Starting phenix.real_space_refine on Wed Sep 17 22:31:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5is0_8119/09_2025/5is0_8119_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5is0_8119/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/5is0_8119/09_2025/5is0_8119_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5is0_8119/09_2025/5is0_8119_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5is0_8119/09_2025/5is0_8119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5is0_8119/09_2025/5is0_8119.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 14, 'HIS:plan': 3, 'ARG:plan': 4, 'TRP:plan': 3, 'TYR:plan': 2, 'ASP:plan': 11, 'ASN:plan1': 4, 'PHE:plan': 5, 'GLN:plan1': 1} 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, D, E Time building chain proxies: 2.59, per 1000 atoms: 0.22 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: 1.21 Conformation dependent library (CDL) restraints added in 561.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.39 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: 1.99 Time building geometry restraints manager: 1.53 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'B' selection = chain 'D' selection = chain 'E' } 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: 0.600 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.410 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.012 0.002 ARG C 743 TYR 0.016 0.003 TYR D 653 PHE 0.035 0.004 PHE D 448 TRP 0.028 0.004 TRP E 697 HIS 0.001 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.01454 (12076) covalent geometry : angle 1.23704 (16404) hydrogen bonds : bond 0.28308 ( 697) hydrogen bonds : angle 9.92700 ( 2055) 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 : 0.511 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: 0.1333 time to fit residues: 55.4261 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 : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 423 GLN D 700 GLN E 410 HIS E 423 GLN E 700 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.113901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.081666 restraints weight = 28086.725| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.01 r_work: 0.2981 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12080 Z= 0.141 Angle : 0.652 9.652 16404 Z= 0.341 Chirality : 0.042 0.172 1896 Planarity : 0.004 0.025 2024 Dihedral : 13.763 117.360 1788 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.12 % Favored : 93.62 % Rotamer: Outliers : 0.94 % Allowed : 9.64 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.19), residues: 1568 helix: -0.94 (0.14), residues: 1000 sheet: -2.62 (0.79), residues: 56 loop : -2.83 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 474 TYR 0.014 0.001 TYR B 565 PHE 0.017 0.002 PHE E 489 TRP 0.022 0.003 TRP C 697 HIS 0.001 0.000 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00299 (12076) covalent geometry : angle 0.65184 (16404) hydrogen bonds : bond 0.04531 ( 697) hydrogen bonds : angle 4.60598 ( 2055) Misc. bond : bond 0.00233 ( 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 306 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 296 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8987 (mm) cc_final: 0.8437 (tt) REVERT: C 570 GLU cc_start: 0.9038 (tt0) cc_final: 0.8803 (tt0) REVERT: C 682 MET cc_start: 0.8734 (mtt) cc_final: 0.8479 (mtt) REVERT: B 571 LYS cc_start: 0.9146 (mmtm) cc_final: 0.8775 (mmmm) REVERT: B 673 LEU cc_start: 0.9168 (tt) cc_final: 0.8713 (mt) REVERT: B 682 MET cc_start: 0.8627 (mtt) cc_final: 0.8217 (mtt) REVERT: D 339 LEU cc_start: 0.8992 (mm) cc_final: 0.8614 (tt) REVERT: D 570 GLU cc_start: 0.9090 (tt0) cc_final: 0.8842 (tt0) REVERT: D 581 MET cc_start: 0.8338 (mmm) cc_final: 0.8063 (ptt) REVERT: E 571 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8766 (mmmm) REVERT: E 589 PHE cc_start: 0.9089 (t80) cc_final: 0.8885 (t80) REVERT: E 592 SER cc_start: 0.9316 (t) cc_final: 0.9116 (m) outliers start: 10 outliers final: 4 residues processed: 300 average time/residue: 0.0998 time to fit residues: 45.0807 Evaluate side-chains 215 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain B residue 574 LEU 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 119 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 HIS C 551 ASN C 700 GLN B 410 HIS B 423 GLN B 676 ASN D 410 HIS D 700 GLN E 410 HIS E 423 GLN E 676 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.112642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.083419 restraints weight = 28183.643| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.91 r_work: 0.2969 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12080 Z= 0.132 Angle : 0.565 6.923 16404 Z= 0.301 Chirality : 0.041 0.153 1896 Planarity : 0.003 0.019 2024 Dihedral : 13.027 112.479 1788 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.59 % Allowed : 12.