Starting phenix.real_space_refine on Tue Jul 7 02:21:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x0x_66448/07_2026/9x0x_66448.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x0x_66448/07_2026/9x0x_66448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x0x_66448/07_2026/9x0x_66448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x0x_66448/07_2026/9x0x_66448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x0x_66448/07_2026/9x0x_66448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x0x_66448/07_2026/9x0x_66448.map" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 154 5.16 5 C 26362 2.51 5 N 6958 2.21 5 O 7966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41454 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "B" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "C" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "D" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "E" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "F" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "G" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "H" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "I" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "J" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "K" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "L" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "M" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "N" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "O" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "S" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "P" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "Q" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "R" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "T" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "V" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "W" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "X" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "Y" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "Z" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "b" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 100 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.69, per 1000 atoms: 0.19 Number of scatterers: 41454 At special positions: 0 Unit cell: (172.53, 174.15, 138.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 14 15.00 O 7966 8.00 N 6958 7.00 C 26362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 499 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS E 506 " distance=2.03 Simple disulfide: pdb=" SG CYS F 499 " - pdb=" SG CYS F 506 " distance=2.03 Simple disulfide: pdb=" SG CYS G 499 " - pdb=" SG CYS G 506 " distance=2.03 Simple disulfide: pdb=" SG CYS H 499 " - pdb=" SG CYS H 506 " distance=2.03 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS I 506 " distance=2.03 Simple disulfide: pdb=" SG CYS J 499 " - pdb=" SG CYS J 506 " distance=2.03 Simple disulfide: pdb=" SG CYS K 499 " - pdb=" SG CYS K 506 " distance=2.03 Simple disulfide: pdb=" SG CYS L 499 " - pdb=" SG CYS L 506 " distance=2.03 Simple disulfide: pdb=" SG CYS M 499 " - pdb=" SG CYS M 506 " distance=2.03 Simple disulfide: pdb=" SG CYS N 499 " - pdb=" SG CYS N 506 " distance=2.03 Simple disulfide: pdb=" SG CYS O 101 " - pdb=" SG CYS O 104 " distance=2.03 Simple disulfide: pdb=" SG CYS S 101 " - pdb=" SG CYS S 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 101 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 101 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS T 101 " - pdb=" SG CYS T 104 " distance=2.03 Simple disulfide: pdb=" SG CYS U 101 " - pdb=" SG CYS U 104 " distance=2.03 Simple disulfide: pdb=" SG CYS V 101 " - pdb=" SG CYS V 104 " distance=2.03 Simple disulfide: pdb=" SG CYS W 101 " - pdb=" SG CYS W 104 " distance=2.03 Simple disulfide: pdb=" SG CYS X 101 " - pdb=" SG CYS X 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 101 " - pdb=" SG CYS Y 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 101 " - pdb=" SG CYS Z 104 " distance=2.03 Simple disulfide: pdb=" SG CYS a 101 " - pdb=" SG CYS a 104 " distance=2.03 Simple disulfide: pdb=" SG CYS b 101 " - pdb=" SG CYS b 104 " 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: 2.71 Conformation dependent library (CDL) restraints added in 1.2 seconds 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9800 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 58 sheets defined 27.0% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 388 through 400 Processing helix chain 'A' and resid 429 through 444 Processing helix chain 'A' and resid 627 through 630 removed outlier: 4.077A pdb=" N MET A 630 " --> pdb=" O TYR A 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 627 through 630' Processing helix chain 'A' and resid 673 through 677 Processing helix chain 'A' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG A 682 " --> pdb=" O TYR A 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 400 Processing helix chain 'B' and resid 429 through 444 Processing helix chain 'B' and resid 627 through 630 removed outlier: 4.076A pdb=" N MET B 630 " --> pdb=" O TYR B 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 627 through 630' Processing helix chain 'B' and resid 673 through 677 Processing helix chain 'B' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG B 682 " --> pdb=" O TYR B 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 400 Processing helix chain 'C' and resid 429 through 444 Processing helix chain 'C' and resid 627 through 630 removed outlier: 4.077A pdb=" N MET C 630 " --> pdb=" O TYR C 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 627 through 630' Processing helix chain 'C' and resid 673 through 677 Processing helix chain 'C' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG C 682 " --> pdb=" O TYR C 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 400 Processing helix chain 'D' and resid 429 through 444 Processing helix chain 'D' and resid 627 through 630 removed outlier: 4.076A pdb=" N MET D 630 " --> pdb=" O TYR D 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 627 through 630' Processing helix chain 'D' and resid 673 through 677 Processing helix chain 'D' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG D 682 " --> pdb=" O TYR D 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 400 Processing helix chain 'E' and resid 429 through 444 Processing helix chain 'E' and resid 627 through 630 removed outlier: 4.076A pdb=" N MET E 630 " --> pdb=" O TYR E 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 627 through 630' Processing helix chain 'E' and resid 673 through 677 Processing helix chain 'E' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG E 682 " --> pdb=" O TYR E 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 