Starting phenix.real_space_refine on Wed Nov 20 06:43:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flv_50540/11_2024/9flv_50540.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flv_50540/11_2024/9flv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flv_50540/11_2024/9flv_50540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flv_50540/11_2024/9flv_50540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flv_50540/11_2024/9flv_50540.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flv_50540/11_2024/9flv_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 11.98, per 1000 atoms: 0.58 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: 5.17 Conformation dependent library (CDL) restraints added in 3.4 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: 3.92 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: 8.95 Time building geometry restraints manager: 5.98 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 50.840 Find NCS groups from input model: 0.780 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.230 ------------------------------------------------------------------------------- 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 : 2.220 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: 0.2461 time to fit residues: 176.9600 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 : 2.360 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2393 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6350 (t80) REVERT: A 2520 SER cc_start: 0.8675 (t) cc_final: 0.8265 (p) REVERT: A 2678 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8275 (t0) REVERT: A 2772 MET cc_start: 0.6805 (ttm) cc_final: 0.6331 (pmm) REVERT: B 2393 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6199 (t80) REVERT: B 2461 ASN cc_start: 0.8116 (m-40) cc_final: 0.7280 (m-40) REVERT: B 2520 SER cc_start: 0.8727 (t) cc_final: 0.8343 (p) REVERT: B 2772 MET cc_start: 0.6767 (ttm) cc_final: 0.6408 (pmm) REVERT: C 2393 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.5876 (t80) REVERT: C 2497 MET cc_start: 0.8588 (mtm) cc_final: 0.8257 (mtm) REVERT: C 2634 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8348 (m) REVERT: D 2393 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.5846 (t80) REVERT: D 2461 ASN cc_start: 0.8011 (m-40) cc_final: 0.7328 (m-40) REVERT: D 2772 MET cc_start: 0.6926 (ttm) cc_final: 0.6494 (pmm) REVERT: E 2393 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.5882 (t80) REVERT: E 2461 ASN cc_start: 0.7942 (m-40) cc_final: 0.7320 (m-40) REVERT: E 2772 MET cc_start: 0.6784 (ttm) cc_final: 0.6551 (pmm) REVERT: F 2393 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.5882 (t80) REVERT: F 2405 PHE cc_start: 0.7537 (m-80) cc_final: 0.7320 (m-10) REVERT: F 2461 ASN cc_start: 0.7847 (m-40) cc_final: 0.7361 (m-40) REVERT: G 2393 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6416 (t80) REVERT: G 2461 ASN cc_start: 0.8064 (m-40) cc_final: 0.7233 (m-40) REVERT: G 2483 MET cc_start: 0.8198 (ttt) cc_final: 0.7760 (ttt) REVERT: G 2520 SER cc_start: 0.8456 (t) cc_final: 0.8182 (p) REVERT: G 2765 ILE cc_start: 0.9282 (mp) cc_final: 0.9009 (mt) outliers start: 50 outliers final: 20 residues processed: 278 average time/residue: 0.2355 time to fit residues: 115.4102 Evaluate side-chains 164 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 2.018 ------------------------------------------------------------------------------- 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 144 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 209 optimal weight: 0.2980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 21266 Z= 0.426 Angle : 0.629 6.790 29463 Z= 0.341 Chirality : 0.049 0.172 3703 Planarity : 0.005 0.036 3864 Dihedral : 4.924 23.410 3010 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.79 % Allowed : 8.25 % 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: 0.65 (0.14), residues: 2891 helix: None (None), residues: 0 sheet: 1.07 (0.15), residues: 1043 loop : 0.11 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F2674 HIS 0.003 0.001 HIS B2641 PHE 0.021 0.003 PHE D2704 TYR 0.015 0.002 TYR A2672 ARG 0.001 0.000 ARG G2755 *********************** 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 226 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 159 time to evaluate : 2.161 Fit side-chains REVERT: A 2393 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6677 (t80) REVERT: A 2400 SER cc_start: 0.9114 (t) cc_final: 0.8852 (p) REVERT: A 2420 VAL cc_start: 0.9237 (t) cc_final: 0.8952 (p) REVERT: A 2520 SER cc_start: 0.8686 (t) cc_final: 0.8326 (p) REVERT: A 2556 MET cc_start: 0.7852 (tpp) cc_final: 