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.21), residues: 1568 helix: 0.52 (0.16), residues: 972 sheet: -2.72 (0.74), residues: 56 loop : -2.30 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 474 TYR 0.014 0.001 TYR B 511 PHE 0.012 0.001 PHE E 489 TRP 0.013 0.002 TRP C 697 HIS 0.002 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00288 (12076) covalent geometry : angle 0.56453 (16404) hydrogen bonds : bond 0.03648 ( 697) hydrogen bonds : angle 4.13967 ( 2055) Misc. bond : bond 0.00126 ( 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 272 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 255 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8928 (mm) cc_final: 0.8445 (tt) REVERT: C 359 GLU cc_start: 0.6949 (tt0) cc_final: 0.6490 (mp0) REVERT: C 401 TYR cc_start: 0.8071 (m-10) cc_final: 0.7402 (m-80) REVERT: C 419 ASN cc_start: 0.9089 (m-40) cc_final: 0.8737 (m-40) REVERT: C 511 TYR cc_start: 0.8215 (t80) cc_final: 0.7847 (t80) REVERT: C 581 MET cc_start: 0.8331 (mmm) cc_final: 0.8099 (ptt) REVERT: C 646 ASP cc_start: 0.9058 (t0) cc_final: 0.8840 (t0) REVERT: C 682 MET cc_start: 0.8743 (mtt) cc_final: 0.8326 (mtp) REVERT: C 706 LEU cc_start: 0.9505 (mp) cc_final: 0.9290 (mt) REVERT: B 359 GLU cc_start: 0.6938 (tt0) cc_final: 0.6531 (mp0) REVERT: B 401 TYR cc_start: 0.8023 (m-10) cc_final: 0.7340 (m-80) REVERT: B 419 ASN cc_start: 0.9068 (m-40) cc_final: 0.8744 (m-40) REVERT: B 511 TYR cc_start: 0.8195 (t80) cc_final: 0.7844 (t80) REVERT: B 571 LYS cc_start: 0.9094 (mmtm) cc_final: 0.8777 (mmmm) REVERT: B 646 ASP cc_start: 0.9075 (t0) cc_final: 0.8836 (t0) REVERT: B 706 LEU cc_start: 0.9503 (mp) cc_final: 0.9295 (mt) REVERT: D 339 LEU cc_start: 0.8670 (mm) cc_final: 0.8248 (tt) REVERT: D 359 GLU cc_start: 0.6939 (tt0) cc_final: 0.6570 (mp0) REVERT: D 401 TYR cc_start: 0.8177 (m-10) cc_final: 0.7941 (m-80) REVERT: D 419 ASN cc_start: 0.9034 (m-40) cc_final: 0.8731 (m-40) REVERT: D 511 TYR cc_start: 0.8199 (t80) cc_final: 0.7798 (t80) REVERT: D 581 MET cc_start: 0.8347 (mmm) cc_final: 0.8116 (ptt) REVERT: D 636 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8951 (mm-30) REVERT: D 646 ASP cc_start: 0.9092 (t0) cc_final: 0.8859 (t0) REVERT: E 359 GLU cc_start: 0.6920 (tt0) cc_final: 0.6549 (mp0) REVERT: E 401 TYR cc_start: 0.8062 (m-10) cc_final: 0.7838 (m-80) REVERT: E 419 ASN cc_start: 0.9077 (m-40) cc_final: 0.8778 (m-40) REVERT: E 511 TYR cc_start: 0.8207 (t80) cc_final: 0.7819 (t80) REVERT: E 571 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8664 (mmmm) REVERT: E 581 MET cc_start: 0.8380 (mmm) cc_final: 0.8154 (ptt) REVERT: E 646 ASP cc_start: 0.9070 (t0) cc_final: 0.8847 (t0) outliers start: 17 outliers final: 12 residues processed: 270 average time/residue: 0.1052 time to fit residues: 41.8675 Evaluate side-chains 236 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 224 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 442 CYS 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 72 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 143 optimal weight: 0.3980 chunk 111 optimal weight: 0.3980 chunk 155 optimal weight: 50.0000 chunk 114 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 533 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.114356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081757 restraints weight = 27845.619| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.05 r_work: 0.2998 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12080 Z= 0.107 Angle : 0.533 9.339 16404 Z= 0.284 Chirality : 0.041 0.153 1896 Planarity : 0.002 0.020 2024 Dihedral : 12.561 109.895 1788 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.50 % Allowed : 13.76 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.22), residues: 1568 helix: 0.76 (0.17), residues: 