400 Processing helix chain 'F' and resid 429 through 444 Processing helix chain 'F' and resid 627 through 630 removed outlier: 4.077A pdb=" N MET F 630 " --> pdb=" O TYR F 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 627 through 630' Processing helix chain 'F' and resid 673 through 677 Processing helix chain 'F' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG F 682 " --> pdb=" O TYR F 679 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 400 Processing helix chain 'G' and resid 429 through 444 Processing helix chain 'G' and resid 627 through 630 removed outlier: 4.076A pdb=" N MET G 630 " --> pdb=" O TYR G 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 627 through 630' Processing helix chain 'G' and resid 673 through 677 Processing helix chain 'G' and resid 679 through 683 removed outlier: 4.069A pdb=" N ARG G 682 " --> pdb=" O TYR G 679 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 400 Processing helix chain 'H' and resid 429 through 444 Processing helix chain 'H' and resid 627 through 630 removed outlier: 4.076A pdb=" N MET H 630 " --> pdb=" O TYR H 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 627 through 630' Processing helix chain 'H' and resid 673 through 677 Processing helix chain 'H' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG H 682 " --> pdb=" O TYR H 679 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 400 Processing helix chain 'I' and resid 429 through 444 Processing helix chain 'I' and resid 627 through 630 removed outlier: 4.076A pdb=" N MET I 630 " --> pdb=" O TYR I 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 627 through 630' Processing helix chain 'I' and resid 673 through 677 Processing helix chain 'I' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG I 682 " --> pdb=" O TYR I 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 388 through 400 Processing helix chain 'J' and resid 429 through 444 Processing helix chain 'J' and resid 627 through 630 removed outlier: 4.076A pdb=" N MET J 630 " --> pdb=" O TYR J 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 627 through 630' Processing helix chain 'J' and resid 673 through 677 Processing helix chain 'J' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG J 682 " --> pdb=" O TYR J 679 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 400 Processing helix chain 'K' and resid 429 through 444 Processing helix chain 'K' and resid 627 through 630 removed outlier: 4.075A pdb=" N MET K 630 " --> pdb=" O TYR K 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 627 through 630' Processing helix chain 'K' and resid 673 through 677 Processing helix chain 'K' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG K 682 " --> pdb=" O TYR K 679 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 400 Processing helix chain 'L' and resid 429 through 444 Processing helix chain 'L' and resid 627 through 630 removed outlier: 4.076A pdb=" N MET L 630 " --> pdb=" O TYR L 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 627 through 630' Processing helix chain 'L' and resid 673 through 677 Processing helix chain 'L' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG L 682 " --> pdb=" O TYR L 679 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 400 Processing helix chain 'M' and resid 429 through 444 Processing helix chain 'M' and resid 627 through 630 removed outlier: 4.076A pdb=" N MET M 630 " --> pdb=" O TYR M 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 627 through 630' Processing helix chain 'M' and resid 673 through 677 Processing helix chain 'M' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG M 682 " --> pdb=" O TYR M 679 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 400 Processing helix chain 'N' and resid 429 through 444 Processing helix chain 'N' and resid 627 through 630 removed outlier: 4.075A pdb=" N MET N 630 " --> pdb=" O TYR N 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 627 through 630' Processing helix chain 'N' and resid 673 through 677 Processing helix chain 'N' and resid 679 through 683 removed outlier: 4.068A pdb=" N ARG N 682 " --> pdb=" O TYR N 679 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 53 removed outlier: 4.032A pdb=" N ALA O 46 " --> pdb=" O PRO O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 72 Processing helix chain 'O' and resid 72 through 80 Processing helix chain 'O' and resid 81 through 90 Processing helix chain 'O' and resid 90 through 99 removed outlier: 3.579A pdb=" N GLU O 96 " --> pdb=" O ASP O 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 53 removed outlier: 4.033A pdb=" N ALA S 46 " --> pdb=" O PRO S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 72 Processing helix chain 'S' and resid 72 through 80 Processing helix chain 'S' and resid 81 through 90 Processing helix chain 'S' and resid 90 through 99 removed outlier: 3.579A pdb=" N GLU S 96 " --> pdb=" O ASP S 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 53 removed outlier: 4.033A pdb=" N ALA P 46 " --> pdb=" O PRO P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 72 Processing helix chain 'P' and resid 72 through 80 Processing helix chain 'P' and resid 81 through 90 Processing helix chain 'P' and resid 90 through 99 removed outlier: 3.579A pdb=" N GLU P 96 " --> pdb=" O ASP P 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.032A pdb=" N ALA Q 46 " --> pdb=" O PRO Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 72 Processing helix chain 'Q' and resid 72 through 80 Processing helix chain 'Q' and resid 81 through 90 Processing helix chain 'Q' and resid 90 through 99 removed outlier: 3.579A pdb=" N GLU Q 96 " --> pdb=" O ASP Q 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 53 removed outlier: 4.033A pdb=" N ALA R 46 " --> pdb=" O PRO R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 72 Processing helix chain 'R' and resid 72 through 80 Processing helix chain 'R' and resid 81 through 90 Processing helix chain 'R' and resid 90 through 99 removed outlier: 3.579A pdb=" N GLU R 96 " --> pdb=" O ASP R 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 53 removed outlier: 4.032A pdb=" N ALA T 46 " --> pdb=" O PRO T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 72 Processing helix chain 'T' and resid 72 through 80 Processing helix chain 'T' and resid 81 through 90 Processing helix chain 'T' and resid 90 through 99 removed outlier: 3.580A pdb=" N GLU T 96 " --> pdb=" O ASP T 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 53 removed outlier: 4.032A pdb=" N ALA U 46 " --> pdb=" O PRO U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 72 Processing helix chain 'U' and resid 72 through 80 Processing helix chain 'U' and resid 81 through 90 Processing helix chain 'U' and resid 90 through 99 removed outlier: 