646 ASP cc_start: 0.9137 (t0) cc_final: 0.8824 (t0) REVERT: D 359 GLU cc_start: 0.6764 (tt0) cc_final: 0.6305 (mp0) REVERT: D 419 ASN cc_start: 0.9188 (m-40) cc_final: 0.8978 (m-40) REVERT: D 533 GLN cc_start: 0.8612 (mm110) cc_final: 0.8411 (mm110) REVERT: D 581 MET cc_start: 0.8646 (mmm) cc_final: 0.8330 (ptt) REVERT: E 419 ASN cc_start: 0.9192 (m-40) cc_final: 0.8987 (m-40) REVERT: E 511 TYR cc_start: 0.8362 (t80) cc_final: 0.8130 (t80) REVERT: E 571 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8438 (mmmm) REVERT: E 581 MET cc_start: 0.8613 (mmm) cc_final: 0.8289 (ptt) outliers start: 38 outliers final: 34 residues processed: 251 average time/residue: 0.1988 time to fit residues: 77.0652 Evaluate side-chains 248 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 483 SER Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 83 optimal weight: 40.0000 chunk 105 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 40.0000 chunk 133 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.113928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.081316 restraints weight = 27666.467| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.98 r_work: 0.2975 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12080 Z= 0.135 Angle : 0.675 14.490 16404 Z= 0.338 Chirality : 0.042 0.143 1896 Planarity : 0.003 0.023 2024 Dihedral : 11.965 106.910 1788 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.72 % Allowed : 17.60 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.02 (0.22), residues: 1568 helix: 1.12 (0.17), residues: 1008 sheet: -2.85 (0.50), residues: 56 loop : -1.94 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 697 HIS 0.001 0.000 HIS B 410 PHE 0.010 0.001 PHE D 496 TYR 0.021 0.001 TYR D 511 ARG 0.003 0.000 ARG C 420 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 697) hydrogen bonds : angle 3.90613 ( 2055) covalent geometry : bond 0.00310 (12076) covalent geometry : angle 0.67481 (16404) Misc. bond : bond 0.00061 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6044.73 seconds wall clock time: 107 minutes 25.20 seconds (6445.20 seconds total)