Starting phenix.real_space_refine on Fri Jan 24 01:24:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flv_50540/01_2025/9flv_50540.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flv_50540/01_2025/9flv_50540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9flv_50540/01_2025/9flv_50540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flv_50540/01_2025/9flv_50540.map" model { file = "/net/cci-nas-00/data/ceres_data/9flv_50540/01_2025/9flv_50540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flv_50540/01_2025/9flv_50540.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 12852 2.51 5 N 3416 2.21 5 O 4452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 20818 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2974 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Chain: "B" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2974 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Chain: "C" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2974 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Chain: "D" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2974 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Chain: "E" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2974 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Chain: "F" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2974 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2974 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Time building chain proxies: 11.89, per 1000 atoms: 0.57 Number of scatterers: 20818 At special positions: 0 Unit cell: (94.785, 95.85, 222.585, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 4452 8.00 N 3416 7.00 C 12852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A2490 " - pdb=" SG CYS A2629 " distance=2.04 Simple disulfide: pdb=" SG CYS A2656 " - pdb=" SG CYS A2796 " distance=2.03 Simple disulfide: pdb=" SG CYS B2490 " - pdb=" SG CYS B2629 " distance=2.04 Simple disulfide: pdb=" SG CYS B2656 " - pdb=" SG CYS B2796 " distance=2.03 Simple disulfide: pdb=" SG CYS C2490 " - pdb=" SG CYS C2629 " distance=2.04 Simple disulfide: pdb=" SG CYS C2656 " - pdb=" SG CYS C2796 " distance=2.03 Simple disulfide: pdb=" SG CYS D2490 " - pdb=" SG CYS D2629 " distance=2.04 Simple disulfide: pdb=" SG CYS D2656 " - pdb=" SG CYS D2796 " distance=2.03 Simple disulfide: pdb=" SG CYS E2490 " - pdb=" SG CYS E2629 " distance=2.04 Simple disulfide: pdb=" SG CYS E2656 " - pdb=" SG CYS E2796 " distance=2.03 Simple disulfide: pdb=" SG CYS F2490 " - pdb=" SG CYS F2629 " distance=2.04 Simple disulfide: pdb=" SG CYS F2656 " - pdb=" SG CYS F2796 " distance=2.03 Simple disulfide: pdb=" SG CYS G2490 " - pdb=" SG CYS G2629 " distance=2.04 Simple disulfide: pdb=" SG CYS G2656 " - pdb=" SG CYS G2796 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.59 Conformation dependent library (CDL) restraints added in 3.1 seconds 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5432 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 70 sheets defined 3.1% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 2446 through 2450 Processing helix chain 'A' and resid 2677 through 2679 No H-bonds generated for 'chain 'A' and resid 2677 through 2679' Processing helix chain 'A' and resid 2694 through 2698 Processing helix chain 'B' and resid 2446 through 2450 Processing helix chain 'B' and resid 2677 through 2679 No H-bonds generated for 'chain 'B' and resid 2677 through 2679' Processing helix chain 'B' and resid 2694 through 2698 Processing helix chain 'C' and resid 2446 through 2450 Processing helix chain 'C' and resid 2677 through 2679 No H-bonds generated for 'chain 'C' and resid 2677 through 2679' Processing helix chain 'C' and resid 2694 through 2698 Processing helix chain 'D' and resid 2446 through 2450 Processing helix chain 'D' and resid 2677 through 2679 No H-bonds generated for 'chain 'D' and resid 2677 through 2679' Processing helix chain 'D' and resid 2694 through 2698 Processing helix chain 'E' and resid 2446 through 2450 Processing helix chain 'E' and resid 2677 through 2679 No H-bonds generated for 'chain 'E' and resid 2677 through 2679' Processing helix chain 'E' and resid 2694 through 2698 Processing helix chain 'F' and resid 2446 through 2450 Processing helix chain 'F' and resid 2677 through 2679 No H-bonds generated for 'chain 'F' and resid 2677 through 2679' Processing helix chain 'F' and resid 2694 through 2698 Processing helix chain 'G' and resid 2446 through 2450 Processing helix chain 'G' and resid 2677 through 2679 No H-bonds generated for 'chain 'G' and resid 2677 through 2679' Processing helix chain 'G' and resid 2694 through 2698 Processing sheet with id=AA1, first strand: chain 'A' and resid 2405 through 2408 removed outlier: 6.677A pdb=" N PHE A2405 " --> pdb=" O THR A2473 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASN A2475 " --> pdb=" O PHE A2405 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A2407 " --> pdb=" O ASN A2475 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2483 through 2485 Processing sheet with id=AA3, first strand: chain 'A' and resid 2488 through 2490 removed outlier: 6.855A pdb=" N ILE A2489 " --> pdb=" O ASN A2560 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2567 through 2568 Processing sheet with id=AA5, first strand: chain 'A' and resid 2579 through 2580 Processing sheet with id=AA6, first strand: chain 'A' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP A2593 " --> pdb=" O ILE A2603 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP A2593 " --> pdb=" O ILE A2603 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2653 through 2656 removed outlier: 6.799A pdb=" N PHE A2653 " --> pdb=" O GLY A2721 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASN A2723 " --> pdb=" O PHE A2653 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A2655 " --> pdb=" O ASN A2723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2731 through 2732 Processing sheet with id=AB1, first strand: chain 'A' and resid 2763 through 2766 removed outlier: 4.856A pdb=" N THR A2753 " --> pdb=" O GLN A2791 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A2791 " --> pdb=" O THR A2753 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2405 through 2408 removed outlier: 6.677A pdb=" N PHE B2405 " --> pdb=" O THR B2473 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASN B2475 " --> pdb=" O PHE B2405 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B2407 " --> pdb=" O ASN B2475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2483 through 2485 Processing sheet with id=AB4, first strand: chain 'B' and resid 2488 through 2490 removed outlier: 6.855A pdb=" N ILE B2489 " --> pdb=" O ASN B2560 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 2567 through 2568 Processing sheet with id=AB6, first strand: chain 'B' and resid 2579 through 2580 Processing sheet with id=AB7, first strand: chain 'B' and resid 2602 through 2604 removed outlier: 6.809A pdb=" N TRP B2593 " --> pdb=" O ILE B2603 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 2602 through 2604 removed outlier: 6.809A pdb=" N TRP B2593 " --> pdb=" O ILE B2603 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 2653 through 2656 removed outlier: 6.800A pdb=" N PHE B2653 " --> pdb=" O GLY B2721 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASN B2723 " --> pdb=" O PHE B2653 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B2655 " --> pdb=" O ASN B2723 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 2731 through 2732 Processing sheet with id=AC2, first strand: chain 'B' and resid 2763 through 2766 removed outlier: 4.856A pdb=" N THR B2753 " --> pdb=" O GLN B2791 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B2791 " --> pdb=" O THR B2753 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 2405 through 2408 removed outlier: 6.676A pdb=" N PHE C2405 " --> pdb=" O THR C2473 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASN C2475 " --> pdb=" O PHE C2405 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C2407 " --> pdb=" O ASN C2475 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 2483 through 2485 Processing sheet with id=AC5, first strand: chain 'C' and resid 2488 through 2490 removed outlier: 6.855A pdb=" N ILE C2489 " --> pdb=" O ASN C2560 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 2567 through 2568 Processing sheet with id=AC7, first strand: chain 'C' and resid 2579 through 2580 Processing sheet with id=AC8, first strand: chain 'C' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP C2593 " --> pdb=" O ILE C2603 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP C2593 " --> pdb=" O ILE C2603 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 2653 through 2656 removed outlier: 6.799A pdb=" N PHE C2653 " --> pdb=" O GLY C2721 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASN C2723 " --> pdb=" O PHE C2653 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C2655 " --> pdb=" O