3.580A pdb=" N GLU U 96 " --> pdb=" O ASP U 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 53 removed outlier: 4.032A pdb=" N ALA V 46 " --> pdb=" O PRO V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 72 Processing helix chain 'V' and resid 72 through 80 Processing helix chain 'V' and resid 81 through 90 Processing helix chain 'V' and resid 90 through 99 removed outlier: 3.579A pdb=" N GLU V 96 " --> pdb=" O ASP V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 53 removed outlier: 4.033A pdb=" N ALA W 46 " --> pdb=" O PRO W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 72 Processing helix chain 'W' and resid 72 through 80 Processing helix chain 'W' and resid 81 through 90 Processing helix chain 'W' and resid 90 through 99 removed outlier: 3.579A pdb=" N GLU W 96 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 53 removed outlier: 4.032A pdb=" N ALA X 46 " --> pdb=" O PRO X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 72 Processing helix chain 'X' and resid 72 through 80 Processing helix chain 'X' and resid 81 through 90 Processing helix chain 'X' and resid 90 through 99 removed outlier: 3.580A pdb=" N GLU X 96 " --> pdb=" O ASP X 92 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 53 removed outlier: 4.033A pdb=" N ALA Y 46 " --> pdb=" O PRO Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 72 Processing helix chain 'Y' and resid 72 through 80 Processing helix chain 'Y' and resid 81 through 90 Processing helix chain 'Y' and resid 90 through 99 removed outlier: 3.579A pdb=" N GLU Y 96 " --> pdb=" O ASP Y 92 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 53 removed outlier: 4.032A pdb=" N ALA Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 72 Processing helix chain 'Z' and resid 72 through 80 Processing helix chain 'Z' and resid 81 through 90 Processing helix chain 'Z' and resid 90 through 99 removed outlier: 3.580A pdb=" N GLU Z 96 " --> pdb=" O ASP Z 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 53 removed outlier: 4.032A pdb=" N ALA a 46 " --> pdb=" O PRO a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 72 Processing helix chain 'a' and resid 72 through 80 Processing helix chain 'a' and resid 81 through 90 Processing helix chain 'a' and resid 90 through 99 removed outlier: 3.579A pdb=" N GLU a 96 " --> pdb=" O ASP a 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 53 removed outlier: 4.033A pdb=" N ALA b 46 " --> pdb=" O PRO b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 72 Processing helix chain 'b' and resid 72 through 80 Processing helix chain 'b' and resid 81 through 90 Processing helix chain 'b' and resid 90 through 99 removed outlier: 3.578A pdb=" N GLU b 96 " --> pdb=" O ASP b 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 383 Processing sheet with id=AA2, first strand: chain 'A' and resid 414 through 418 Processing sheet with id=AA3, first strand: chain 'A' and resid 449 through 476 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 480 through 483 current: chain 'A' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 541 through 567 current: chain 'A' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 685 through 705 current: chain 'B' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 480 through 483 current: chain 'B' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 541 through 567 current: chain 'B' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 685 through 705 current: chain 'C' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 480 through 483 current: chain 'C' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 541 through 567 current: chain 'C' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 685 through 705 current: chain 'D' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 480 through 483 current: chain 'D' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 541 through 567 current: chain 'D' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 685 through 705 current: chain 'E' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 480 through 483 current: chain 'E' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 541 through 567 current: chain 'E' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 685 through 705 current: chain 'F' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 480 through 483 current: chain 'F' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 541 through 567 current: chain 'F' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 685 through 705 current: chain 'G' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 480 through 483 current: chain 'G' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 541 through 567 current: chain 'G' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 685 through 705 current: chain 'H' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 480 through 483 current: chain 'H' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 541 through 567 current: chain 'H' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 685 through 705 current: chain 'I' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 480 through 483 current: chain 'I' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 541 through 567 current: chain 'I' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 685 through 705 current: chain 'J' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 480 through 483 current: chain 'J' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 541 through 567 current: chain 'J' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 685 through 705 current: chain 'K' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 480 through 483 current: chain 'K' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 541 through 567 current: chain 'K' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 685 through 705 current: chain 'L' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 480 through 483 current: chain 'L' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 541 through 567 current: chain 'L' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 685 through 705 current: chain 'M' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 480 through 483 current: chain 'M' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 541 through 567 current: chain 'M' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 685 through 705 current: chain 'N' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 480 through 483 current: chain 'N' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 541 through 567 current: chain 'N' and resid 685 through 705 Processing sheet with id=AA4, first strand: chain 'A' and resid 490 through 492 Processing sheet with id=AA5, first strand: chain 'A' and resid 498 through 499 Processing sheet with