0.7409 (ttt) REVERT: A 2678 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8395 (t0) REVERT: A 2745 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8180 (mm) REVERT: B 2393 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6130 (t80) REVERT: B 2461 ASN cc_start: 0.8258 (m-40) cc_final: 0.7606 (m-40) REVERT: C 2393 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6418 (t80) REVERT: D 2393 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.5979 (t80) REVERT: D 2461 ASN cc_start: 0.8170 (m-40) cc_final: 0.7784 (m-40) REVERT: E 2393 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.6212 (t80) REVERT: E 2461 ASN cc_start: 0.8232 (m-40) cc_final: 0.7904 (m-40) REVERT: E 2796 CYS cc_start: 0.6303 (m) cc_final: 0.5956 (m) REVERT: F 2393 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.6013 (t80) REVERT: F 2461 ASN cc_start: 0.8376 (m-40) cc_final: 0.8057 (m110) REVERT: G 2393 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.6255 (t80) REVERT: G 2461 ASN cc_start: 0.8144 (m-40) cc_final: 0.7807 (m-40) REVERT: G 2520 SER cc_start: 0.8515 (t) cc_final: 0.8311 (p) REVERT: G 2796 CYS cc_start: 0.6373 (m) cc_final: 0.5918 (m) outliers start: 67 outliers final: 36 residues processed: 207 average time/residue: 0.2357 time to fit residues: 87.0210 Evaluate side-chains 163 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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 2626 VAL Chi-restraints excluded: chain B residue 2641 HIS Chi-restraints excluded: chain B residue 2671 SER Chi-restraints excluded: chain B residue 2675 THR 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 2549 SER 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 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 2549 SER 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 F residue 2549 SER 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 2637 THR Chi-restraints excluded: chain G residue 2713 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2795 ASN B2795 ASN F2795 ASN G2712 GLN G2795 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21266 Z= 0.171 Angle : 0.505 5.896 29463 Z= 0.269 Chirality : 0.045 0.141 3703 Planarity : 0.005 0.036 3864 Dihedral : 4.244 19.288 3010 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.17 % Allowed : 10.45 % Favored : 87.38 % 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: 0.86 (0.14), residues: 2891 helix: None (None), residues: 0 sheet: 1.15 (0.14), residues: 1057 loop : 0.30 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2674 HIS 0.001 0.001 HIS D2641 PHE 0.018 0.002 PHE G2704 TYR 0.009 0.001 TYR B2672 ARG 0.003 0.000 ARG D2755 *********************** 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 199 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 2.148 Fit side-chains REVERT: A 2393 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.6252 (t80) REVERT: A 2420 VAL cc_start: 0.9255 (t) cc_final: 0.8992 (p) REVERT: A 2556 MET cc_start: 0.7722 (tpp) cc_final: 0.7334 (ttt) REVERT: A 2745 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8152 (mm) REVERT: A 2772 MET cc_start: 0.7517 (tpp) cc_final: 0.6192 (pmm) REVERT: B 2393 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.5961 (t80) REVERT: B 2461 ASN cc_start: 0.8276 (m-40) cc_final: 0.7518 (m-40) REVERT: C 2393 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.5759 (t80) REVERT: D 2393 TYR cc_start: 0.6312 (OUTLIER) cc_final: 0.5594 (t80) REVERT: D 2461 ASN cc_start: 0.8156 (m-40) cc_final: 0.7685 (m-40) REVERT: E 2393 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.5914 (t80) REVERT: E 2461 ASN cc_start: 0.8155 (m-40) cc_final: 0.7788 (m-40) REVERT: F 2393 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.5630 (t80) REVERT: F 2461 ASN cc_start: 0.8378 (m-40) cc_final: 0.7894 (m-40) REVERT: F 2772 MET cc_start: 0.7363 (tpp) cc_final: 0.6023 (pmm) REVERT: G 2393 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.5970 (t80) REVERT: G 2461 ASN cc_start: 0.8230 (m-40) cc_final: 0.7712 (m-40) REVERT: G 2772 MET cc_start: 0.7561 (tpp) cc_final: 0.6158 (pmm) REVERT: G 2796 CYS cc_start: 0.6242 (m) cc_final: 0.5860 (m) outliers start: 52 outliers final: 22 residues processed: 189 average time/residue: 0.2380 time to fit residues: 80.7840 Evaluate side-chains 149 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2393 TYR 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 2552 SER 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 2615 THR Chi-restraints excluded: chain C residue 2626 VAL Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2408 CYS Chi-restraints excluded: chain D residue 2615 THR 