1008 sheet: -2.68 (0.66), residues: 56 loop : -2.44 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 474 TYR 0.011 0.001 TYR E 511 PHE 0.010 0.001 PHE E 489 TRP 0.009 0.001 TRP D 697 HIS 0.000 0.000 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00227 (12076) covalent geometry : angle 0.53329 (16404) hydrogen bonds : bond 0.03342 ( 697) hydrogen bonds : angle 3.91549 ( 2055) Misc. bond : bond 0.00109 ( 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 256 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8260 (tt) REVERT: C 359 GLU cc_start: 0.7068 (tt0) cc_final: 0.6631 (mp0) REVERT: C 401 TYR cc_start: 0.7920 (m-10) cc_final: 0.7594 (m-80) REVERT: C 419 ASN cc_start: 0.9093 (m-40) cc_final: 0.8744 (m-40) REVERT: C 581 MET cc_start: 0.8395 (mmm) cc_final: 0.8141 (ptt) REVERT: C 646 ASP cc_start: 0.9016 (t0) cc_final: 0.8765 (t0) REVERT: C 682 MET cc_start: 0.8819 (mtt) cc_final: 0.8517 (mtt) REVERT: B 359 GLU cc_start: 0.7006 (tt0) cc_final: 0.6603 (mp0) REVERT: B 401 TYR cc_start: 0.7957 (m-10) cc_final: 0.7657 (m-80) REVERT: B 419 ASN cc_start: 0.9017 (m-40) cc_final: 0.8675 (m-40) REVERT: B 571 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8708 (mmmm) REVERT: B 572 MET cc_start: 0.8530 (ttm) cc_final: 0.7913 (ttm) REVERT: B 646 ASP cc_start: 0.9016 (t0) cc_final: 0.8761 (t0) REVERT: B 682 MET cc_start: 0.8533 (mtt) cc_final: 0.7464 (mtt) REVERT: D 339 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8095 (tt) REVERT: D 359 GLU cc_start: 0.6978 (tt0) cc_final: 0.6640 (mp0) REVERT: D 419 ASN cc_start: 0.9028 (m-40) cc_final: 0.8704 (m-40) REVERT: D 581 MET cc_start: 0.8336 (mmm) cc_final: 0.8123 (ptt) REVERT: D 636 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8888 (mm-30) REVERT: D 646 ASP cc_start: 0.9047 (t0) cc_final: 0.8799 (t0) REVERT: E 359 GLU cc_start: 0.6897 (tt0) cc_final: 0.6559 (mp0) REVERT: E 401 TYR cc_start: 0.8058 (m-10) cc_final: 0.7837 (m-80) REVERT: E 419 ASN cc_start: 0.9058 (m-40) cc_final: 0.8737 (m-40) REVERT: E 564 ILE cc_start: 0.9023 (mt) cc_final: 0.8735 (mm) REVERT: E 571 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8576 (mmmm) REVERT: E 646 ASP cc_start: 0.9055 (t0) cc_final: 0.8825 (t0) REVERT: E 677 MET cc_start: 0.8321 (tpp) cc_final: 0.7165 (tpp) outliers start: 16 outliers final: 8 residues processed: 250 average time/residue: 0.1068 time to fit residues: 39.6104 Evaluate side-chains 230 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 220 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 339 LEU 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 339 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 573 ILE 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 13 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 75 optimal weight: 0.0370 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 2 optimal weight: 0.0050 chunk 133 optimal weight: 8.9990 overall best weight: 0.5074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.115935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083132 restraints weight = 27816.853| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.06 r_work: 0.3024 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12080 Z= 0.107 Angle : 0.537 9.639 16404 Z= 0.280 Chirality : 0.040 0.159 1896 Planarity : 0.002 0.019 2024 Dihedral : 12.065 105.717 1788 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.69 % Allowed : 14.89 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.22), residues: 1568 helix: 0.99 (0.17), residues: 1008 sheet: -2.58 (0.62), residues: 56 loop : -2.43 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 474 TYR 0.010 0.001 TYR C 565 PHE 0.012 0.001 PHE C 496 TRP 0.007 0.001 TRP E 697 HIS 0.001 0.000 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00228 (12076) covalent geometry : angle 0.53703 (16404) hydrogen bonds : bond 0.03183 ( 697) hydrogen bonds : angle 3.80221 ( 2055) Misc. bond : bond 0.00074 ( 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 282 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8215 (tt) REVERT: C 359 GLU cc_start: 0.7101 (tt0) cc_final: 0.6710 (mp0) REVERT: C 401 TYR cc_start: 0.8085 (m-10) cc_final: 0.7741 (m-80) REVERT: C 419 ASN cc_start: 0.9056 (m-40) cc_final: 0.8785 (m-40) REVERT: C 581 MET cc_start: 0.8363 (mmm) cc_final: 0.8074 (ptt) REVERT: C 646 ASP