ASN C2723 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 2731 through 2732 Processing sheet with id=AD3, first strand: chain 'C' and resid 2763 through 2766 removed outlier: 4.856A pdb=" N THR C2753 " --> pdb=" O GLN C2791 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C2791 " --> pdb=" O THR C2753 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 2405 through 2408 removed outlier: 6.677A pdb=" N PHE D2405 " --> pdb=" O THR D2473 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ASN D2475 " --> pdb=" O PHE D2405 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL D2407 " --> pdb=" O ASN D2475 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 2483 through 2485 Processing sheet with id=AD6, first strand: chain 'D' and resid 2488 through 2490 removed outlier: 6.855A pdb=" N ILE D2489 " --> pdb=" O ASN D2560 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 2567 through 2568 Processing sheet with id=AD8, first strand: chain 'D' and resid 2579 through 2580 Processing sheet with id=AD9, first strand: chain 'D' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP D2593 " --> pdb=" O ILE D2603 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP D2593 " --> pdb=" O ILE D2603 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 2653 through 2656 removed outlier: 6.800A pdb=" N PHE D2653 " --> pdb=" O GLY D2721 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASN D2723 " --> pdb=" O PHE D2653 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D2655 " --> pdb=" O ASN D2723 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 2731 through 2732 Processing sheet with id=AE4, first strand: chain 'D' and resid 2763 through 2766 removed outlier: 4.856A pdb=" N THR D2753 " --> pdb=" O GLN D2791 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN D2791 " --> pdb=" O THR D2753 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 2405 through 2408 removed outlier: 6.677A pdb=" N PHE E2405 " --> pdb=" O THR E2473 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASN E2475 " --> pdb=" O PHE E2405 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL E2407 " --> pdb=" O ASN E2475 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 2483 through 2485 Processing sheet with id=AE7, first strand: chain 'E' and resid 2488 through 2490 removed outlier: 6.855A pdb=" N ILE E2489 " --> pdb=" O ASN E2560 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 2567 through 2568 Processing sheet with id=AE9, first strand: chain 'E' and resid 2579 through 2580 Processing sheet with id=AF1, first strand: chain 'E' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP E2593 " --> pdb=" O ILE E2603 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP E2593 " --> pdb=" O ILE E2603 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 2653 through 2656 removed outlier: 6.799A pdb=" N PHE E2653 " --> pdb=" O GLY E2721 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASN E2723 " --> pdb=" O PHE E2653 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL E2655 " --> pdb=" O ASN E2723 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 2731 through 2732 Processing sheet with id=AF5, first strand: chain 'E' and resid 2763 through 2766 removed outlier: 4.855A pdb=" N THR E2753 " --> pdb=" O GLN E2791 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN E2791 " --> pdb=" O THR E2753 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 2405 through 2408 removed outlier: 6.677A pdb=" N PHE F2405 " --> pdb=" O THR F2473 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASN F2475 " --> pdb=" O PHE F2405 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL F2407 " --> pdb=" O ASN F2475 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 2483 through 2485 Processing sheet with id=AF8, first strand: chain 'F' and resid 2488 through 2490 removed outlier: 6.855A pdb=" N ILE F2489 " --> pdb=" O ASN F2560 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 2567 through 2568 Processing sheet with id=AG1, first strand: chain 'F' and resid 2579 through 2580 Processing sheet with id=AG2, first strand: chain 'F' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP F2593 " --> pdb=" O ILE F2603 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP F2593 " --> pdb=" O ILE F2603 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 2653 through 2656 removed outlier: 6.800A pdb=" N PHE F2653 " --> pdb=" O GLY F2721 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASN F2723 " --> pdb=" O PHE F2653 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL F2655 " --> pdb=" O ASN F2723 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 2731 through 2732 Processing sheet with id=AG6, first strand: chain 'F' and resid 2763 through 2766 removed outlier: 4.857A pdb=" N THR F2753 " --> pdb=" O GLN F2791 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN F2791 " --> pdb=" O THR F2753 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 2405 through 2408 removed outlier: 6.677A pdb=" N PHE G2405 " --> pdb=" O THR G2473 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASN G2475 " --> pdb=" O PHE G2405 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL G2407 " --> pdb=" O ASN G2475 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 2483 through 2485 Processing sheet with id=AG9, first strand: chain 'G' and resid 2488 through 2490 removed outlier: 6.854A pdb=" N ILE G2489 " --> pdb=" O ASN G2560 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 2567 through 2568 Processing sheet with id=AH2, first strand: chain 'G' and resid 2579 through 2580 Processing sheet with id=AH3, first strand: chain 'G' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP G2593 " --> pdb=" O ILE G2603 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 2602 through 2604 removed outlier: 6.808A pdb=" N TRP G2593 " --> pdb=" O ILE G2603 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 2653 through 2656 removed outlier: 6.799A pdb=" N PHE G2653 " --> pdb=" O GLY G2721 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASN G2723 " --> pdb=" O PHE G2653 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL G2655 " --> pdb=" O ASN G2723 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 2731 through 2732 Processing sheet with id=AH7, first strand: chain 'G' and resid 2763 through 2766 removed outlier: 4.856A pdb=" N THR G2753 " --> pdb=" O GLN G2791 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN G2791 " --> pdb=" O THR G2753 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1512 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: 8.75 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3749 1.30 - 1.43: 5301 1.43 - 1.56: 12017 1.56 - 1.69: 73 1.69 - 1.82: 126 Bond restraints: 21266 Sorted by residual: bond pdb=" CA SER C2434 " pdb=" CB SER C2434 " ideal model delta sigma weight residual 1.532 1.441 0.092 1.68e-02 3.54e+03 2.98e+01 bond pdb=" CA SER D2434 " pdb=" CB SER D2434 " ideal model delta sigma weight residual 1.532 1.441 0.092 1.68e-02 3.54e+03 2.97e+01 bond pdb=" CA SER A2434 " pdb=" CB SER A2434 " ideal model delta sigma weight residual 1.532 1.441 0.092 1.68e-02 3.54e+03 2.97e+01 bond pdb=" CA SER F2434 " pdb=" CB SER F2434 " ideal model delta sigma weight residual 1.532 1.441 0.092 1.68e-02 3.54e+03 2.97e+01 bond pdb=" CA SER G2434 " pdb=" CB SER G2434 " ideal model delta sigma weight residual 1.532 1.441 0.091 1.68e-02 3.54e+03 2.96e+01 ... (remaining 21261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 25216 2.44 - 4.89: 3284 4.89 - 7.33: 802 7.33 - 9.78: 126 9.78 - 12.22: 35 Bond angle restraints: 29463 Sorted by residual: angle pdb=" CA PHE B2405 " pdb=" CB PHE B2405 " pdb=" CG PHE B2405 " ideal model delta sigma weight residual 113.80 122.73 -8.93 1.00e+00 1.00e+00 7.98e+01 angle pdb=" CA PHE D2405 " pdb=" CB PHE D2405 " pdb=" CG PHE D2405 " ideal model delta sigma weight residual 113.80 122.72 -8.92 1.00e+00 1.00e+00 7.96e+01 angle pdb=" CA PHE G2405 " pdb=" CB PHE G2405 " pdb=" CG PHE G2405 " ideal model delta sigma weight residual 113.80 122.72 -8.92 1.00e+00 1.00e+00 7.96e+01 angle pdb=" CA PHE A2405 " pdb=" CB PHE A2405 " pdb=" CG PHE A2405 " ideal model delta sigma weight residual 113.80 122.71 -8.91 1.00e+00 1.00e+00 7.94e+01 angle pdb=" CA PHE E2405 " pdb=" CB PHE E2405 " pdb=" CG PHE E2405 " ideal model delta sigma weight residual 113.80 122.70 -8.90 1.00e+00 1.00e+00 7.92e+01 ... (remaining 29458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 12278 17.85 - 35.70: 224 35.70 - 53.55: 77 53.55 - 71.40: 0 71.40 - 89.25: 14 Dihedral angle restraints: 12593 sinusoidal: 4179 harmonic: 8414 Sorted by residual: dihedral pdb=" CB CYS F2656 " pdb=" SG CYS F2656 " pdb=" SG CYS F2796 " pdb=" CB CYS F2796 " ideal model delta sinusoidal sigma weight residual 93.00 145.51 -52.51 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CB CYS C2656 " pdb=" SG CYS C2656 " pdb=" SG CYS C2796 " pdb=" CB CYS C2796 " ideal model delta sinusoidal sigma