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 2641 HIS Chi-restraints excluded: chain E residue 2659 GLU Chi-restraints excluded: chain E residue 2705 ILE Chi-restraints excluded: chain F residue 2393 TYR Chi-restraints excluded: chain F residue 2479 THR 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 2549 SER Chi-restraints excluded: chain G residue 2637 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 206 optimal weight: 0.0170 chunk 114 optimal weight: 0.4980 chunk 236 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2795 ASN B2712 GLN C2712 GLN C2795 ASN D2712 GLN D2795 ASN E2712 GLN E2795 ASN F2712 GLN G2607 GLN G2641 HIS G2795 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21266 Z= 0.150 Angle : 0.486 6.019 29463 Z= 0.255 Chirality : 0.045 0.152 3703 Planarity : 0.005 0.039 3864 Dihedral : 3.957 16.959 3010 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.67 % Allowed : 10.70 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 1.24 (0.14), residues: 1050 loop : 0.32 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F2674 HIS 0.001 0.001 HIS C2641 PHE 0.019 0.002 PHE C2704 TYR 0.008 0.001 TYR C2672 ARG 0.002 0.000 ARG G2755 *********************** 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 208 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 144 time to evaluate : 2.243 Fit side-chains REVERT: A 2393 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.6022 (t80) REVERT: A 2420 VAL cc_start: 0.9293 (t) cc_final: 0.9028 (p) REVERT: A 2461 ASN cc_start: 0.8099 (m-40) cc_final: 0.7571 (m-40) REVERT: A 2745 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8112 (mm) REVERT: B 2393 TYR cc_start: 0.6674 (OUTLIER) cc_final: 0.5826 (t80) REVERT: B 2461 ASN cc_start: 0.8238 (m-40) cc_final: 0.7470 (m-40) REVERT: B 2772 MET cc_start: 0.7637 (tpp) cc_final: 0.5607 (pmm) REVERT: B 2795 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8062 (t0) REVERT: C 2393 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.5482 (t80) REVERT: C 2772 MET cc_start: 0.7485 (tpp) cc_final: 0.5720 (pmm) REVERT: D 2393 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5287 (t80) REVERT: D 2461 ASN cc_start: 0.8228 (m-40) cc_final: 0.7691 (m-40) REVERT: D 2772 MET cc_start: 0.7679 (tpp) cc_final: 0.5839 (pmm) REVERT: E 2393 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.5825 (t80) REVERT: E 2461 ASN cc_start: 0.8107 (m-40) cc_final: 0.7625 (m-40) REVERT: E 2772 MET cc_start: 0.7312 (tpp) cc_final: 0.5013 (pmm) REVERT: E 2796 CYS cc_start: 0.6212 (m) cc_final: 0.5883 (m) REVERT: F 2393 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5474 (t80) REVERT: F 2461 ASN cc_start: 0.8373 (m-40) cc_final: 0.7837 (m-40) REVERT: F 2772 MET cc_start: 0.7295 (tpp) cc_final: 0.5996 (pmm) REVERT: G 2393 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.5653 (t80) REVERT: G 2461 ASN cc_start: 0.8304 (m-40) cc_final: 0.7691 (m-40) REVERT: G 2641 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.7232 (m170) REVERT: G 2772 MET cc_start: 0.7475 (tpp) cc_final: 0.6169 (pmm) outliers start: 64 outliers final: 33 residues processed: 186 average time/residue: 0.2307 time to fit residues: 76.7437 Evaluate side-chains 166 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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 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 2420 VAL Chi-restraints excluded: chain B residue 2552 SER Chi-restraints excluded: chain B residue 2641 HIS Chi-restraints excluded: chain B residue 2795 ASN 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 2626 VAL 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 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 E residue 2393 TYR Chi-restraints excluded: chain E residue 2490 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 2705 ILE 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 2420 VAL Chi-restraints excluded: chain F residue 2479 THR 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 2637 THR Chi-restraints excluded: chain G residue 2641 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 0.7980 chunk 249 optimal weight: 6.9990 chunk 54 optimal weight: 0.4980 chunk 162 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 230 optimal weight: 0.4980 chunk 128 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2795 ASN G2641 HIS G2678 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21266 Z= 0.298 Angle : 0.544 6.173 29463 Z= 0.286 Chirality : 0.047 0.214 3703 Planarity : 0.005 0.039 3864 Dihedral : 4.310 20.064 3010 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.96 % Allowed : 10.91 % Favored : 86.13 % 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: 