id=AA6, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AA7, first strand: chain 'A' and resid 572 through 580 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 613 through 622 current: chain 'A' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 613 through 622 current: chain 'B' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 613 through 622 current: chain 'C' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 613 through 622 current: chain 'D' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 613 through 622 current: chain 'E' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 613 through 622 current: chain 'F' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 613 through 622 current: chain 'G' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 613 through 622 current: chain 'H' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 613 through 622 current: chain 'I' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 613 through 622 current: chain 'J' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 613 through 622 current: chain 'K' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 613 through 622 current: chain 'L' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 613 through 622 current: chain 'M' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 613 through 622 current: chain 'N' and resid 637 through 649 Processing sheet with id=AA8, first strand: chain 'B' and resid 414 through 418 Processing sheet with id=AA9, first strand: chain 'B' and resid 490 through 492 Processing sheet with id=AB1, first strand: chain 'B' and resid 498 through 499 Processing sheet with id=AB2, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AB3, first strand: chain 'C' and resid 414 through 418 Processing sheet with id=AB4, first strand: chain 'C' and resid 490 through 492 Processing sheet with id=AB5, first strand: chain 'C' and resid 498 through 499 Processing sheet with id=AB6, first strand: chain 'C' and resid 510 through 511 Processing sheet with id=AB7, first strand: chain 'D' and resid 414 through 418 Processing sheet with id=AB8, first strand: chain 'D' and resid 490 through 492 Processing sheet with id=AB9, first strand: chain 'D' and resid 498 through 499 Processing sheet with id=AC1, first strand: chain 'D' and resid 510 through 511 Processing sheet with id=AC2, first strand: chain 'E' and resid 414 through 418 Processing sheet with id=AC3, first strand: chain 'E' and resid 490 through 492 Processing sheet with id=AC4, first strand: chain 'E' and resid 498 through 499 Processing sheet with id=AC5, first strand: chain 'E' and resid 510 through 511 Processing sheet with id=AC6, first strand: chain 'F' and resid 414 through 418 Processing sheet with id=AC7, first strand: chain 'F' and resid 490 through 492 Processing sheet with id=AC8, first strand: chain 'F' and resid 498 through 499 Processing sheet with id=AC9, first strand: chain 'F' and resid 510 through 511 Processing sheet with id=AD1, first strand: chain 'G' and resid 414 through 418 Processing sheet with id=AD2, first strand: chain 'G' and resid 490 through 492 Processing sheet with id=AD3, first strand: chain 'G' and resid 498 through 499 Processing sheet with id=AD4, first strand: chain 'G' and resid 510 through 511 Processing sheet with id=AD5, first strand: chain 'H' and resid 414 through 418 Processing sheet with id=AD6, first strand: chain 'H' and resid 490 through 492 Processing sheet with id=AD7, first strand: chain 'H' and resid 498 through 499 Processing sheet with id=AD8, first strand: chain 'H' and resid 510 through 511 Processing sheet with id=AD9, first strand: chain 'I' and resid 414 through 418 Processing sheet with id=AE1, first strand: chain 'I' and resid 490 through 492 Processing sheet with id=AE2, first strand: chain 'I' and resid 498 through 499 Processing sheet with id=AE3, first strand: chain 'I' and resid 510 through 511 Processing sheet with id=AE4, first strand: chain 'J' and resid 414 through 418 Processing sheet with id=AE5, first strand: chain 'J' and resid 490 through 492 Processing sheet with id=AE6, first strand: chain 'J' and resid 498 through 499 Processing sheet with id=AE7, first strand: chain 'J' and resid 510 through 511 Processing sheet with id=AE8, first strand: chain 'K' and resid 414 through 418 Processing sheet with id=AE9, first strand: chain 'K' and resid 490 through 492 Processing sheet with id=AF1, first strand: chain 'K' and resid 498 through 499 Processing sheet with id=AF2, first strand: chain 'K' and resid 510 through 511 Processing sheet with id=AF3, first strand: chain 'L' and resid 414 through 418 Processing sheet with id=AF4, first strand: chain 'L' and resid 490 through 492 Processing sheet with id=AF5, first strand: chain 'L' and resid 498 through 499 Processing sheet with id=AF6, first strand: chain 'L' and resid 510 through 511 Processing sheet with id=AF7, first strand: chain 'M' and resid 414 through 418 Processing sheet with id=AF8, first strand: chain 'M' and resid 490 through 492 Processing sheet with id=AF9, first strand: chain 'M' and resid 498 through 499 Processing sheet with id=AG1, first strand: chain 'M' and resid 510 through 511 Processing sheet with id=AG2, first strand: chain 'N' and resid 490 through 492 Processing sheet with id=AG3, first strand: chain 'N' and resid 498 through 499 Processing sheet with id=AG4, first strand: chain 'N' and resid 510 through 511 1520 hydrogen bonds defined for protein. 4017 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: 7.43 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10667 1.33 - 1.45: 6514 1.45 - 1.57: 24637 1.57 - 1.69: 28 1.69 - 1.81: 252 Bond restraints: 42098 Sorted by residual: bond pdb=" C30 PTY U 801 " pdb=" O4 PTY U 801 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C30 PTY Z 801 " pdb=" O4 PTY Z 801 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C30 PTY P 801 " pdb=" O4 PTY P 801 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C30 PTY a 801 " pdb=" O4 PTY a 801 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C30 PTY Q 801 " pdb=" O4 PTY Q 801 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.73e+01 ... (remaining 42093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 55119 2.04 - 4.08: 1435 4.08 - 6.12: 244 6.12 - 8.17: 70 8.17 - 10.21: 28 Bond angle restraints: 56896 Sorted by residual: angle pdb=" N SER S 107 " pdb=" CA SER S 107 " pdb=" C SER S 107 " ideal model delta sigma weight residual 109.95 115.54 -5.59 1.59e+00 3.96e-01 1.24e+01 angle pdb=" N SER Z 107 " pdb=" CA SER Z 107 " pdb=" C SER Z 107 " ideal model delta sigma weight residual 109.95 115.53 -5.58 1.59e+00 3.96e-01 1.23e+01 angle pdb=" N SER P 107 " pdb=" CA SER P 107 " pdb=" C SER P 107 " ideal model delta sigma weight residual 109.95 115.52 -5.57 1.59e+00 3.96e-01 