weight residual 93.00 145.49 -52.49 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS B2656 " pdb=" SG CYS B2656 " pdb=" SG CYS B2796 " pdb=" CB CYS B2796 " ideal model delta sinusoidal sigma weight residual 93.00 145.49 -52.49 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 12590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2631 0.084 - 0.168: 785 0.168 - 0.253: 203 0.253 - 0.337: 63 0.337 - 0.421: 21 Chirality restraints: 3703 Sorted by residual: chirality pdb=" CB VAL E2807 " pdb=" CA VAL E2807 " pdb=" CG1 VAL E2807 " pdb=" CG2 VAL E2807 " both_signs ideal model delta sigma weight residual False -2.63 -3.05 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB VAL A2807 " pdb=" CA VAL A2807 " pdb=" CG1 VAL A2807 " pdb=" CG2 VAL A2807 " both_signs ideal model delta sigma weight residual False -2.63 -3.05 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CB VAL B2807 " pdb=" CA VAL B2807 " pdb=" CG1 VAL B2807 " pdb=" CG2 VAL B2807 " both_signs ideal model delta sigma weight residual False -2.63 -3.05 0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 3700 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C2753 " -0.028 2.00e-02 2.50e+03 5.57e-02 3.10e+01 pdb=" C THR C2753 " 0.096 2.00e-02 2.50e+03 pdb=" O THR C2753 " -0.036 2.00e-02 2.50e+03 pdb=" N PHE C2754 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B2753 " -0.028 2.00e-02 2.50e+03 5.56e-02 3.10e+01 pdb=" C THR B2753 " 0.096 2.00e-02 2.50e+03 pdb=" O THR B2753 " -0.036 2.00e-02 2.50e+03 pdb=" N PHE B2754 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F2753 " 0.028 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C THR F2753 " -0.096 2.00e-02 2.50e+03 pdb=" O THR F2753 " 0.036 2.00e-02 2.50e+03 pdb=" N PHE F2754 " 0.032 2.00e-02 2.50e+03 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 14 1.94 - 2.68: 1057 2.68 - 3.42: 27815 3.42 - 4.16: 51739 4.16 - 4.90: 84631 Nonbonded interactions: 165256 Sorted by model distance: nonbonded pdb=" NH2 ARG B2755 " pdb=" OD2 ASP B2763 " model vdw 1.202 3.120 nonbonded pdb=" NH2 ARG F2755 " pdb=" OD2 ASP F2763 " model vdw 1.202 3.120 nonbonded pdb=" NH2 ARG A2755 " pdb=" OD2 ASP A2763 " model vdw 1.203 3.120 nonbonded pdb=" NH2 ARG D2755 " pdb=" OD2 ASP D2763 " model vdw 1.203 3.120 nonbonded pdb=" NH2 ARG E2755 " pdb=" OD2 ASP E2763 " model vdw 1.203 3.120 ... (remaining 165251 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 49.880 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.018 0.120 21266 Z= 1.204 Angle : 1.887 12.220 29463 Z= 1.304 Chirality : 0.095 0.421 3703 Planarity : 0.013 0.221 3864 Dihedral : 8.987 89.246 7119 Min Nonbonded Distance : 1.202 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.14), residues: 2891 helix: None (None), residues: 0 sheet: 1.67 (0.15), residues: 980 loop : 0.50 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.010 TRP B2674 HIS 0.006 0.004 HIS F2641 PHE 0.039 0.010 PHE F2405 TYR 0.082 0.010 TYR B2393 ARG 0.003 0.001 ARG F2755 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2412 ASP cc_start: 0.7969 (m-30) cc_final: 0.7714 (m-30) REVERT: A 2608 ASN cc_start: 0.8887 (m110) cc_final: 0.8290 (m-40) REVERT: A 2610 THR cc_start: 0.8817 (m) cc_final: 0.8589 (p) REVERT: A 2634 VAL cc_start: 0.8399 (t) cc_final: 0.8083 (m) REVERT: A 2772 MET cc_start: 0.6756 (ttm) cc_final: 0.6128 (pmm) REVERT: B 2420 VAL cc_start: 0.8892 (t) cc_final: 0.8677 (m) REVERT: B 2483 MET cc_start: 0.8360 (ttm) cc_final: 0.8128 (ttt) REVERT: B 2772 MET cc_start: 0.6887 (ttm) cc_final: 0.6362 (pmm) REVERT: C 2420 VAL cc_start: 0.8962 (t) cc_final: 0.8693 (m) REVERT: C 2444 ASN cc_start: 0.8339 (t0) cc_final: 0.8131 (t0) REVERT: C 2483 MET cc_start: 0.8281 (ttm) cc_final: 0.8051 (ttt) REVERT: C 2625 THR cc_start: 0.8729 (m) cc_final: 0.8480 (p) REVERT: C 2772 MET cc_start: 0.6803 (ttm) cc_final: 0.6359 (pmm) REVERT: D 2420 VAL cc_start: 0.8899 (t) cc_final: 0.8668 (m) REVERT: D 2496 VAL cc_start: 0.8708 (t) cc_final: 0.8491 (p) REVERT: D 2772 MET cc_start: 0.6899 (ttm) cc_final: 0.6470 (pmm) REVERT: E 2420 VAL cc_start: 0.8862 (t) cc_final: 0.8660 (m) REVERT: E 2483 MET cc_start: 0.8399 (ttm) cc_final: 0.8117 (ttt) REVERT: E 2608 ASN cc_start: 0.8865 (m110) cc_final: 0.8590 (m-40) REVERT: E 2610 THR cc_start: 0.8742 (m) cc_final: 0.8428 (p) REVERT: E 2625 THR cc_start: 0.8688 (m) cc_final: 0.8404 (p) REVERT: E 2772 MET cc_start: 0.6741 (ttm) cc_final: 0.6303 (pmm) REVERT: F 2772 MET cc_start: 0.6459 (ttm) cc_final: 0.6167 (pmm) REVERT: G 2420 VAL cc_start: 0.8996 (t) cc_final: 0.8747 (m) REVERT: G 2608 ASN cc_start: 0.8851 (m110) cc_final: 0.8542 (m-40) REVERT: G 2678 ASN cc_start: 0.8318 (m-40) cc_final: 0.7878 (t0) REVERT: G 2772 MET cc_start: 0.6679 (ttm) cc_final: 0.6122 (pmm) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.2466 time to fit residues: 178.0216 Evaluate side-chains 194 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 116 optimal weight: 9.9990 chunk 224 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 260 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2760 ASN B2582 ASN B2608 ASN B2760 ASN C2461 ASN C2608 ASN C2760 ASN D2582 ASN D2607 GLN D2608 ASN D2760 ASN E2760 ASN F2444 ASN F2760 ASN G2760 ASN G2795 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.138594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.104598 restraints weight = 25682.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.102283 restraints weight = 44989.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.103794 restraints weight = 42353.604| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21266 Z= 0.195 Angle : 0.571 6.388 29463 Z= 0.316 Chirality : 0.048 0.171 3703 Planarity : 0.005 0.031 3864 Dihedral : 4.634 17.456 3010 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.08 % Allowed : 5.87 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 1.32 (0.14), residues: 1085 loop : 0.37 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F2674 HIS 0.001 0.000 HIS G2641 PHE 0.019 0.002 PHE B2704 TYR 0.014 0.001 TYR C2672 ARG 0.001 0.000 ARG D2755 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2393 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6383 (t80) REVERT: A 2520 SER cc_start: 0.8537 (t) cc_final: 0.8150 (p) REVERT: A 2678 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8253 (t0) REVERT: A 2772 MET cc_start: 0.6623 (ttm) cc_final: 0.6351 (pmm) REVERT: B 2393 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6262 (t80) REVERT: B 2461 ASN cc_start: 0.7977 (m-40) cc_final: 0.7299 (m-40) REVERT: B 2520 SER cc_start: 0.8731 (t) cc_final: 0.8354 (p) REVERT: C 2393 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.5942 (t80) REVERT: C 2497 MET cc_start: 0.8578 (mtm) cc_final: 0.8246 (mtm) REVERT: C 2634 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8220 (m) REVERT: D 2393 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.5899 (t80) REVERT: D 2461 ASN cc_start: 0.7923 (m-40) cc_final: 0.7317 (m-40) REVERT: D 2772 MET cc_start: 0.6862 (ttm) cc_final: 0.6555 (pmm) REVERT: E 2393 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.5938 (t80) REVERT: E 2461 ASN cc_start: 0.7875 (m-40) cc_final: 0.7317 (m-40) REVERT: F 2393 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.5952 (t80) REVERT: F 2405 PHE cc_start: 0.7535 (m-80) cc_final: 0.7320 (m-10) REVERT: F 2461 ASN cc_start: 0.7734 (m-40) cc_final: 0.7383 (m-40) REVERT: F 2582 ASN cc_start: 0.8008 (t0) cc_final: 0.7768 (m-40) REVERT: G 2393 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6478 (t80) REVERT: G 2461 ASN cc_start: 0.7865 (m-40) cc_final: 0.7215 (m-40) REVERT: G 2483 MET cc_start: 0.8167 (ttt) cc_final: 0.7734 (ttt) REVERT: G 2520 SER cc_start: 0.8435 (t) cc_final: 0.8171 (p) REVERT: G 2765 ILE cc_start: 0.9283 (mp) cc_final: 0.9005 (mt) outliers start: 50 outliers final: 20 residues processed: 278 average time/residue: 0.2363 time to fit residues: 115.4170 Evaluate side-chains 165 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2393 TYR Chi-restraints excluded: chain A residue 2408 CYS Chi-restraints excluded: chain A residue 2678 ASN Chi-restraints excluded: chain A residue 2787 THR Chi-restraints excluded: chain B residue 2393 TYR Chi-restraints excluded: chain B residue 2408 CYS Chi-restraints excluded: chain B residue 2552 SER Chi-restraints excluded: chain B residue 2641 HIS Chi-restraints excluded: chain C residue 2393 TYR Chi-restraints excluded: chain C residue 2408 CYS Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2641 HIS Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2408 CYS Chi-restraints excluded: chain D residue 2415 LEU Chi-restraints excluded: chain D residue 2700 SER Chi-restraints excluded: chain E residue 2393 TYR Chi-restraints excluded: chain E residue 2408 CYS Chi-restraints excluded: chain E residue 2552 SER Chi-restraints excluded: chain E residue 2641 HIS Chi-restraints excluded: chain E residue 2659 GLU Chi-restraints excluded: chain E residue 2787 THR Chi-restraints excluded: chain F residue 2393 TYR Chi-restraints excluded: chain F residue 2408 CYS Chi-restraints excluded: chain G residue 2393 TYR Chi-restraints excluded: chain G residue 2408 CYS Chi-restraints excluded: chain G residue 2490 CYS Chi-restraints excluded: chain G residue 2787 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 163 optimal weight: 0.4980 chunk 250 optimal weight: 0.1980 chunk 41 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 280 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2795 ASN B2607 GLN B2795 ASN C2438 ASN C2795 ASN D2795 ASN E2582 ASN E2607 GLN E2795 ASN F2795 ASN G2582 ASN G2607 GLN G2678 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.133108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.097400 restraints weight = 25427.