0.65 (0.14), residues: 2891 helix: None (None), residues: 0 sheet: 1.00 (0.14), residues: 1050 loop : 0.16 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F2674 HIS 0.008 0.002 HIS G2641 PHE 0.022 0.002 PHE G2704 TYR 0.010 0.001 TYR G2532 ARG 0.002 0.000 ARG D2755 *********************** 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 203 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 132 time to evaluate : 2.245 Fit side-chains REVERT: A 2393 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6340 (t80) REVERT: A 2420 VAL cc_start: 0.9256 (t) cc_final: 0.9037 (p) REVERT: A 2556 MET cc_start: 0.7837 (tpp) cc_final: 0.7336 (ttt) REVERT: A 2745 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8081 (mm) REVERT: B 2393 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.5861 (t80) REVERT: B 2420 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8984 (p) REVERT: B 2461 ASN cc_start: 0.8350 (m-40) cc_final: 0.7573 (m-40) REVERT: C 2393 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.5651 (t80) REVERT: C 2772 MET cc_start: 0.7536 (tpp) cc_final: 0.5854 (pmm) REVERT: D 2393 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5505 (t80) REVERT: D 2461 ASN cc_start: 0.8254 (m-40) cc_final: 0.7741 (m-40) REVERT: D 2795 ASN cc_start: 0.8597 (m-40) cc_final: 0.8289 (t0) REVERT: E 2393 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.5915 (t80) REVERT: E 2420 VAL cc_start: 0.9336 (t) cc_final: 0.9131 (p) REVERT: E 2461 ASN cc_start: 0.8213 (m-40) cc_final: 0.7798 (m-40) REVERT: F 2393 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.5811 (t80) REVERT: F 2772 MET cc_start: 0.7314 (tpp) cc_final: 0.6063 (pmm) REVERT: G 2393 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.5790 (t80) REVERT: G 2420 VAL cc_start: 0.9346 (t) cc_final: 0.9101 (p) REVERT: G 2461 ASN cc_start: 0.8400 (m-40) cc_final: 0.7818 (m-40) REVERT: G 2640 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7446 (mp) REVERT: G 2772 MET cc_start: 0.7671 (tpp) cc_final: 0.6366 (pmm) REVERT: G 2795 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8147 (t0) outliers start: 71 outliers final: 44 residues processed: 180 average time/residue: 0.2409 time to fit residues: 77.5930 Evaluate side-chains 173 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2393 TYR Chi-restraints excluded: chain A residue 2400 SER Chi-restraints excluded: chain A residue 2408 CYS 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 2703 LEU Chi-restraints excluded: chain A residue 2745 LEU Chi-restraints excluded: chain B residue 2393 TYR Chi-restraints excluded: chain B residue 2395 LEU Chi-restraints excluded: chain B residue 2408 CYS Chi-restraints excluded: chain B residue 2420 VAL 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 2745 LEU 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 2626 VAL 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 2395 LEU Chi-restraints excluded: chain D residue 2408 CYS Chi-restraints excluded: chain D residue 2420 VAL 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 2490 CYS 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 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 2497 MET 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 2538 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 2745 LEU Chi-restraints excluded: chain G residue 2795 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 233 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 173 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2795 ASN B2607 GLN C2795 ASN D2607 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4263 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= 0.309 Angle : 0.543 6.094 29463 Z= 0.286 Chirality : 0.047 0.197 3703 Planarity : 0.005 0.037 3864 Dihedral : 4.418 21.137 3010 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.58 % Allowed : 10.83 % 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: 0.49 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 0.82 (0.14), residues: 1050 loop : 0.09 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F2674 HIS 0.002 0.001 HIS B2641 PHE 0.020 0.003 PHE E2704 TYR 0.011 0.001 TYR G2532 ARG 0.002 0.000 ARG C2755 *********************** 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 221 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 135 time to evaluate : 2.097 Fit side-chains REVERT: A 2393 TYR cc_start: 0.6496 (OUTLIER) cc_final: 0.6015 (t80) REVERT: A 2556 MET cc_start: 0.7808 (tpp) cc_final: 0.7311 (ttt) REVERT: B 2393 TYR cc_start: 0.6730 (OUTLIER) cc_final: 0.5783 (t80) REVERT: C 2393 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.5393 (t80) REVERT: C 2772 MET cc_start: 0.7635 (tpp) cc_final: 0.5919 (pmm) REVERT: D 2393 TYR cc_start: 0.6301 (OUTLIER) cc_final: 0.5548 (t80) REVERT: D 2420 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.9057 (p) REVERT: D 2461 ASN cc_start: 0.8281 (m-40) cc_final: 0.7761 (m-40) REVERT: E 2393 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.5584 (t80) REVERT: E 2461 ASN cc_start: 0.8288 (m-40) cc_final: 0.7876 (m110) REVERT: F 2393 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.5861 (t80) REVERT: G 2393 TYR cc_start: 0.6667 (OUTLIER) cc_final: 0.5738 (t80) REVERT: G 2461 ASN cc_start: 0.8434 (m-40) cc_final: 0.7973 (m110) REVERT: G 2795 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7991 (t0) outliers start: 86 outliers final: 52 residues processed: 201 average time/residue: 0.2312 time to fit residues: 83.0788 Evaluate side-chains 183 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 122 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2393 TYR Chi-restraints excluded: chain A residue 2400 SER Chi-restraints excluded: chain A residue 2408 CYS Chi-restraints excluded: chain A residue 2422 SER 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 2395 LEU Chi-restraints excluded: chain B residue 2408 CYS 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 2641 HIS Chi-restraints excluded: chain B residue 2745 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 2479 THR Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2549 SER Chi-restraints excluded: chain C residue 2615 THR Chi-restraints excluded: chain C residue 2626 VAL Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2795 ASN 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 2603 ILE Chi-restraints excluded: chain D residue 2615 THR Chi-restraints excluded: chain D residue 2700 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 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 2411 ASP Chi-restraints excluded: chain F residue 2420 VAL Chi-restraints excluded: chain F residue 2479 THR 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 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 2479 THR Chi-restraints excluded: chain G residue 2538 THR 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 2745 LEU Chi-restraints excluded: chain G residue 2795 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 165 optimal weight: 0.3980 chunk 83 optimal weight: 0.0170 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 136 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2712 GLN A2795 ASN C2795 ASN ** E2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.002 0.035 21266 Z= 0.142 Angle : 0.483 5.919 29463 Z= 0.252 Chirality : 0.045 0.144 3703 Planarity : 0.004 0.037 3864 Dihedral : 3.947 19.710 3010 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.33 % Allowed : 12.00 % Favored : 85.67 % 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: 0.77 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 1.05 (0.14), residues: 1050 loop : 0.27 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G2674 HIS 0.002 0.001 HIS G2641 PHE 0.017 0.001 PHE E2704 TYR 0.006 0.000 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 216 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 2.158 Fit side-chains REVERT: A 2393 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.5788 (t80) REVERT: B 2393 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.5332 (t80) REVERT: C 2393 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.5081 (t80) REVERT: C 2772 MET cc_start: 0.7609 (tpp) cc_final: 0.5876 (pmm) REVERT: D 2393 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.5309 (t80) REVERT: D 2420 VAL cc_start: 0.9283 (OUTLIER) cc_final: 0.9022 (p) REVERT: D 2461 ASN cc_start: 0.8164 (m-40) cc_final: 0.7676 (m-40) REVERT: E 2393 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5286 (t80) REVERT: E 2461 ASN cc_start: 0.8086 (m-40) cc_final: 0.7730 (m-40) REVERT: F 2393 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.5483 (t80) REVERT: F 2772 MET cc_start: 0.7432 (tpp) cc_final: 0.5737 (pmm) REVERT: G 2393 TYR cc_start: 0.6555 (OUTLIER) cc_final: 0.5462 (t80) REVERT: G 2461 ASN cc_start: 0.8269 (m-40) cc_final: 0.7652 (m-40) REVERT: G 2772 MET cc_start: 0.7518 (tpp) cc_final: 0.5879 (pmm) outliers start: 56 outliers final: 40 residues processed: 199 average time/residue: 0.2362 time to fit residues: 84.3094 Evaluate side-chains 186 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 2.150 ------------------------------------------------------------------------------- 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 2422 