1.23e+01 angle pdb=" N SER Q 107 " pdb=" CA SER Q 107 " pdb=" C SER Q 107 " ideal model delta sigma weight residual 109.95 115.51 -5.56 1.59e+00 3.96e-01 1.22e+01 angle pdb=" N SER U 107 " pdb=" CA SER U 107 " pdb=" C SER U 107 " ideal model delta sigma weight residual 109.95 115.50 -5.55 1.59e+00 3.96e-01 1.22e+01 ... (remaining 56891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.39: 23702 23.39 - 46.78: 1765 46.78 - 70.17: 321 70.17 - 93.56: 84 93.56 - 116.95: 14 Dihedral angle restraints: 25886 sinusoidal: 10598 harmonic: 15288 Sorted by residual: dihedral pdb=" CB CYS V 101 " pdb=" SG CYS V 101 " pdb=" SG CYS V 104 " pdb=" CB CYS V 104 " ideal model delta sinusoidal sigma weight residual -86.00 -124.34 38.34 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CB CYS Y 101 " pdb=" SG CYS Y 101 " pdb=" SG CYS Y 104 " pdb=" CB CYS Y 104 " ideal model delta sinusoidal sigma weight residual -86.00 -124.33 38.33 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CB CYS T 101 " pdb=" SG CYS T 101 " pdb=" SG CYS T 104 " pdb=" CB CYS T 104 " ideal model delta sinusoidal sigma weight residual -86.00 -124.33 38.33 1 1.00e+01 1.00e-02 2.07e+01 ... (remaining 25883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 5266 0.067 - 0.133: 1234 0.133 - 0.200: 52 0.200 - 0.267: 14 0.267 - 0.334: 14 Chirality restraints: 6580 Sorted by residual: chirality pdb=" CB ILE I 574 " pdb=" CA ILE I 574 " pdb=" CG1 ILE I 574 " pdb=" CG2 ILE I 574 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB ILE N 574 " pdb=" CA ILE N 574 " pdb=" CG1 ILE N 574 " pdb=" CG2 ILE N 574 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE G 574 " pdb=" CA ILE G 574 " pdb=" CG1 ILE G 574 " pdb=" CG2 ILE G 574 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 6577 not shown) Planarity restraints: 7322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU U 73 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO U 74 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO U 74 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO U 74 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 73 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO R 74 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO R 74 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 74 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU W 73 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO W 74 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO W 74 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO W 74 " 0.030 5.00e-02 4.00e+02 ... (remaining 7319 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 11619 2.81 - 3.33: 34705 3.33 - 3.86: 73635 3.86 - 4.38: 89504 4.38 - 4.90: 149539 Nonbonded interactions: 359002 Sorted by model distance: nonbonded pdb=" OH TYR E 483 " pdb=" OD1 ASP F 544 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 483 " pdb=" OD1 ASP B 544 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR L 483 " pdb=" OD1 ASP M 544 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR H 483 " pdb=" OD1 ASP I 544 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR D 483 " pdb=" OD1 ASP E 544 " model vdw 2.289 3.040 ... (remaining 358997 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' and resid 375 through 706) selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'O' and resid 36 through 109) selection = (chain 'P' and resid 36 through 109) selection = (chain 'Q' and resid 36 through 109) selection = (chain 'R' and resid 36 through 109) selection = (chain 'S' and resid 36 through 109) selection = (chain 'T' and resid 36 through 109) selection = (chain 'U' and resid 36 through 109) selection = (chain 'V' and resid 36 through 109) selection = (chain 'W' and resid 36 through 109) selection = (chain 'X' and resid 36 through 109) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 109) selection = (chain 'a' and resid 36 through 109) selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 31.120 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 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 : 0.009 0.122 42126 Z= 0.387 Angle : 0.820 10.208 56952 Z= 0.401 Chirality : 0.055 0.334 6580 Planarity : 0.006 0.053 7322 Dihedral : 17.112 116.953 16002 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.94 % Allowed : 20.13 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.10), residues: 5278 helix: -2.76 (0.11), residues: 1134 sheet: 0.36 (0.10), residues: 2240 loop : -1.36 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG T 55 TYR 0.019 0.002 TYR b 37 PHE 0.011 0.003 PHE N 673 TRP 0.012 0.002 TRP L 471 HIS 0.002 0.001 HIS E 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00872 / 0.39 (42098) covalent geometry : angle 0.82002 / 0.40 (56896) SS BOND : bond 0.00208 / 0.14 ( 28) SS BOND : angle 0.82257 / 0.58 ( 56) hydrogen bonds : bond 0.18497 / 12.43 ( 1520) hydrogen bonds : angle 8.40153 / 5.75 ( 4017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 618 time to evaluate : 1.733 Fit side-chains REVERT: C 394 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8577 (mtmm) REVERT: D 453 GLU cc_start: 0.8445 (tt0) cc_final: 0.8077 (tm-30) REVERT: D 630 MET cc_start: 0.8763 (tpp) cc_final: 0.8375 (tpp) REVERT: E 492 LYS cc_start: 0.8172 (tttm) cc_final: 0.7972 (tttm) REVERT: E 497 MET cc_start: 0.7288 (mmp) cc_final: 0.7041 (mmm) REVERT: F 705 MET cc_start: 0.8713 (mtm) cc_final: 0.8268 (mtp) REVERT: J 394 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8606 (mtmm) REVERT: K 453 GLU cc_start: 0.8444 (tt0) cc_final: 0.8029 (tm-30) REVERT: L 492 LYS cc_start: 0.8192 (tttm) cc_final: 0.7988 (tttm) REVERT: L 497 MET cc_start: 0.7291 (mmp) cc_final: 0.7047 (mmm) REVERT: M 394 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8378 (mttp) REVERT: M 705 MET cc_start: 0.8648 (mtm) cc_final: 0.8194 (mtp) REVERT: O 95 LYS cc_start: 0.8405 (tttt) cc_final: 0.7611 (mptt) REVERT: S 95 LYS cc_start: 0.8501 (tttt) cc_final: 0.7692 (mptt) REVERT: P 95 LYS cc_start: 0.8367 (tttt) cc_final: 0.7586 (mptt) REVERT: Q 95 LYS cc_start: 0.8498 (tttt) cc_final: 0.7701 (mptt) REVERT: R 95 LYS cc_start: 0.8292 (tttt) cc_final: 0.7542 (mptt) REVERT: T 95 LYS cc_start: 0.8468 (tttt) cc_final: 0.7704 (mptt) REVERT: U 95 LYS cc_start: 0.8378 (tttt) cc_final: 0.7587 (mptt) REVERT: V 95 LYS cc_start: 0.8431 (tttt) cc_final: 0.7628 (mptt) REVERT: W 95 LYS cc_start: 0.8407 (tttt) cc_final: 0.7596 (mptt) REVERT: X 95 LYS cc_start: 0.8512 (tttt) cc_final: 0.7707 (mptt) REVERT: Y 95 LYS cc_start: 0.8411 (tttt) cc_final: 0.7592 (mptt) REVERT: Z 95 LYS cc_start: 0.8503 (tttt) cc_final: 0.7686 (mptt) REVERT: a 95 LYS cc_start: 0.8470 (tttt) cc_final: 0.7706 (mptt) REVERT: b 95 LYS cc_start: 0.8377 (tttt) cc_final: 0.7618 (mptt) outliers start: 42 outliers final: 25 