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.097751 restraints weight = 57952.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.099192 restraints weight = 49221.410| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21266 Z= 0.337 Angle : 0.589 6.580 29463 Z= 0.318 Chirality : 0.048 0.148 3703 Planarity : 0.005 0.035 3864 Dihedral : 4.675 21.795 3010 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.54 % Allowed : 8.50 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 2891 helix: None (None), residues: 0 sheet: 1.19 (0.15), residues: 1043 loop : 0.21 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F2674 HIS 0.002 0.001 HIS C2641 PHE 0.023 0.003 PHE D2704 TYR 0.015 0.001 TYR A2672 ARG 0.001 0.000 ARG D2755 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 153 time to evaluate : 2.276 Fit side-chains REVERT: A 2393 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6608 (t80) REVERT: A 2400 SER cc_start: 0.9120 (t) cc_final: 0.8894 (p) REVERT: A 2520 SER cc_start: 0.8510 (t) cc_final: 0.8169 (p) REVERT: A 2556 MET cc_start: 0.7895 (tpp) cc_final: 0.7451 (ttt) REVERT: A 2678 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8375 (t0) REVERT: A 2745 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8246 (mm) REVERT: B 2393 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.6137 (t80) REVERT: B 2461 ASN cc_start: 0.8274 (m-40) cc_final: 0.7708 (m-40) REVERT: C 2393 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6299 (t80) REVERT: C 2497 MET cc_start: 0.8748 (mtm) cc_final: 0.8393 (mtm) REVERT: D 2393 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5725 (t80) REVERT: D 2461 ASN cc_start: 0.8011 (m-40) cc_final: 0.7698 (m-40) REVERT: E 2393 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.6123 (t80) REVERT: E 2420 VAL cc_start: 0.9084 (t) cc_final: 0.8776 (p) REVERT: E 2461 ASN cc_start: 0.8065 (m-40) cc_final: 0.7751 (m-40) REVERT: E 2796 CYS cc_start: 0.6190 (m) cc_final: 0.5869 (m) REVERT: F 2393 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.6287 (t80) REVERT: F 2461 ASN cc_start: 0.8273 (m-40) cc_final: 0.7961 (m110) REVERT: G 2393 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6194 (t80) REVERT: G 2461 ASN cc_start: 0.8028 (m-40) cc_final: 0.7759 (m-40) REVERT: G 2520 SER cc_start: 0.8496 (t) cc_final: 0.8277 (p) REVERT: G 2796 CYS cc_start: 0.6410 (m) cc_final: 0.5989 (m) outliers start: 61 outliers final: 32 residues processed: 198 average time/residue: 0.2347 time to fit residues: 82.9363 Evaluate side-chains 154 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2393 TYR Chi-restraints excluded: chain A residue 2408 CYS Chi-restraints excluded: chain A residue 2549 SER Chi-restraints excluded: chain A residue 2678 ASN Chi-restraints excluded: chain A residue 2745 LEU Chi-restraints excluded: chain A residue 2787 THR Chi-restraints excluded: chain B residue 2393 TYR Chi-restraints excluded: chain B residue 2408 CYS Chi-restraints excluded: chain B residue 2549 SER Chi-restraints excluded: chain B residue 2552 SER Chi-restraints excluded: chain B residue 2641 HIS Chi-restraints excluded: chain B residue 2671 SER Chi-restraints excluded: chain C residue 2393 TYR Chi-restraints excluded: chain C residue 2408 CYS Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2626 VAL Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2641 HIS Chi-restraints excluded: chain C residue 2795 ASN Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2408 CYS Chi-restraints excluded: chain D residue 2443 THR Chi-restraints excluded: chain D residue 2603 ILE Chi-restraints excluded: chain D residue 2640 LEU Chi-restraints excluded: chain D residue 2700 SER Chi-restraints excluded: chain D residue 2795 ASN Chi-restraints excluded: chain E residue 2393 TYR Chi-restraints excluded: chain E residue 2408 CYS Chi-restraints excluded: chain E residue 2490 CYS Chi-restraints excluded: chain E residue 2552 SER Chi-restraints excluded: chain E residue 2659 GLU Chi-restraints excluded: chain E residue 2787 THR Chi-restraints excluded: chain E residue 2795 ASN Chi-restraints excluded: chain F residue 2393 TYR Chi-restraints excluded: chain F residue 2408 CYS Chi-restraints excluded: chain F residue 2479 THR Chi-restraints excluded: chain G residue 2393 TYR Chi-restraints excluded: chain G residue 2408 CYS Chi-restraints excluded: chain G residue 2549 SER Chi-restraints excluded: chain G residue 2626 VAL Chi-restraints excluded: chain G residue 2637 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 285 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2795 ASN B2795 ASN D2607 GLN F2795 ASN G2678 ASN G2795 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.128506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.091083 restraints weight = 25996.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.091763 restraints weight = 54929.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.093067 restraints weight = 46317.265| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 21266 Z= 0.556 Angle : 0.680 7.129 29463 Z= 0.367 Chirality : 0.051 0.162 3703 Planarity : 0.006 0.050 3864 Dihedral : 5.222 25.732 3010 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.71 % Allowed : 9.37 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 2891 helix: None (None), residues: 0 sheet: 0.60 (0.14), residues: 1029 loop : -0.20 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D2537 HIS 0.003 0.002 HIS C2641 PHE 0.023 0.004 PHE G2704 TYR 0.014 0.002 TYR C2506 ARG 0.003 0.000 ARG G2755 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 141 time to evaluate : 2.368 Fit side-chains REVERT: A 2400 SER cc_start: 0.9102 (t) cc_final: 0.8844 (p) REVERT: A 2520 SER cc_start: 0.8557 (t) cc_final: 0.8335 (p) REVERT: A 2556 MET cc_start: 0.7894 (tpp) cc_final: 0.7502 (ttt) REVERT: A 2745 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8299 (mm) REVERT: A 2795 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8171 (t0) REVERT: B 2393 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.6364 (t80) REVERT: B 2461 ASN cc_start: 0.8280 (m-40) cc_final: 0.7858 (m110) REVERT: C 2393 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6617 (t80) REVERT: C 2497 MET cc_start: 0.8803 (mtm) cc_final: 0.8482 (mtm) REVERT: C 2772 MET cc_start: 0.7471 (tpp) cc_final: 0.6033 (pmm) REVERT: D 2393 TYR cc_start: 0.6368 (OUTLIER) cc_final: 0.5933 (t80) REVERT: D 2461 ASN cc_start: 0.8189 (m-40) cc_final: 0.7969 (m110) REVERT: E 2393 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.6382 (t80) REVERT: E 2420 VAL cc_start: 0.9323 (t) cc_final: 0.9109 (p) REVERT: E 2461 ASN cc_start: 0.8278 (m-40) cc_final: 0.7963 (m110) REVERT: E 2772 MET cc_start: 0.7576 (tpp) cc_final: 0.6056 (pmm) REVERT: F 2393 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.6374 (t80) REVERT: F 2772 MET cc_start: 0.7324 (tpp) cc_final: 0.5881 (pmm) REVERT: G 2393 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6229 (t80) REVERT: G 2420 VAL cc_start: 0.9334 (t) cc_final: 0.9116 (p) REVERT: G 2461 ASN cc_start: 0.8288 (m-40) cc_final: 0.8064 (m-40) REVERT: G 2772 MET cc_start: 0.7631 (tpp) cc_final: 0.6339 (pmm) REVERT: G 2796 CYS cc_start: 0.6379 (m) cc_final: 0.6037 (m) outliers start: 89 outliers final: 47 residues processed: 212 average time/residue: 0.2353 time to fit residues: 88.6384 Evaluate side-chains 162 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 107 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2408 CYS Chi-restraints excluded: chain A residue 2549 SER Chi-restraints excluded: chain A residue 2745 LEU Chi-restraints excluded: chain A residue 2757 ILE Chi-restraints excluded: chain A residue 2787 THR Chi-restraints excluded: chain A residue 2795 ASN Chi-restraints excluded: chain B residue 2393 TYR Chi-restraints excluded: chain B residue 2549 SER Chi-restraints excluded: chain B residue 2552 SER Chi-restraints excluded: chain B residue 2603 ILE Chi-restraints excluded: chain B residue 2671 SER Chi-restraints excluded: chain B residue 2731 LEU Chi-restraints excluded: chain C residue 2393 TYR Chi-restraints excluded: chain C residue 2408 CYS