SER Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2549 SER 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 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 2745 LEU 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 2420 VAL Chi-restraints excluded: chain C residue 2479 THR Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2615 THR Chi-restraints excluded: chain C residue 2636 THR 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 2420 VAL Chi-restraints excluded: chain D residue 2615 THR Chi-restraints excluded: chain D residue 2636 THR 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 2479 THR Chi-restraints excluded: chain E residue 2490 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 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 2420 VAL Chi-restraints excluded: chain F residue 2636 THR Chi-restraints excluded: chain F residue 2705 ILE Chi-restraints excluded: chain G residue 2393 TYR Chi-restraints excluded: chain G residue 2422 SER Chi-restraints excluded: chain G residue 2479 THR Chi-restraints excluded: chain G residue 2637 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 0.1980 chunk 265 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 232 optimal weight: 3.9990 chunk 243 optimal weight: 20.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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** A2795 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21266 Z= 0.306 Angle : 0.542 6.255 29463 Z= 0.286 Chirality : 0.047 0.190 3703 Planarity : 0.006 0.102 3864 Dihedral : 4.281 20.400 3010 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.33 % Allowed : 12.58 % Favored : 85.09 % 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: 0.48 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 0.75 (0.15), residues: 1043 loop : 0.14 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C2674 HIS 0.002 0.001 HIS C2641 PHE 0.022 0.002 PHE E2704 TYR 0.011 0.001 TYR G2532 ARG 0.002 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 191 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 2.250 Fit side-chains REVERT: A 2393 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5998 (t80) REVERT: B 2393 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5549 (t80) REVERT: C 2393 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5219 (t80) REVERT: C 2772 MET cc_start: 0.7685 (tpp) cc_final: 0.5921 (pmm) REVERT: C 2795 ASN cc_start: 0.8063 (t0) cc_final: 0.7752 (t0) REVERT: D 2393 TYR cc_start: 0.6382 (OUTLIER) cc_final: 0.5608 (t80) REVERT: D 2420 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.9055 (p) REVERT: D 2461 ASN cc_start: 0.8207 (m-40) cc_final: 0.7775 (m110) REVERT: E 2393 TYR cc_start: 0.6231 (OUTLIER) cc_final: 0.5483 (t80) REVERT: E 2461 ASN cc_start: 0.8273 (m-40) cc_final: 0.7854 (m110) REVERT: F 2393 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.5379 (t80) REVERT: G 2393 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.5483 (t80) REVERT: G 2461 ASN cc_start: 0.8373 (m-40) cc_final: 0.7904 (m110) REVERT: G 2772 MET cc_start: 0.7599 (tpp) cc_final: 0.5825 (pmm) outliers start: 56 outliers final: 44 residues processed: 173 average time/residue: 0.2359 time to fit residues: 73.3504 Evaluate side-chains 183 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 2.391 ------------------------------------------------------------------------------- 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 2422 SER Chi-restraints excluded: chain A residue 2515 ASP Chi-restraints excluded: chain A residue 2549 SER 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 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 2641 HIS Chi-restraints excluded: chain B residue 2745 LEU 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 2420 VAL Chi-restraints excluded: chain C residue 2479 THR Chi-restraints excluded: chain C residue 2490 CYS Chi-restraints excluded: chain C residue 2615 THR Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2636 THR Chi-restraints excluded: chain C residue 2641 HIS Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2420 VAL Chi-restraints excluded: chain D residue 2615 THR Chi-restraints excluded: chain D residue 2636 THR Chi-restraints excluded: chain E residue 2393 TYR Chi-restraints excluded: chain E residue 2408 CYS Chi-restraints excluded: chain E residue 2479 THR 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 2395 LEU Chi-restraints excluded: chain F residue 2420 VAL Chi-restraints excluded: chain F residue 2549 SER Chi-restraints excluded: chain F residue 2636 THR 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 2479 THR Chi-restraints excluded: chain G residue 2549 