cc_start: 0.9005 (t0) cc_final: 0.8778 (t0) REVERT: C 682 MET cc_start: 0.8801 (mtt) cc_final: 0.8545 (mtt) REVERT: B 359 GLU cc_start: 0.6824 (tt0) cc_final: 0.6429 (mp0) REVERT: B 401 TYR cc_start: 0.7979 (m-10) cc_final: 0.7611 (m-80) REVERT: B 419 ASN cc_start: 0.8990 (m-40) cc_final: 0.8732 (m-40) REVERT: B 560 GLN cc_start: 0.9121 (tt0) cc_final: 0.8909 (tp-100) REVERT: B 571 LYS cc_start: 0.9016 (mmtm) cc_final: 0.8709 (mmmm) REVERT: B 646 ASP cc_start: 0.9029 (t0) cc_final: 0.8800 (t0) REVERT: D 339 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8045 (tt) REVERT: D 359 GLU cc_start: 0.6911 (tt0) cc_final: 0.6547 (mp0) REVERT: D 419 ASN cc_start: 0.9076 (m-40) cc_final: 0.8813 (m-40) REVERT: D 564 ILE cc_start: 0.9012 (mt) cc_final: 0.8603 (mm) REVERT: D 567 VAL cc_start: 0.9520 (t) cc_final: 0.9262 (p) REVERT: D 581 MET cc_start: 0.8341 (mmm) cc_final: 0.8134 (ptt) REVERT: D 636 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8820 (mm-30) REVERT: D 646 ASP cc_start: 0.9020 (t0) cc_final: 0.8797 (t0) REVERT: D 682 MET cc_start: 0.8415 (mtt) cc_final: 0.8082 (mtt) REVERT: E 359 GLU cc_start: 0.6976 (tt0) cc_final: 0.6690 (mp0) REVERT: E 401 TYR cc_start: 0.8100 (m-10) cc_final: 0.7382 (m-80) REVERT: E 419 ASN cc_start: 0.9029 (m-40) cc_final: 0.8761 (m-40) REVERT: E 564 ILE cc_start: 0.9028 (mt) cc_final: 0.8670 (mm) REVERT: E 567 VAL cc_start: 0.9517 (t) cc_final: 0.9215 (p) REVERT: E 571 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8194 (mmmm) REVERT: E 581 MET cc_start: 0.8493 (mmm) cc_final: 0.8182 (ptt) REVERT: E 646 ASP cc_start: 0.9041 (t0) cc_final: 0.8828 (t0) REVERT: E 677 MET cc_start: 0.8177 (tpp) cc_final: 0.7741 (mpp) outliers start: 18 outliers final: 12 residues processed: 275 average time/residue: 0.0946 time to fit residues: 39.7922 Evaluate side-chains 236 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 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 673 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 573 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 124 optimal weight: 0.0970 chunk 113 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2060 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.115110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082381 restraints weight = 28107.780| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.02 r_work: 0.2993 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12080 Z= 0.129 Angle : 0.599 12.909 16404 Z= 0.302 Chirality : 0.041 0.168 1896 Planarity : 0.003 0.020 2024 Dihedral : 11.916 104.361 1788 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.00 % Allowed : 15.36 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.22), residues: 1568 helix: 1.13 (0.17), residues: 1008 sheet: -2.53 (0.61), residues: 56 loop : -2.36 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 743 TYR 0.010 0.001 TYR C 565 PHE 0.012 0.001 PHE B 496 TRP 0.013 0.001 TRP E 697 HIS 0.001 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00290 (12076) covalent geometry : angle 0.59941 (16404) hydrogen bonds : bond 0.03257 ( 697) hydrogen bonds : angle 3.75306 ( 2055) Misc. bond : bond 0.00080 ( 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 266 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8309 (tt) REVERT: C 359 GLU cc_start: 0.6875 (tt0) cc_final: 0.6622 (mp0) REVERT: C 401 TYR cc_start: 0.8111 (m-10) cc_final: 0.7830 (m-80) REVERT: C 419 ASN cc_start: 0.9053 (m-40) cc_final: 0.8752 (m-40) REVERT: C 493 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9118 (pt) REVERT: C 581 MET cc_start: 0.8390 (mmm) cc_final: 0.8106 (ptt) REVERT: C 646 ASP cc_start: 0.9003 (t0) cc_final: 0.8743 (t0) REVERT: C 709 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8572 (tm-30) REVERT: B 359 GLU cc_start: 0.6760 (tt0) cc_final: 0.6504 (mp0) REVERT: B 401 TYR cc_start: 0.8021 (m-10) cc_final: 0.7737 (m-80) REVERT: B 419 ASN cc_start: 0.9013 (m-40) cc_final: 0.8716 (m-40) REVERT: B 571 LYS cc_start: 0.8945 (mmtm) cc_final: 0.8647 (mmmm) REVERT: B 600 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7469 (mp0) REVERT: B 646 ASP cc_start: 0.9018 (t0) cc_final: 0.8795 (t0) REVERT: D 339 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8128 (tt) REVERT: D 419 ASN cc_start: 0.9112 (m-40) cc_final: 0.8869 (m-40) REVERT: D 493 