Chi-restraints excluded: chain C residue 2411 ASP Chi-restraints excluded: chain C residue 2420 VAL Chi-restraints excluded: chain C residue 2483 MET Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2515 ASP Chi-restraints excluded: chain C residue 2549 SER Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2675 THR Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2395 LEU Chi-restraints excluded: chain D residue 2408 CYS Chi-restraints excluded: chain D residue 2420 VAL Chi-restraints excluded: chain D residue 2443 THR Chi-restraints excluded: chain D residue 2490 CYS Chi-restraints excluded: chain D residue 2603 ILE Chi-restraints excluded: chain D residue 2671 SER Chi-restraints excluded: chain D residue 2705 ILE Chi-restraints excluded: chain E residue 2393 TYR Chi-restraints excluded: chain E residue 2408 CYS Chi-restraints excluded: chain E residue 2490 CYS Chi-restraints excluded: chain E residue 2549 SER Chi-restraints excluded: chain E residue 2552 SER Chi-restraints excluded: chain E residue 2659 GLU Chi-restraints excluded: chain E residue 2694 THR Chi-restraints excluded: chain E residue 2731 LEU Chi-restraints excluded: chain E residue 2765 ILE Chi-restraints excluded: chain E residue 2787 THR Chi-restraints excluded: chain F residue 2393 TYR Chi-restraints excluded: chain F residue 2408 CYS Chi-restraints excluded: chain F residue 2411 ASP Chi-restraints excluded: chain F residue 2420 VAL Chi-restraints excluded: chain F residue 2479 THR Chi-restraints excluded: chain F residue 2549 SER Chi-restraints excluded: chain F residue 2705 ILE Chi-restraints excluded: chain G residue 2393 TYR Chi-restraints excluded: chain G residue 2408 CYS Chi-restraints excluded: chain G residue 2422 SER Chi-restraints excluded: chain G residue 2549 SER Chi-restraints excluded: chain G residue 2615 THR Chi-restraints excluded: chain G residue 2637 THR Chi-restraints excluded: chain G residue 2713 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 191 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 97 optimal weight: 0.0980 chunk 217 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 162 optimal weight: 20.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2678 ASN B2678 ASN B2712 GLN C2795 ASN D2712 GLN D2795 ASN E2712 GLN E2795 ASN F2795 ASN G2582 ASN G2712 GLN G2795 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.132849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.096101 restraints weight = 25695.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.097474 restraints weight = 50264.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.098324 restraints weight = 39094.029| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21266 Z= 0.198 Angle : 0.510 6.024 29463 Z= 0.271 Chirality : 0.046 0.161 3703 Planarity : 0.005 0.038 3864 Dihedral : 4.366 20.440 3010 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.96 % Allowed : 10.70 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 2891 helix: None (None), residues: 0 sheet: 0.74 (0.14), residues: 1036 loop : 0.04 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F2674 HIS 0.002 0.001 HIS G2641 PHE 0.017 0.002 PHE D2704 TYR 0.007 0.001 TYR A2672 ARG 0.001 0.000 ARG D2755 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 151 time to evaluate : 2.151 Fit side-chains REVERT: A 2400 SER cc_start: 0.9100 (t) cc_final: 0.8877 (p) REVERT: A 2556 MET cc_start: 0.7884 (tpp) cc_final: 0.7430 (ttt) REVERT: A 2745 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8191 (mm) REVERT: B 2393 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.6021 (t80) REVERT: B 2772 MET cc_start: 0.7562 (tpp) cc_final: 0.5490 (pmm) REVERT: C 2393 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.5746 (t80) REVERT: C 2400 SER cc_start: 0.9023 (t) cc_final: 0.8740 (p) REVERT: C 2497 MET cc_start: 0.8720 (mtm) cc_final: 0.8359 (mtm) REVERT: C 2772 MET cc_start: 0.7430 (tpp) cc_final: 0.6023 (pmm) REVERT: D 2393 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5549 (t80) REVERT: D 2461 ASN cc_start: 0.8083 (m-40) cc_final: 0.7876 (m-40) REVERT: E 2393 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5794 (t80) REVERT: E 2705 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8050 (tt) REVERT: E 2796 CYS cc_start: 0.6185 (m) cc_final: 0.5869 (m) REVERT: F 2393 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.5791 (t80) REVERT: F 2461 ASN cc_start: 0.8288 (m-40) cc_final: 0.8034 (m-40) REVERT: F 2772 MET cc_start: 0.7317 (tpp) cc_final: 0.5857 (pmm) REVERT: G 2393 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.5955 (t80) REVERT: G 2461 ASN cc_start: 0.8216 (m-40) cc_final: 0.7928 (m-40) REVERT: G 2772 MET cc_start: 0.7623 (tpp) cc_final: 0.6384 (pmm) outliers start: 71 outliers final: 33 residues processed: 205 average time/residue: 0.2330 time to fit residues: 85.7553 Evaluate side-chains 171 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2422 SER Chi-restraints excluded: chain A residue 2515 ASP Chi-restraints excluded: chain A residue 2549 SER Chi-restraints excluded: chain A residue 2745 LEU Chi-restraints excluded: chain B residue 2393 TYR Chi-restraints excluded: chain B residue 2479 THR Chi-restraints excluded: chain B residue 2552 SER Chi-restraints excluded: chain B residue 2641 HIS Chi-restraints excluded: chain B residue 2671 SER Chi-restraints excluded: chain C residue 2393 TYR Chi-restraints excluded: chain C residue 2411 ASP Chi-restraints excluded: chain C residue 2479 THR Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2549 SER Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2420 VAL Chi-restraints excluded: chain D residue 2549 SER Chi-restraints excluded: chain D residue 2649 ILE Chi-restraints excluded: chain D residue 2671 SER Chi-restraints excluded: chain D residue 2705 ILE Chi-restraints excluded: chain E residue 2393 TYR Chi-restraints excluded: chain E residue 2411 ASP Chi-restraints excluded: chain E residue 2490 CYS Chi-restraints excluded: chain E residue 2549 SER Chi-restraints excluded: chain E residue 2552 SER Chi-restraints excluded: chain E residue 2659 GLU Chi-restraints excluded: chain E residue 2705 ILE Chi-restraints excluded: chain E residue 2731 LEU Chi-restraints excluded: chain F residue 2393 TYR Chi-restraints excluded: chain F residue 2479 THR Chi-restraints excluded: chain F residue 2549 SER Chi-restraints excluded: chain F residue 2649 ILE Chi-restraints excluded: chain F residue 2705 ILE Chi-restraints excluded: chain F residue 2795 ASN Chi-restraints excluded: chain G residue 2393 TYR Chi-restraints excluded: chain G residue 2479 THR Chi-restraints excluded: chain G residue 2549 SER Chi-restraints excluded: chain G residue 2637 THR Chi-restraints excluded: chain G residue 2640 LEU Chi-restraints excluded: chain G residue 2649 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 56 optimal weight: 6.9990 chunk 186 optimal weight: 0.1980 chunk 196 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 265 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2712 GLN A2795 ASN C2712 GLN C2795 ASN ** E2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2712 GLN ** F2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2795 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.134591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.100527 restraints weight = 25412.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.100653 restraints weight = 53057.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.101760 restraints weight = 48620.703| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21266 Z= 0.161 Angle : 0.492 6.629 29463 Z= 0.257 Chirality : 0.045 0.168 3703 Planarity : 0.005 0.039 3864 Dihedral : 4.057 18.064 3010 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.21 % Allowed : 11.20 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 0.91 (0.14), residues: 1050 loop : 0.13 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F2674 HIS 0.001 0.001 HIS E2641 PHE 0.018 0.002 PHE C2704 TYR 0.007 0.001 TYR C2672 ARG 0.001 0.000 ARG A2755 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 145 time to evaluate : 2.423 Fit side-chains REVERT: A 2745 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 2393 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.5950 (t80) REVERT: B 2461 ASN cc_start: 0.8056 (m-40) cc_final: 0.7551 (m-40) REVERT: B 2772 MET cc_start: 0.7393 (tpp) cc_final: 0.5573 (pmm) REVERT: C 2393 TYR cc_start: 0.6594 (OUTLIER) cc_final: 0.5467 (t80) REVERT: C 2400 SER cc_start: 0.8935 (t) cc_final: 0.8707 (p) REVERT: C 2497 MET cc_start: 0.8650 (mtm) cc_final: 0.8329 (mtm) REVERT: C 2772 MET cc_start: 0.7230 (tpp) cc_final: 0.6028 (pmm) REVERT: D 2393 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5485 (t80) REVERT: D 2461 ASN cc_start: 0.7948 (m-40) cc_final: 0.7747 (m-40) REVERT: E 2393 TYR cc_start: 0.6363 (OUTLIER) cc_final: 0.5069 (t80) REVERT: E 2772 MET cc_start: 0.7119 (tpp) cc_final: 0.5044 (pmm) REVERT: E 2796 CYS cc_start: 0.6163 (m) cc_final: 0.5901 (m) REVERT: F 2393 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5764 (t80) REVERT: G 2393 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.5833 (t80) REVERT: G 2461 ASN cc_start: 0.7989 (m-40) cc_final: 0.7772 (m-40) REVERT: G 2772 MET cc_start: 0.7585 (tpp) cc_final: 0.6484 (pmm) outliers start: 77 outliers final: 49 residues processed: 204 average time/residue: 0.2585 time to fit residues: 94.8177 Evaluate side-chains 179 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 123 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2408 CYS Chi-restraints excluded: chain A residue 2549 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2745 LEU Chi-restraints excluded: chain B residue 2393 TYR Chi-restraints excluded: chain B residue 2470 VAL Chi-restraints excluded: chain B residue 2479 THR Chi-restraints excluded: chain B residue 2552 SER Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2641 HIS Chi-restraints excluded: chain C residue 2393 TYR Chi-restraints excluded: chain C residue 2395 LEU Chi-restraints excluded: chain C residue 2411 ASP Chi-restraints excluded: chain C residue 2420 VAL Chi-restraints excluded: chain C residue 2479 THR Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2549 SER Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2636 THR Chi-restraints excluded: chain C residue 2640 LEU Chi-restraints excluded: chain C residue 2795 ASN Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2408 CYS Chi-restraints excluded: chain D residue 2470 VAL Chi-restraints excluded: chain D residue 2504 ASN Chi-restraints excluded: chain D residue 2549 SER Chi-restraints excluded: chain D residue 2615 THR Chi-restraints excluded: chain D residue 2636 THR Chi-restraints excluded: chain D residue 2649 ILE Chi-restraints excluded: chain D residue 2671 SER Chi-restraints excluded: chain D residue 2705 ILE Chi-restraints excluded: chain E residue 2393 TYR Chi-restraints excluded: chain E residue 2408 CYS Chi-restraints excluded: chain E residue 2411 ASP Chi-restraints excluded: chain E residue 2470 VAL Chi-restraints excluded: chain E residue 2490 CYS Chi-restraints excluded: chain E residue 2549 SER Chi-restraints excluded: chain E residue 2552 SER Chi-restraints excluded: chain E residue 2659 GLU Chi-restraints excluded: chain E residue 2705 ILE Chi-restraints excluded: chain E residue 2731 LEU Chi-restraints excluded: chain F residue 2393 TYR Chi-restraints excluded: chain F residue 2420 VAL Chi-restraints excluded: chain F residue 2479 THR Chi-restraints excluded: chain F residue 2549 SER Chi-restraints excluded: chain F residue 2636 THR Chi-restraints excluded: chain F residue 2649 ILE Chi-restraints excluded: chain F residue 2705 ILE Chi-restraints excluded: chain G residue 2393 TYR Chi-restraints excluded: chain G residue 2408 CYS Chi-restraints excluded: chain G residue 2422 SER Chi-restraints excluded: chain G residue 2470 VAL Chi-restraints excluded: chain G residue 2479 THR Chi-restraints excluded: chain G residue 2549 SER Chi-restraints excluded: chain G residue 2637 THR Chi-restraints excluded: chain G residue 2649 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 196 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2795 ASN ** C2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2795 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.130468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.093327 restraints weight = 25761.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.094329 restraints weight = 46826.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.095249 restraints weight = 46245.137| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21266 Z= 0.377 Angle : 0.577 6.518 29463 Z= 0.305 Chirality : 0.048 0.224 3703 Planarity : 0.005 0.038 3864 Dihedral : 4.600 22.395 3010 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.67 % Allowed : 11.16 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 2891 helix: None (None), residues: 0 sheet: 0.69 (0.15), residues: 1015 loop : -0.11 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F2674 HIS 0.002 0.001 HIS F2641 PHE 0.022 0.003 PHE E2704 TYR 0.009 0.001 TYR A2506 ARG 0.001 0.000 ARG D2755 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 127 time to evaluate : 2.119 Fit side-chains REVERT: A 2556 MET cc_start: 0.7942 (tpp) cc_final: 0.7485 (ttt) REVERT: A 2745 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8151 (mm) REVERT: B 2393 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.5997 (t80) REVERT: C 2393 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5626 (t80) REVERT: C 2400 SER cc_start: 0.9027 (t) cc_final: 0.8767 (p) REVERT: C 2497 MET cc_start: 0.8801 (mtm) cc_final: 0.8408 (mtm) REVERT: D 2393 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5600 (t80) REVERT: D 2420 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.9048 (p) REVERT: D 2461 ASN cc_start: 0.8245 (m-40) cc_final: 0.7883 (m110) REVERT: D 2796 CYS cc_start: 0.6100 (m) cc_final: 0.5847 (m) REVERT: E 2393 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5308 (t80) REVERT: E 2796 CYS cc_start: 0.6172 (m) cc_final: 0.5895 (m) REVERT: F 2393 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.5496 (t80) REVERT: G 2393 TYR cc_start: 0.6291 (OUTLIER) cc_final: 0.5639 (t80) REVERT: G 2461 ASN cc_start: 0.8372 (m-40) cc_final: 0.7976 (m110) outliers start: 88 outliers final: 67 residues processed: 194 average time/residue: 0.2420 time to fit residues: 84.4047 Evaluate side-chains 191 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 116 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2400 SER Chi-restraints excluded: chain A residue 2408 CYS Chi-restraints excluded: chain A residue 2470 VAL Chi-restraints excluded: chain A residue 2515 ASP Chi-restraints excluded: chain A residue 2549 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2703 LEU Chi-restraints excluded: chain A residue 2745 LEU Chi-restraints excluded: chain A residue 2795 ASN Chi-restraints excluded: chain B residue 2393 TYR Chi-restraints excluded: chain B residue 2408 CYS Chi-restraints excluded: chain B residue 2470 VAL Chi-restraints excluded: chain B residue 2479 THR Chi-restraints excluded: chain B residue 2549 SER Chi-restraints excluded: chain B residue 2552 SER Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2745 LEU Chi-restraints excluded: chain B residue 2753 THR Chi-restraints excluded: chain C residue 2393 TYR Chi-restraints excluded: chain C residue 2395 LEU Chi-restraints excluded: chain C residue 2408 CYS Chi-restraints excluded: chain C residue 2411 ASP Chi-restraints excluded: chain C residue 2420 VAL Chi-restraints excluded: chain C residue 2479 THR Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2549 SER Chi-restraints excluded: chain C residue 2626 VAL Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2636 THR Chi-restraints excluded: chain C residue 2640 LEU Chi-restraints excluded: chain C residue 2745 LEU Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2395 LEU Chi-restraints excluded: chain D residue 2408 CYS Chi-restraints excluded: chain D residue 2420 VAL Chi-restraints excluded: chain D residue 2470 VAL Chi-restraints excluded: chain D residue 2549 SER Chi-restraints excluded: chain D residue 2615 THR Chi-restraints excluded: chain D residue 2636 THR Chi-restraints excluded: chain D residue 2649 ILE Chi-restraints excluded: chain D residue 2671 SER Chi-restraints excluded: chain D residue 2745 LEU Chi-restraints excluded: chain E residue 2393 TYR Chi-restraints excluded: chain E residue 2408 CYS Chi-restraints excluded: chain E residue 2470 VAL Chi-restraints excluded: chain E residue 2490 CYS Chi-restraints excluded: chain E residue 2549 SER Chi-restraints excluded: chain E residue 2552 SER Chi-restraints excluded: chain E residue 2603 ILE Chi-restraints excluded: chain E residue 2659 GLU Chi-restraints excluded: chain E residue 2694 THR Chi-restraints excluded: chain E residue 2705 ILE Chi-restraints excluded: chain E residue 2731 LEU Chi-restraints excluded: chain F residue 2393 TYR Chi-restraints excluded: chain F residue 2395 LEU Chi-restraints excluded: chain F residue 2408 CYS Chi-restraints excluded: chain F residue 2420 VAL Chi-restraints excluded: chain F residue 2422 SER Chi-restraints excluded: chain F residue 2479 THR Chi-restraints excluded: chain F residue 2549 SER Chi-restraints excluded: chain F residue 2603 ILE Chi-restraints excluded: chain F residue 2636 THR Chi-restraints excluded: chain F residue 2649 ILE Chi-restraints excluded: chain F residue 2705 ILE Chi-restraints excluded: chain F residue 2795 ASN Chi-restraints excluded: chain G residue 2393 TYR Chi-restraints excluded: chain G residue 2408 CYS Chi-restraints excluded: chain G residue 2422 SER Chi-restraints excluded: chain G residue 2470 VAL Chi-restraints excluded: chain G residue 2479 THR Chi-restraints excluded: chain G residue 2549 SER Chi-restraints excluded: chain G residue 2636 THR Chi-restraints excluded: chain G residue 2637 THR Chi-restraints excluded: chain G residue 2649 ILE Chi-restraints excluded: chain G residue 2745 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 253 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 241 optimal weight: 0.2980 chunk 117 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2795 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.130937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.093906 restraints weight = 25837.