residues processed: 652 average time/residue: 0.7921 time to fit residues: 617.8148 Evaluate side-chains 586 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 561 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain G residue 514 SER Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain J residue 514 SER Chi-restraints excluded: chain K residue 514 SER Chi-restraints excluded: chain L residue 514 SER Chi-restraints excluded: chain M residue 514 SER Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain b residue 99 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 ASN A 628 GLN A 643 ASN B 488 ASN B 628 GLN B 643 ASN C 488 ASN C 643 ASN D 643 ASN E 488 ASN E 628 GLN E 643 ASN F 488 ASN G 488 ASN H 488 ASN H 628 GLN H 643 ASN I 488 ASN I 628 GLN I 643 ASN J 488 ASN J 643 ASN K 643 ASN L 488 ASN L 628 GLN L 643 ASN M 488 ASN N 488 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.113514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.094227 restraints weight = 41894.069| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.27 r_work: 0.2894 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 42126 Z= 0.164 Angle : 0.599 7.469 56952 Z= 0.310 Chirality : 0.047 0.142 6580 Planarity : 0.005 0.040 7322 Dihedral : 9.943 94.169 6353 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.36 % Allowed : 17.54 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.11), residues: 5278 helix: 0.02 (0.14), residues: 1148 sheet: 0.55 (0.10), residues: 2100 loop : -1.19 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 703 TYR 0.012 0.001 TYR Y 37 PHE 0.009 0.001 PHE I 684 TRP 0.006 0.001 TRP F 471 HIS 0.002 0.001 HIS E 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (42098) covalent geometry : angle 0.59801 / 0.31 (56896) SS BOND : bond 0.00039 / 0.03 ( 28) SS BOND : angle 1.45489 / 0.90 ( 56) hydrogen bonds : bond 0.04391 / 2.95 ( 1520) hydrogen bonds : angle 5.60378 / 3.85 ( 4017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 583 time to evaluate : 1.633 Fit side-chains REVERT: A 397 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7816 (tp40) REVERT: A 630 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8305 (tpp) REVERT: B 397 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7704 (tp40) REVERT: B 695 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: C 388 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7912 (mttp) REVERT: C 394 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8451 (mtmm) REVERT: C 397 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7729 (tp40) REVERT: C 453 GLU cc_start: 0.8498 (tt0) cc_final: 0.8191 (tm-30) REVERT: D 397 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7687 (tp40) REVERT: D 453 GLU cc_start: 0.8493 (tt0) cc_final: 0.8163 (tm-30) REVERT: D 630 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8380 (tpp) REVERT: E 492 LYS cc_start: 0.8108 (tttm) cc_final: 0.7900 (tttm) REVERT: E 497 MET cc_start: 0.7533 (mmp) cc_final: 0.7331 (mmm) REVERT: E 695 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: F 705 MET cc_start: 0.8639 (mtm) cc_final: 0.8172 (mtp) REVERT: G 453 GLU cc_start: 0.8525 (tt0) cc_final: 0.8250 (tm-30) REVERT: G 628 GLN cc_start: 0.8614 (mp-120) cc_final: 0.7925 (mp-120) REVERT: G 695 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: H 397 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7807 (tp40) REVERT: H 630 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8303 (tpp) REVERT: I 397 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7677 (tp40) REVERT: I 695 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: J 388 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7906 (mttp) REVERT: J 394 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8446 (mtmm) REVERT: J 397 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7729 (tp40) REVERT: J 453 GLU cc_start: 0.8505 (tt0) cc_final: 0.8200 (tm-30) REVERT: K 397 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7689 (tp40) REVERT: K 453 GLU cc_start: 0.8487 (tt0) cc_final: 0.8155 (tm-30) REVERT: L 492 LYS cc_start: 0.8109 (tttm) cc_final: 0.7900 (tttm) REVERT: L 695 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: L 705 MET cc_start: 0.8578 (mtm) cc_final: 0.8341 (mtp) REVERT: M 394 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8225 (mttp) REVERT: M 705 MET cc_start: 0.8576 (mtm) cc_final: 0.8105 (mtp) REVERT: N 453 GLU cc_start: 0.8512 (tt0) cc_final: 0.8238 (tm-30) REVERT: N 628 GLN cc_start: 0.8613 (mp-120) cc_final: 0.7925 (mp-120) REVERT: N 695 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: O 95 LYS cc_start: 0.8168 (tttt) cc_final: 0.7006 (mptt) REVERT: S 95 LYS cc_start: 0.8300 (tttt) cc_final: 0.7139 (mptt) REVERT: P 95 LYS cc_start: 0.8258 (tttt) cc_final: 0.7075 (mptt) REVERT: Q 95 LYS cc_start: 0.8323 (tttt) cc_final: 0.7144 (mptt) REVERT: R 95 LYS cc_start: 0.8110 (tttt) cc_final: 0.6964 (mptt) REVERT: T 95 LYS cc_start: 0.8194 (tttt) cc_final: 0.7115 (mptt) REVERT: U 95 LYS cc_start: 0.8263 (tttt) cc_final: 0.7119 (mptt) REVERT: V 95 LYS cc_start: 0.8277 (tttt) cc_final: 0.7110 (mptt) REVERT: W 95 LYS cc_start: 0.8273 (tttt) cc_final: 0.7086 (mptt) REVERT: X 95 LYS cc_start: 0.8344 (tttt) cc_final: 0.7179 (mptt) REVERT: Y 95 LYS cc_start: 0.8164 (tttt) cc_final: 0.7029 (mptt) REVERT: Z 95 LYS cc_start: 0.8308 (tttt) cc_final: 0.7157 (mptt) REVERT: a 95 LYS cc_start: 0.8206 (tttt) cc_final: 0.7108 (mptt) REVERT: b 95 LYS cc_start: 0.8231 (tttt) cc_final: 0.7100 (mptt) outliers start: 194 outliers final: 58 residues processed: 700 average time/residue: 0.8343 time to fit residues: 697.7192 Evaluate side-chains 626 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 551 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 492 LYS Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 695 GLU Chi-restraints excluded: chain H residue 397 GLN Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain I residue 397 GLN Chi-restraints excluded: chain I residue 630 MET Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain I residue 695 GLU Chi-restraints excluded: chain J residue 397 GLN Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 397 GLN Chi-restraints excluded: chain K residue 492 LYS Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 646 ILE Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain L residue 695 GLU Chi-restraints excluded: chain M residue 630 MET Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 630 MET Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 695 GLU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain b residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 459 optimal weight: 7.9990 chunk 464 optimal weight: 4.9990 chunk 373 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 470 