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9060 (pt) REVERT: D 561 GLN cc_start: 0.7603 (pm20) cc_final: 0.6962 (pt0) REVERT: D 564 ILE cc_start: 0.9053 (mt) cc_final: 0.8715 (mm) REVERT: D 567 VAL cc_start: 0.9536 (t) cc_final: 0.9244 (p) REVERT: D 636 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8833 (mm-30) REVERT: D 646 ASP cc_start: 0.9006 (t0) cc_final: 0.8786 (t0) REVERT: E 419 ASN cc_start: 0.9090 (m-40) cc_final: 0.8774 (m-40) REVERT: E 499 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6859 (mtm-85) REVERT: E 561 GLN cc_start: 0.7563 (pm20) cc_final: 0.6966 (pt0) REVERT: E 564 ILE cc_start: 0.9090 (mt) cc_final: 0.8717 (mm) REVERT: E 567 VAL cc_start: 0.9559 (t) cc_final: 0.9261 (p) REVERT: E 571 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8305 (mmmt) REVERT: E 581 MET cc_start: 0.8488 (mmm) cc_final: 0.8163 (ptt) REVERT: E 646 ASP cc_start: 0.9042 (t0) cc_final: 0.8823 (t0) outliers start: 32 outliers final: 22 residues processed: 255 average time/residue: 0.0983 time to fit residues: 38.6758 Evaluate side-chains 245 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 493 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 686 VAL 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 D residue 339 LEU 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 493 ILE 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 686 VAL 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 499 ARG Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 573 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 129 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 139 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 116 optimal weight: 30.0000 chunk 93 optimal weight: 0.7980 chunk 38 optimal weight: 40.0000 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.114822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083129 restraints weight = 27869.619| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.12 r_work: 0.2977 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12080 Z= 0.132 Angle : 0.603 11.643 16404 Z= 0.304 Chirality : 0.041 0.176 1896 Planarity : 0.002 0.020 2024 Dihedral : 11.807 103.370 1788 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.09 % Allowed : 15.26 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.23), residues: 1568 helix: 1.14 (0.17), residues: 1012 sheet: -2.61 (0.60), residues: 56 loop : -2.31 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 579 TYR 0.011 0.001 TYR C 565 PHE 0.010 0.001 PHE E 448 TRP 0.014 0.001 TRP C 697 HIS 0.001 0.000 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00303 (12076) covalent geometry : angle 0.60327 (16404) hydrogen bonds : bond 0.03215 ( 697) hydrogen bonds : angle 3.73349 ( 2055) Misc. bond : bond 0.00077 ( 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 268 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8373 (tt) REVERT: C 359 GLU cc_start: 0.6874 (tt0) cc_final: 0.6648 (mp0) REVERT: C 401 TYR cc_start: 0.8229 (m-10) cc_final: 0.7982 (m-80) REVERT: C 419 ASN cc_start: 0.9114 (m-40) cc_final: 0.8844 (m-40) REVERT: C 423 GLN cc_start: 0.9109 (tp40) cc_final: 0.8831 (tp-100) REVERT: C 493 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9145 (pt) REVERT: C 581 MET cc_start: 0.8414 (mmm) cc_final: 0.8092 (ptt) REVERT: C 646 ASP cc_start: 0.8995 (t0) cc_final: 0.8766 (t0) REVERT: C 709 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8655 (tm-30) REVERT: B 359 GLU cc_start: 0.6778 (tt0) cc_final: 0.6520 (mp0) REVERT: B 401 TYR cc_start: 0.8061 (m-10) cc_final: 0.7741 (m-80) REVERT: B 419 ASN cc_start: 0.9112 (m-40) cc_final: 0.8912 (m-40) REVERT: B 571 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8599 (mmmm) REVERT: B 600 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7435 (mp0) REVERT: B 646 ASP cc_start: 0.9027 (t0) cc_final: 0.8776 (t0) REVERT: B 691 GLN cc_start: 0.8533 (pm20) cc_final: 0.8293 (mp10) REVERT: D 339 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8205 (tt) REVERT: D 419 ASN cc_start: 0.9127 (m-40) cc_final: 0.8891 (m-40) REVERT: D 493 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9102 (pt) REVERT: D 564 ILE cc_start: 0.9068 (mt) cc_final: 0.8647 (mm) REVERT: D 567 VAL cc_start: 0.9530 (t) cc_final: 0.9222 (p) REVERT: D 581 MET cc_start: 0.8472 (mmm) cc_final: 0.8132 (ptt) REVERT: D 636 