SER Chi-restraints excluded: chain G residue 2637 THR 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 256 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 272 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 189 optimal weight: 0.0570 chunk 285 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 227 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2795 ASN ** E2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21266 Z= 0.157 Angle : 0.487 5.880 29463 Z= 0.255 Chirality : 0.045 0.149 3703 Planarity : 0.005 0.092 3864 Dihedral : 3.989 19.007 3010 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.08 % Allowed : 12.74 % 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: 0.69 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 0.97 (0.15), residues: 1043 loop : 0.23 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F2674 HIS 0.001 0.001 HIS D2641 PHE 0.018 0.002 PHE E2704 TYR 0.008 0.001 TYR G2532 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 190 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 2.069 Fit side-chains REVERT: A 2393 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5600 (t80) REVERT: B 2393 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5339 (t80) REVERT: C 2393 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5094 (t80) REVERT: C 2772 MET cc_start: 0.7670 (tpp) cc_final: 0.5886 (pmm) REVERT: D 2393 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.5278 (t80) REVERT: D 2420 VAL cc_start: 0.9304 (OUTLIER) cc_final: 0.9049 (p) REVERT: D 2461 ASN cc_start: 0.8191 (m-40) cc_final: 0.7755 (m110) REVERT: D 2691 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7375 (mm-40) REVERT: E 2393 TYR cc_start: 0.6175 (OUTLIER) cc_final: 0.5376 (t80) REVERT: E 2461 ASN cc_start: 0.8166 (m-40) cc_final: 0.7790 (m110) REVERT: F 2393 TYR cc_start: 0.5954 (OUTLIER) cc_final: 0.5120 (t80) REVERT: G 2772 MET cc_start: 0.7637 (tpp) cc_final: 0.5871 (pmm) outliers start: 50 outliers final: 41 residues processed: 175 average time/residue: 0.2435 time to fit residues: 75.6550 Evaluate side-chains 183 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 2.539 ------------------------------------------------------------------------------- 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 2515 ASP Chi-restraints excluded: chain A residue 2549 SER 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 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 2745 LEU 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 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 2615 THR Chi-restraints excluded: chain C residue 2634 VAL Chi-restraints excluded: chain C residue 2636 THR Chi-restraints excluded: chain C residue 2641 HIS Chi-restraints excluded: chain D residue 2393 TYR Chi-restraints excluded: chain D residue 2420 VAL Chi-restraints excluded: chain D residue 2490 CYS Chi-restraints excluded: chain D residue 2615 THR Chi-restraints excluded: chain D residue 2636 THR 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 2479 THR 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 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 2420 VAL Chi-restraints excluded: chain F residue 2636 THR Chi-restraints excluded: chain F residue 2705 ILE Chi-restraints excluded: chain G residue 2422 SER 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 2745 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 95 optimal weight: 0.0570 chunk 234 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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** A2641 HIS ** D2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2723 ASN D2794 ASN ** E2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.103295 restraints weight = 25449.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.103777 restraints weight = 54770.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.104558 restraints weight = 46861.935| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21266 Z= 0.163 Angle : 0.485 5.884 29463 Z= 0.253 Chirality : 0.045 0.149 3703 Planarity : 0.005 0.084 3864 Dihedral : 3.869 17.011 3010 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.54 % Allowed : 12.37 % Favored : 85.09 % 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: 0.74 (0.15), residues: 2891 helix: None (None), residues: 0 sheet: 1.05 (0.15), residues: 1043 loop : 0.24 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F2674 HIS 0.001 0.001 HIS D2641 PHE 0.018 0.002 PHE E2704 TYR 0.007 0.001 TYR C2672 ARG 0.001 0.000 ARG A2755 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.04 seconds wall clock time: 62 minutes 24.67 seconds (3744.67 seconds total)