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.094708 restraints weight = 47023.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.095662 restraints weight = 50065.113| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21266 Z= 0.329 Angle : 0.549 6.305 29463 Z= 0.289 Chirality : 0.047 0.216 3703 Planarity : 0.005 0.038 3864 Dihedral : 4.502 21.726 3010 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.54 % Allowed : 11.25 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 0.53 (0.15), residues: 1029 loop : -0.08 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F2674 HIS 0.002 0.001 HIS D2641 PHE 0.021 0.002 PHE E2704 TYR 0.008 0.001 TYR C2672 ARG 0.002 0.000 ARG A2755 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 125 time to evaluate : 2.663 Fit side-chains REVERT: A 2556 MET cc_start: 0.7892 (tpp) cc_final: 0.7271 (ttt) REVERT: B 2393 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.5893 (t80) REVERT: C 2393 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.5618 (t80) REVERT: C 2400 SER cc_start: 0.9034 (t) cc_final: 0.8765 (p) REVERT: C 2497 MET cc_start: 0.8694 (mtm) cc_final: 0.8324 (mtm) REVERT: D 2393 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.5424 (t80) REVERT: D 2420 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.9008 (p) REVERT: D 2461 ASN cc_start: 0.8169 (m-40) cc_final: 0.7772 (m-40) REVERT: E 2393 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5280 (t80) REVERT: E 2796 CYS cc_start: 0.6124 (m) cc_final: 0.5843 (m) REVERT: F 2393 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.5620 (t80) REVERT: G 2393 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.5649 (t80) REVERT: G 2461 ASN cc_start: 0.8330 (m-40) cc_final: 0.8017 (m110) REVERT: G 2772 MET cc_start: 0.7561 (tpp) cc_final: 0.5774 (pmm) outliers start: 85 outliers final: 65 residues processed: 189 average time/residue: 0.2346 time to fit residues: 79.4776 Evaluate side-chains 193 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 121 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2408 CYS Chi-restraints excluded: chain A residue 2470 VAL Chi-restraints excluded: chain A residue 2515 ASP Chi-restraints excluded: chain A residue 2549 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2703 LEU Chi-restraints excluded: chain A residue 2745 LEU Chi-restraints excluded: chain B residue 2393 TYR Chi-restraints excluded: chain B residue 2408 CYS Chi-restraints excluded: chain B residue 2470 VAL Chi-restraints excluded: chain B residue 2479 THR Chi-restraints excluded: chain B residue 2489 ILE Chi-restraints excluded: chain B residue 2549 SER Chi-restraints excluded: chain B residue 2552 SER Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2671 SER Chi-restraints excluded: chain B residue 2745 LEU Chi-restraints excluded: chain B residue 2753 THR Chi-restraints excluded: chain C residue 2393 TYR Chi-restraints excluded: chain C residue 2395 LEU Chi-restraints excluded: chain C residue 2408 CYS Chi-restraints excluded: chain C residue 2411 ASP Chi-restraints excluded: chain C residue 2479 THR Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2549 SER Chi-restraints excluded: chain C residue 2626 VAL Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2636 THR Chi-restraints excluded: chain C residue 2640 LEU Chi-restraints excluded: chain C residue 2745 LEU Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2395 LEU Chi-restraints excluded: chain D residue 2408 CYS Chi-restraints excluded: chain D residue 2420 VAL Chi-restraints excluded: chain D residue 2470 VAL Chi-restraints excluded: chain D residue 2549 SER Chi-restraints excluded: chain D residue 2603 ILE Chi-restraints excluded: chain D residue 2615 THR Chi-restraints excluded: chain D residue 2636 THR Chi-restraints excluded: chain D residue 2649 ILE Chi-restraints excluded: chain D residue 2671 SER Chi-restraints excluded: chain D residue 2745 LEU Chi-restraints excluded: chain E residue 2393 TYR Chi-restraints excluded: chain E residue 2408 CYS Chi-restraints excluded: chain E residue 2411 ASP Chi-restraints excluded: chain E residue 2470 VAL Chi-restraints excluded: chain E residue 2490 CYS Chi-restraints excluded: chain E residue 2549 SER Chi-restraints excluded: chain E residue 2552 SER Chi-restraints excluded: chain E residue 2659 GLU Chi-restraints excluded: chain E residue 2694 THR Chi-restraints excluded: chain E residue 2705 ILE Chi-restraints excluded: chain E residue 2731 LEU Chi-restraints excluded: chain F residue 2393 TYR Chi-restraints excluded: chain F residue 2408 CYS Chi-restraints excluded: chain F residue 2420 VAL Chi-restraints excluded: chain F residue 2422 SER Chi-restraints excluded: chain F residue 2479 THR Chi-restraints excluded: chain F residue 2549 SER Chi-restraints excluded: chain F residue 2636 THR Chi-restraints excluded: chain F residue 2649 ILE Chi-restraints excluded: chain G residue 2393 TYR Chi-restraints excluded: chain G residue 2408 CYS Chi-restraints excluded: chain G residue 2422 SER Chi-restraints excluded: chain G residue 2470 VAL Chi-restraints excluded: chain G residue 2479 THR Chi-restraints excluded: chain G residue 2549 SER Chi-restraints excluded: chain G residue 2636 THR Chi-restraints excluded: chain G residue 2637 THR Chi-restraints excluded: chain G residue 2640 LEU Chi-restraints excluded: chain G residue 2649 ILE Chi-restraints excluded: chain G residue 2745 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 155 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 226 optimal weight: 0.3980 chunk 262 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2795 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.134191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.099586 restraints weight = 25569.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.099947 restraints weight = 53788.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.101103 restraints weight = 50002.070| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21266 Z= 0.162 Angle : 0.487 5.861 29463 Z= 0.253 Chirality : 0.045 0.150 3703 Planarity : 0.004 0.036 3864 Dihedral : 4.056 18.525 3010 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.00 % Allowed : 11.54 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 0.79 (0.15), residues: 1022 loop : 0.01 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G2674 HIS 0.002 0.001 HIS D2641 PHE 0.018 0.002 PHE E2704 TYR 0.006 0.000 TYR C2672 ARG 0.001 0.000 ARG A2755 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 141 time to evaluate : 2.290 Fit side-chains REVERT: A 2497 MET cc_start: 0.8804 (mtm) cc_final: 0.8592 (mtm) REVERT: B 2393 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.5661 (t80) REVERT: B 2461 ASN cc_start: 0.8130 (m-40) cc_final: 0.7747 (m110) REVERT: C 2393 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.5561 (t80) REVERT: C 2400 SER cc_start: 0.9004 (t) cc_final: 0.8775 (p) REVERT: C 2497 MET cc_start: 0.8603 (mtm) cc_final: 0.8229 (mtm) REVERT: C 2772 MET cc_start: 0.7417 (tpp) cc_final: 0.5332 (pmm) REVERT: D 2393 TYR cc_start: 0.5929 (OUTLIER) cc_final: 0.5420 (t80) REVERT: D 2420 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8945 (p) REVERT: D 2461 ASN cc_start: 0.7985 (m-40) cc_final: 0.7732 (m110) REVERT: E 2393 TYR cc_start: 0.6269 (OUTLIER) cc_final: 0.5186 (t80) REVERT: F 2393 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.5312 (t80) REVERT: G 2393 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5465 (t80) REVERT: G 2461 ASN cc_start: 0.8069 (m-40) cc_final: 0.7791 (m110) REVERT: G 2772 MET cc_start: 0.7485 (tpp) cc_final: 0.5762 (pmm) REVERT: G 2795 ASN cc_start: 0.8451 (m-40) cc_final: 0.8181 (t0) outliers start: 72 outliers final: 53 residues processed: 193 average time/residue: 0.2289 time to fit residues: 79.7490 Evaluate side-chains 192 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2408 CYS Chi-restraints excluded: chain A residue 2470 VAL Chi-restraints excluded: chain A residue 2515 ASP Chi-restraints excluded: chain A residue 2549 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2745 LEU Chi-restraints excluded: chain B residue 2393 TYR Chi-restraints excluded: chain B residue 2470 VAL Chi-restraints excluded: chain B residue 2479 THR Chi-restraints excluded: chain B residue 2552 SER Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2641 