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8864 (mm-30) REVERT: D 646 ASP cc_start: 0.9015 (t0) cc_final: 0.8782 (t0) REVERT: E 401 TYR cc_start: 0.8140 (m-80) cc_final: 0.7710 (m-80) REVERT: E 561 GLN cc_start: 0.7496 (pm20) cc_final: 0.6876 (pt0) REVERT: E 564 ILE cc_start: 0.9096 (mt) cc_final: 0.8680 (mm) REVERT: E 567 VAL cc_start: 0.9514 (t) cc_final: 0.9135 (p) REVERT: E 571 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8428 (mmmm) REVERT: E 581 MET cc_start: 0.8528 (mmm) cc_final: 0.8181 (ptt) REVERT: E 646 ASP cc_start: 0.8980 (t0) cc_final: 0.8772 (t0) outliers start: 33 outliers final: 27 residues processed: 258 average time/residue: 0.0879 time to fit residues: 35.8114 Evaluate side-chains 258 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 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 B residue 686 VAL Chi-restraints excluded: chain D residue 339 LEU 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 493 ILE 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 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 Chi-restraints excluded: chain E residue 670 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 94 optimal weight: 0.0170 chunk 95 optimal weight: 7.9990 chunk 65 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 142 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.118823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085424 restraints weight = 27936.246| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.10 r_work: 0.3050 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12080 Z= 0.110 Angle : 0.588 14.426 16404 Z= 0.297 Chirality : 0.040 0.142 1896 Planarity : 0.002 0.023 2024 Dihedral : 11.407 99.500 1788 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.34 % Allowed : 15.64 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.22), residues: 1568 helix: 1.21 (0.17), residues: 1008 sheet: -2.52 (0.58), residues: 56 loop : -2.20 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 743 TYR 0.013 0.001 TYR C 511 PHE 0.010 0.001 PHE B 496 TRP 0.006 0.001 TRP C 697 HIS 0.000 0.000 HIS E 410 Details of bonding type rmsd covalent geometry : bond 0.00244 (12076) covalent geometry : angle 0.58767 (16404) hydrogen bonds : bond 0.03063 ( 697) hydrogen bonds : angle 3.67650 ( 2055) Misc. bond : bond 0.00031 ( 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 286 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8202 (tt) REVERT: C 359 GLU cc_start: 0.7027 (tt0) cc_final: 0.6799 (mp0) REVERT: C 401 TYR cc_start: 0.8234 (m-10) cc_final: 0.7943 (m-80) REVERT: C 419 ASN cc_start: 0.9128 (m-40) cc_final: 0.8917 (m-40) REVERT: C 423 GLN cc_start: 0.9063 (tp40) cc_final: 0.8751 (tp-100) REVERT: C 493 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9145 (pt) REVERT: C 709 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8570 (tm-30) REVERT: B 359 GLU cc_start: 0.6691 (tt0) cc_final: 0.6328 (mp0) REVERT: B 401 TYR cc_start: 0.8177 (m-10) cc_final: 0.7827 (m-80) REVERT: B 419 ASN cc_start: 0.9075 (m-40) cc_final: 0.8860 (m-40) REVERT: B 493 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9136 (pt) REVERT: B 535 LYS cc_start: 0.9286 (tppt) cc_final: 0.9083 (tppt) REVERT: B 571 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8369 (mmmm) REVERT: B 691 GLN cc_start: 0.8505 (pm20) cc_final: 0.8265 (mp10) REVERT: D 339 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8068 (tt) REVERT: D 419 ASN cc_start: 0.9105 (m-40) cc_final: 0.8881 (m-40) REVERT: D 493 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9106 (pt) REVERT: D 564 ILE cc_start: 0.9027 (mt) cc_final: 0.8664 (mm) REVERT: D 567 VAL cc_start: 0.9543 (t) cc_final: 0.9220 (p) REVERT: D 581 MET cc_start: 0.8485 (mmm) cc_final: 0.8211 (ptt) REVERT: D 636 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8781 (mm-30) REVERT: E 419 ASN cc_start: 0.8815 (m-40) cc_final: 0.8281 (m-40) REVERT: E 493 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9111 (pt) REVERT: E 511 TYR cc_start: 0.8184 (t80) cc_final: 0.7957 (t80) REVERT: E 564 ILE cc_start: 0.9004 (mt) cc_final: 0.8683 (mm) REVERT: E 567 VAL cc_start: 0.9548 (t) cc_final: 0.9204 (p) REVERT: E 571 LYS cc_start: 0.8670 (mmtm) cc_final: 0.8349 (mmmm) REVERT: E 581 MET cc_start: 0.8475 (mmm) cc_final: 0.8219 (ptt) outliers start: 25 outliers final: 14 residues