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 408 optimal weight: 1.9990 chunk 345 optimal weight: 1.9990 chunk 407 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 ASN A 628 GLN A 643 ASN B 643 ASN C 546 GLN C 643 ASN D 643 ASN E 643 ASN H 612 ASN H 628 GLN H 643 ASN I 643 ASN J 643 ASN K 643 ASN L 643 ASN U 87 GLN b 87 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.093917 restraints weight = 41912.914| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.27 r_work: 0.2888 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 42126 Z= 0.197 Angle : 0.608 8.080 56952 Z= 0.313 Chirality : 0.048 0.141 6580 Planarity : 0.005 0.040 7322 Dihedral : 9.975 93.298 6335 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.93 % Allowed : 17.77 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.11), residues: 5278 helix: 1.45 (0.15), residues: 1148 sheet: 0.74 (0.10), residues: 2100 loop : -1.08 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 432 TYR 0.013 0.001 TYR O 37 PHE 0.012 0.002 PHE I 684 TRP 0.007 0.001 TRP F 471 HIS 0.002 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (42098) covalent geometry : angle 0.60456 / 0.31 (56896) SS BOND : bond 0.00123 / 0.09 ( 28) SS BOND : angle 2.26966 / 1.33 ( 56) hydrogen bonds : bond 0.04210 / 2.82 ( 1520) hydrogen bonds : angle 5.41803 / 3.73 ( 4017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 589 time to evaluate : 1.803 Fit side-chains REVERT: A 397 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7765 (tp40) REVERT: A 574 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8859 (tp) REVERT: A 630 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8321 (tpp) REVERT: B 397 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7719 (tp40) REVERT: B 695 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: C 388 LYS cc_start: 0.8443 (mtpt) cc_final: 0.7932 (mttp) REVERT: C 394 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8466 (mtmm) REVERT: C 397 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7729 (tp40) REVERT: D 378 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7423 (mtt-85) REVERT: D 397 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7713 (tp40) REVERT: D 453 GLU cc_start: 0.8496 (tt0) cc_final: 0.8169 (tm-30) REVERT: D 630 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8374 (tpp) REVERT: E 397 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7806 (tp40) REVERT: E 492 LYS cc_start: 0.8116 (tttm) cc_final: 0.7906 (tttm) REVERT: E 497 MET cc_start: 0.7505 (mmp) cc_final: 0.7298 (mmm) REVERT: E 574 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8809 (tp) REVERT: E 695 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: F 705 MET cc_start: 0.8571 (mtm) cc_final: 0.8087 (mtp) REVERT: G 574 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.8887 (tp) REVERT: G 628 GLN cc_start: 0.8616 (mp-120) cc_final: 0.7873 (mp-120) REVERT: G 695 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: H 397 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7778 (tp40) REVERT: H 574 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.8838 (tp) REVERT: H 630 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8321 (tpp) REVERT: I 397 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7726 (tp40) REVERT: I 695 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: J 388 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7919 (mttp) REVERT: J 394 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8466 (mtmm) REVERT: J 397 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: K 378 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7408 (mtt-85) REVERT: K 397 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7713 (tp40) REVERT: K 453 GLU cc_start: 0.8491 (tt0) cc_final: 0.8164 (tm-30) REVERT: L 397 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7785 (tp40) REVERT: L 492 LYS cc_start: 0.8109 (tttm) cc_final: 0.7867 (tttm) REVERT: L 574 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8805 (tp) REVERT: L 695 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: M 394 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8237 (mttp) REVERT: M 705 MET cc_start: 0.8579 (mtm) cc_final: 0.8097 (mtp) REVERT: N 574 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8889 (tp) REVERT: N 628 GLN cc_start: 0.8625 (mp-120) cc_final: 0.7884 (mp-120) REVERT: N 695 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: S 95 LYS cc_start: 0.8302 (tttt) cc_final: 0.7186 (mptt) REVERT: P 95 LYS cc_start: 0.8275 (tttt) cc_final: 0.7123 (mptt) REVERT: Q 95 LYS cc_start: 0.8345 (tttt) cc_final: 0.7096 (mptt) REVERT: R 95 LYS cc_start: 0.8182 (tttt) cc_final: 0.7007 (mptt) REVERT: T 95 LYS cc_start: 0.8248 (tttt) cc_final: 0.7141 (mptt) REVERT: U 95 LYS cc_start: 0.8308 (tttt) cc_final: 0.7195 (mptt) REVERT: V 95 LYS cc_start: 0.8347 (tttt) cc_final: 0.7120 (mptt) REVERT: W 38 THR cc_start: 0.8870 (t) cc_final: 0.8593 (m) REVERT: W 95 LYS cc_start: 0.8307 (tttt) cc_final: 0.7139 (mptt) REVERT: X 95 LYS cc_start: 0.8372 (tttt) cc_final: 0.7133 (mptt) REVERT: Y 95 LYS cc_start: 0.8215 (tttt) cc_final: 0.7033 (mptt) REVERT: Z 95 LYS cc_start: 0.8299 (tttt) cc_final: 0.7212 (mptt) REVERT: a 95 LYS cc_start: 0.8234 (tttt) cc_final: 0.7102 (mptt) REVERT: b 95 LYS cc_start: 0.8267 (tttt) cc_final: 0.7169 (mptt) outliers start: 175 outliers final: 78 residues processed: 678 average time/residue: 0.8536 time to fit residues: 690.2649 Evaluate side-chains 668 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 563 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 492 LYS Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 397 GLN Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 695 GLU Chi-restraints excluded: chain H residue 397 GLN Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 646 ILE Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain I residue 397 GLN Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 630 MET Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain I residue 695 GLU Chi-restraints excluded: chain J residue 397 GLN Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 646 ILE Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 397 GLN Chi-restraints excluded: chain K residue 492 LYS Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 646 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 397 GLN Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 646 ILE Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain L residue 695 GLU Chi-restraints excluded: chain M residue 630 MET Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 646 ILE Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 695 GLU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 107 SER Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 107 