HIS Chi-restraints excluded: chain B residue 2671 SER Chi-restraints excluded: chain B residue 2745 LEU Chi-restraints excluded: chain B residue 2753 THR Chi-restraints excluded: chain C residue 2393 TYR Chi-restraints excluded: chain C residue 2395 LEU Chi-restraints excluded: chain C residue 2408 CYS Chi-restraints excluded: chain C residue 2411 ASP Chi-restraints excluded: chain C residue 2479 THR Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2549 SER Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2636 THR Chi-restraints excluded: chain C residue 2745 LEU Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2420 VAL Chi-restraints excluded: chain D residue 2470 VAL Chi-restraints excluded: chain D residue 2549 SER Chi-restraints excluded: chain D residue 2552 SER Chi-restraints excluded: chain D residue 2615 THR Chi-restraints excluded: chain D residue 2636 THR Chi-restraints excluded: chain D residue 2649 ILE Chi-restraints excluded: chain E residue 2393 TYR Chi-restraints excluded: chain E residue 2408 CYS Chi-restraints excluded: chain E residue 2411 ASP Chi-restraints excluded: chain E residue 2470 VAL Chi-restraints excluded: chain E residue 2490 CYS Chi-restraints excluded: chain E residue 2549 SER Chi-restraints excluded: chain E residue 2552 SER Chi-restraints excluded: chain E residue 2659 GLU Chi-restraints excluded: chain E residue 2694 THR Chi-restraints excluded: chain E residue 2705 ILE Chi-restraints excluded: chain F residue 2393 TYR Chi-restraints excluded: chain F residue 2420 VAL Chi-restraints excluded: chain F residue 2422 SER Chi-restraints excluded: chain F residue 2549 SER Chi-restraints excluded: chain F residue 2636 THR Chi-restraints excluded: chain F residue 2649 ILE Chi-restraints excluded: chain F residue 2705 ILE Chi-restraints excluded: chain F residue 2795 ASN Chi-restraints excluded: chain G residue 2393 TYR Chi-restraints excluded: chain G residue 2422 SER Chi-restraints excluded: chain G residue 2470 VAL Chi-restraints excluded: chain G residue 2479 THR Chi-restraints excluded: chain G residue 2549 SER Chi-restraints excluded: chain G residue 2636 THR Chi-restraints excluded: chain G residue 2637 THR Chi-restraints excluded: chain G residue 2649 ILE Chi-restraints excluded: chain G residue 2745 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 98 optimal weight: 5.9990 chunk 213 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2733 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 = 0.3397 r_free = 0.3397 target = 0.132541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.096180 restraints weight = 25522.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.097937 restraints weight = 48128.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.098508 restraints weight = 44474.183| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21266 Z= 0.264 Angle : 0.522 6.238 29463 Z= 0.272 Chirality : 0.046 0.173 3703 Planarity : 0.005 0.099 3864 Dihedral : 4.231 19.833 3010 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.04 % Allowed : 11.41 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 0.69 (0.15), residues: 1029 loop : 0.03 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F2674 HIS 0.002 0.001 HIS B2641 PHE 0.020 0.002 PHE E2704 TYR 0.008 0.001 TYR C2672 ARG 0.001 0.000 ARG A2755 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 133 time to evaluate : 2.218 Fit side-chains REVERT: B 2393 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.5744 (t80) REVERT: C 2393 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.5631 (t80) REVERT: C 2400 SER cc_start: 0.9017 (t) cc_final: 0.8773 (p) REVERT: C 2497 MET cc_start: 0.8720 (mtm) cc_final: 0.8348 (mtm) REVERT: C 2772 MET cc_start: 0.7477 (tpp) cc_final: 0.5349 (pmm) REVERT: D 2393 TYR cc_start: 0.5796 (OUTLIER) cc_final: 0.5352 (t80) REVERT: D 2420 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.9010 (p) REVERT: E 2393 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.5471 (t80) REVERT: F 2393 TYR cc_start: 0.5889 (OUTLIER) cc_final: 0.4927 (t80) REVERT: G 2393 TYR cc_start: 0.6269 (OUTLIER) cc_final: 0.5582 (t80) REVERT: G 2461 ASN cc_start: 0.8240 (m-40) cc_final: 0.7920 (m110) REVERT: G 2772 MET cc_start: 0.7535 (tpp) cc_final: 0.5762 (pmm) REVERT: G 2795 ASN cc_start: 0.8570 (m-40) cc_final: 0.8223 (t0) outliers start: 73 outliers final: 61 residues processed: 183 average time/residue: 0.2540 time to fit residues: 82.2836 Evaluate side-chains 196 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 128 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2400 SER Chi-restraints excluded: chain A residue 2408 CYS Chi-restraints excluded: chain A residue 2470 VAL Chi-restraints excluded: chain A residue 2515 ASP Chi-restraints excluded: chain A residue 2549 SER Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2745 LEU Chi-restraints excluded: chain B residue 2393 TYR Chi-restraints excluded: chain B residue 2470 VAL Chi-restraints excluded: chain B residue 2479 THR Chi-restraints excluded: chain B residue 2552 SER Chi-restraints excluded: chain B residue 2636 THR Chi-restraints excluded: chain B residue 2641 HIS Chi-restraints excluded: chain B residue 2671 SER Chi-restraints excluded: chain B residue 2745 LEU Chi-restraints excluded: chain B residue 2753 THR Chi-restraints excluded: chain C residue 2393 TYR Chi-restraints excluded: chain C residue 2395 LEU Chi-restraints excluded: chain C residue 2408 CYS Chi-restraints excluded: chain C residue 2411 ASP Chi-restraints excluded: chain C residue 2479 THR Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2549 SER Chi-restraints excluded: chain C residue 2626 VAL Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2636 THR Chi-restraints excluded: chain C residue 2745 LEU Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2408 CYS Chi-restraints excluded: chain D residue 2420 VAL Chi-restraints excluded: chain D residue 2470 VAL Chi-restraints excluded: chain D residue 2549 SER Chi-restraints excluded: chain D residue 2552 SER Chi-restraints excluded: chain D residue 2603 ILE Chi-restraints excluded: chain D residue 2615 THR Chi-restraints excluded: chain D residue 2636 THR Chi-restraints excluded: chain D residue 2649 ILE Chi-restraints excluded: chain D residue 2745 LEU Chi-restraints excluded: chain E residue 2393 TYR Chi-restraints excluded: chain E residue 2408 CYS Chi-restraints excluded: chain E residue 2411 ASP Chi-restraints excluded: chain E residue 2470 VAL Chi-restraints excluded: chain E residue 2490 CYS Chi-restraints excluded: chain E residue 2549 SER Chi-restraints excluded: chain E residue 2552 SER Chi-restraints excluded: chain E residue 2654 VAL Chi-restraints excluded: chain E residue 2659 GLU Chi-restraints excluded: chain E residue 2694 THR Chi-restraints excluded: chain E residue 2705 ILE Chi-restraints excluded: chain F residue 2393 TYR Chi-restraints excluded: chain F residue 2420 VAL Chi-restraints excluded: chain F residue 2422 SER Chi-restraints excluded: chain F residue 2497 MET Chi-restraints excluded: chain F residue 2549 SER Chi-restraints excluded: chain F residue 2636 THR Chi-restraints excluded: chain F residue 2649 ILE Chi-restraints excluded: chain F residue 2705 ILE Chi-restraints excluded: chain G residue 2393 TYR Chi-restraints excluded: chain G residue 2408 CYS Chi-restraints excluded: chain G residue 2422 SER Chi-restraints excluded: chain G residue 2470 VAL Chi-restraints excluded: chain G residue 2479 THR Chi-restraints excluded: chain G residue 2549 SER Chi-restraints excluded: chain G residue 2636 THR Chi-restraints excluded: chain G residue 2637 THR Chi-restraints excluded: chain G residue 2640 LEU Chi-restraints excluded: chain G residue 2649 ILE Chi-restraints excluded: chain G residue 2745 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 233 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 237 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2678 ASN ** E2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.130821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.094277 restraints weight = 25839.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.094896 restraints weight = 50635.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.095954 restraints weight = 48732.391| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21266 Z= 0.353 Angle : 0.562 6.614 29463 Z= 0.295 Chirality : 0.048 0.200 3703 Planarity : 0.005 0.093 3864 Dihedral : 4.534 22.261 3010 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.21 % Allowed : 11.20 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 0.50 (0.15), residues: 1029 loop : -0.13 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F2674 HIS 0.002 0.001 HIS F2641 PHE 0.022 0.003 PHE E2704 TYR 0.009 0.001 TYR D2506 ARG 0.003 0.000 ARG E2755 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.22 seconds wall clock time: 88 minutes 15.87 seconds (5295.87 seconds total)