processed: 276 average time/residue: 0.0888 time to fit residues: 38.5426 Evaluate side-chains 262 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 493 ILE Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 493 ILE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 153 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 133 optimal weight: 0.4980 chunk 120 optimal weight: 0.0970 chunk 81 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.116844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083238 restraints weight = 27684.042| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.03 r_work: 0.3004 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4992 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= 0.141 Angle : 0.668 14.860 16404 Z= 0.328 Chirality : 0.042 0.158 1896 Planarity : 0.002 0.024 2024 Dihedral : 11.369 99.441 1788 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.34 % Allowed : 18.07 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.22), residues: 1568 helix: 1.23 (0.17), residues: 1008 sheet: -2.64 (0.55), residues: 56 loop : -2.14 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 575 TYR 0.020 0.001 TYR D 511 PHE 0.010 0.001 PHE D 448 TRP 0.015 0.001 TRP B 697 HIS 0.001 0.000 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00326 (12076) covalent geometry : angle 0.66802 (16404) hydrogen bonds : bond 0.03267 ( 697) hydrogen bonds : angle 3.72238 ( 2055) Misc. bond : bond 0.00055 ( 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 267 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.545 Fit side-chains REVERT: C 359 GLU cc_start: 0.7034 (tt0) cc_final: 0.6803 (mp0) REVERT: C 401 TYR cc_start: 0.8229 (m-10) cc_final: 0.8009 (m-80) REVERT: C 419 ASN cc_start: 0.9151 (m-40) cc_final: 0.8867 (m-40) REVERT: C 423 GLN cc_start: 0.9094 (tp40) cc_final: 0.8810 (tp-100) REVERT: C 523 MET cc_start: 0.9153 (tpt) cc_final: 0.8933 (mmm) REVERT: C 540 SER cc_start: 0.9443 (m) cc_final: 0.9209 (p) REVERT: C 709 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8617 (tm-30) REVERT: B 359 GLU cc_start: 0.6896 (tt0) cc_final: 0.6525 (mp0) REVERT: B 401 TYR cc_start: 0.8241 (m-10) cc_final: 0.7958 (m-80) REVERT: B 419 ASN cc_start: 0.9145 (m-40) cc_final: 0.8939 (m-40) REVERT: B 493 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9170 (pt) REVERT: B 511 TYR cc_start: 0.8280 (t80) cc_final: 0.8001 (t80) REVERT: B 567 VAL cc_start: 0.9531 (t) cc_final: 0.9286 (p) REVERT: B 571 LYS cc_start: 0.8482 (mmtm) cc_final: 0.8157 (mmmt) REVERT: B 677 MET cc_start: 0.8743 (tpp) cc_final: 0.8482 (tpp) REVERT: B 691 GLN cc_start: 0.8570 (pm20) cc_final: 0.8301 (mp10) REVERT: D 339 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8139 (tt) REVERT: D 419 ASN cc_start: 0.9145 (m-40) cc_final: 0.8870 (m-40) REVERT: D 511 TYR cc_start: 0.8218 (t80) cc_final: 0.7938 (t80) REVERT: D 540 SER cc_start: 0.9452 (m) cc_final: 0.9200 (p) REVERT: D 564 ILE cc_start: 0.9029 (mt) cc_final: 0.8686 (mm) REVERT: D 567 VAL cc_start: 0.9548 (t) cc_final: 0.9180 (p) REVERT: D 581 MET cc_start: 0.8460 (mmm) cc_final: 0.8220 (ptt) REVERT: D 636 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8810 (mm-30) REVERT: E 419 ASN cc_start: 0.8917 (m-40) cc_final: 0.8704 (m-40) REVERT: E 493 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9124 (pt) REVERT: E 564 ILE cc_start: 0.9028 (mt) cc_final: 0.8706 (mm) REVERT: E 567 VAL cc_start: 0.9555 (t) cc_final: 0.9256 (p) REVERT: E 571 LYS cc_start: 0.8551 (mmtm) cc_final: 0.8188 (mmmm) REVERT: E 581 MET cc_start: 0.8425 (mmm) cc_final: 0.8211 (ptt) outliers start: 25 outliers final: 21 residues processed: 258 average time/residue: 0.0931 time to fit residues: 37.6214 Evaluate side-chains 257 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 686 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 493 ILE 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 339 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 140 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 15 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.118381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.088573 restraints weight = 27877.861| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.14 r_work: 0.3041 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12080 Z= 0.121 Angle : 0.652 14.136 16404 Z= 0.322 Chirality : 0.041 0.148 1896 Planarity : 0.003 0.023 2024 Dihedral : 11.131 96.610 1788 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.06 % Allowed : 17.32 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.22), residues: 1568 helix: 1.24 (0.17), residues: 1008 sheet: -2.66 (0.53), residues: 56 loop : -2.08 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 743 TYR 0.021 0.001 TYR C 511 PHE 0.010 0.001 PHE B 496 TRP 0.013 0.001 TRP B 697 HIS 0.001 0.000 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00272 (12076) covalent geometry : angle 0.65183 (16404) hydrogen bonds : bond 0.03203 ( 697) hydrogen bonds : angle 3.75269 ( 2055) Misc. bond : bond 0.00026 ( 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 266 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: C 339 LEU cc_start: 0.8802 (mm) cc_final: 0.8359 (tt) REVERT: C 359 GLU cc_start: 0.7112 (tt0) cc_final: 0.6756 (mp0) REVERT: C 401 TYR cc_start: 0.8224 (m-10) cc_final: 0.7995 (m-80) REVERT: C 419 ASN cc_start: 0.9194 (m-40) cc_final: 0.8903 (m-40) REVERT: C 423 GLN cc_start: 0.9073 (tp40) cc_final: 0.8770 (tp-100) REVERT: C 540 SER cc_start: 0.9456 (m) cc_final: 0.9239 (p) REVERT: C 673 LEU cc_start: 0.9094 (mt) cc_final: 0.8872 (tt) REVERT: C 709 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8687 (tm-30) REVERT: B 359 GLU cc_start: 0.7020 (tt0) cc_final: 0.6670 (mp0) REVERT: B 401 TYR cc_start: 0.8177 (m-10) cc_final: 0.7848 (m-80) REVERT: B 493 ILE cc_start: 0.9528 (OUTLIER) cc_final: 0.9144 (pt) REVERT: B 567 VAL cc_start: 0.9525 (t) cc_final: 0.9251 (p) REVERT: B 571 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8190 (mmmm) REVERT: B 677 MET cc_start: 0.8748 (tpp) cc_final: 0.8493 (tpp) REVERT: B 691 GLN cc_start: 0.8557 (pm20) cc_final: 0.8273 (mp10) REVERT: D 339 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8123 (tt) REVERT: D 419 ASN cc_start: 0.9172 (m-40) cc_final: 0.8883 (m-40) REVERT: D 511 TYR cc_start: 0.8267 (t80) cc_final: 0.8006 (t80) REVERT: D 540 SER cc_start: 0.9474 (m) cc_final: 0.9237 (p) REVERT: D 564 ILE cc_start: 0.9003 (mt) cc_final: 0.8662 (mm) REVERT: D 567 VAL cc_start: 0.9523 (t) cc_final: 0.9147 (p) REVERT: D 581 MET cc_start: 0.8449 (mmm) cc_final: 0.8196 (ptt) REVERT: D 636 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8821 (mm-30) REVERT: E 419 ASN cc_start: 0.8887 (m-40) cc_final: 0.8650 (m-40) REVERT: E 493 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9123 (pt) REVERT: E 511 TYR cc_start: 0.8280 (t80) cc_final: 0.8035 (t80) REVERT: E 564 ILE cc_start: 0.9019 (mt) cc_final: 0.8657 (mm) REVERT: E 567 VAL cc_start: 0.9541 (t) cc_final: 0.9230 (p) REVERT: E 571 LYS cc_start: 0.8344 (mmtm) cc_final: 0.7931 (mmmm) REVERT: E 581 MET cc_start: 0.8410 (mmm) cc_final: 0.8193 (ptt) outliers start: 22 outliers final: 19 residues processed: 259 average time/residue: 0.0878 time to fit residues: 35.8872 Evaluate side-chains 256 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 670 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain B residue 493 ILE 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 339 LEU Chi-restraints excluded: chain D residue 349 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 76 optimal weight: 50.0000 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.088777 restraints weight = 27621.420| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.07 r_work: 0.3037 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12080 Z= 0.131 Angle : 0.676 14.196 16404 Z= 0.331 Chirality : 0.041 0.150 1896 Planarity : 0.002 0.020 2024 Dihedral : 10.991 96.263 1788 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.34 % Allowed : 17.79 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.22), residues: 1568 helix: 1.42 (0.17), residues: 988 sheet: -2.68 (0.52), residues: 56 loop : -1.79 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 743 TYR 0.018 0.001 TYR D 511 PHE 0.009 0.001 PHE C 496 TRP 0.009 0.001 TRP B 697 HIS 0.001 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00300 (12076) covalent geometry : angle 0.67592 (16404) hydrogen bonds : bond 0.03215 ( 697) hydrogen bonds : angle 3.76572 ( 2055) Misc. bond : bond 0.00028 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2964.61 seconds wall clock time: 51 minutes 40.09 seconds (3100.09 seconds total)