SER Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 99 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 183 optimal weight: 0.6980 chunk 526 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 518 optimal weight: 0.7980 chunk 416 optimal weight: 7.9990 chunk 408 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 285 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 ASN A 628 GLN A 643 ASN B 643 ASN C 643 ASN D 643 ASN E 643 ASN H 612 ASN H 628 GLN H 643 ASN I 643 ASN J 643 ASN K 643 ASN L 643 ASN Y 87 GLN b 87 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.095050 restraints weight = 41786.774| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.27 r_work: 0.2905 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 42126 Z= 0.160 Angle : 0.583 10.991 56952 Z= 0.300 Chirality : 0.047 0.162 6580 Planarity : 0.005 0.038 7322 Dihedral : 9.833 91.316 6335 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.31 % Allowed : 17.52 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.11), residues: 5278 helix: 2.05 (0.15), residues: 1148 sheet: 0.79 (0.10), residues: 2100 loop : -1.03 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 432 TYR 0.010 0.001 TYR R 37 PHE 0.008 0.001 PHE B 684 TRP 0.006 0.001 TRP N 471 HIS 0.001 0.001 HIS M 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (42098) covalent geometry : angle 0.57794 / 0.30 (56896) SS BOND : bond 0.00584 / 0.43 ( 28) SS BOND : angle 2.46666 / 2.16 ( 56) hydrogen bonds : bond 0.03843 / 2.58 ( 1520) hydrogen bonds : angle 5.24906 / 3.62 ( 4017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 592 time to evaluate : 1.715 Fit side-chains REVERT: A 397 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7749 (tp40) REVERT: A 574 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8798 (tp) REVERT: A 630 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8324 (tpp) REVERT: B 397 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7703 (tp40) REVERT: B 695 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: C 388 LYS cc_start: 0.8437 (mtpt) cc_final: 0.7925 (mttp) REVERT: C 397 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7718 (tp40) REVERT: C 453 GLU cc_start: 0.8492 (tt0) cc_final: 0.8183 (tm-30) REVERT: D 378 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7379 (mtt-85) REVERT: D 397 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7697 (tp40) REVERT: D 453 GLU cc_start: 0.8485 (tt0) cc_final: 0.8167 (tm-30) REVERT: D 532 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8896 (tp) REVERT: D 630 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8389 (tpp) REVERT: E 397 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7773 (tp40) REVERT: E 492 LYS cc_start: 0.8096 (tttm) cc_final: 0.7855 (tttm) REVERT: E 497 MET cc_start: 0.7473 (mmp) cc_final: 0.7262 (mmm) REVERT: E 574 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8728 (tp) REVERT: E 695 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: F 613 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8310 (mtt180) REVERT: F 705 MET cc_start: 0.8578 (mtm) cc_final: 0.8127 (mtp) REVERT: G 574 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8847 (tp) REVERT: G 695 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: H 397 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7744 (tp40) REVERT: H 574 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8789 (tp) REVERT: H 630 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8320 (tpp) REVERT: I 397 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7694 (tp40) REVERT: I 695 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: J 388 LYS cc_start: 0.8423 (mtpt) cc_final: 0.7910 (mttp) REVERT: J 394 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8453 (mtmm) REVERT: J 397 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7709 (tp40) REVERT: J 453 GLU cc_start: 0.8508 (tt0) cc_final: 0.8201 (tm-30) REVERT: K 378 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7354 (mtt-85) REVERT: K 397 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7672 (tp40) REVERT: K 453 GLU cc_start: 0.8482 (tt0) cc_final: 0.8164 (tm-30) REVERT: K 532 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8895 (tp) REVERT: L 397 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7765 (tp40) REVERT: L 492 LYS cc_start: 0.8095 (tttm) cc_final: 0.7854 (tttm) REVERT: L 574 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8726 (tp) REVERT: L 695 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: M 394 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8245 (mttp) REVERT: M 613 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8311 (mtt180) REVERT: M 705 MET cc_start: 0.8582 (mtm) cc_final: 0.8129 (mtp) REVERT: N 397 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7718 (tp40) REVERT: N 574 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8844 (tp) REVERT: N 695 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: S 95 LYS cc_start: 0.8331 (tttt) cc_final: 0.7235 (mptt) REVERT: P 38 THR cc_start: 0.8830 (t) cc_final: 0.8532 (m) REVERT: P 95 LYS cc_start: 0.8273 (tttt) cc_final: 0.7125 (mptt) REVERT: R 95 LYS cc_start: 0.8214 (tttt) cc_final: 0.7055 (mptt) REVERT: T 95 LYS cc_start: 0.8265 (tttt) cc_final: 0.7120 (mptt) REVERT: U 95 LYS cc_start: 0.8257 (tttt) cc_final: 0.7180 (mptt) REVERT: V 95 LYS cc_start: 0.8343 (tttt) cc_final: 0.7078 (mptt) REVERT: W 38 THR cc_start: 0.8818 (t) cc_final: 0.8550 (m) REVERT: W 95 LYS cc_start: 0.8275 (tttt) cc_final: 0.7131 (mptt) REVERT: Y 95 LYS cc_start: 0.8238 (tttt) cc_final: 0.7031 (mptt) REVERT: Z 95 LYS cc_start: 0.8346 (tttt) cc_final: 0.7221 (mptt) REVERT: a 95 LYS cc_start: 0.8232 (tttt) cc_final: 0.7053 (mptt) REVERT: b 95 LYS cc_start: 0.8256 (tttt) cc_final: 0.7192 (mptt) outliers start: 192 outliers final: 86 residues processed: 700 average time/residue: 0.8381 time to fit residues: 702.0424 Evaluate side-chains 690 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 574 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 539 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 492 LYS Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 397 GLN Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 613 ARG Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 695 GLU Chi-restraints excluded: chain H residue 397 GLN Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 646 ILE Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain I residue 397 GLN Chi-restraints excluded: chain I residue 630 MET Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain I residue 695 GLU Chi-restraints excluded: chain J residue 397 GLN Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 646 ILE Chi-restraints excluded: chain K residue 397 GLN Chi-restraints excluded: chain K residue 532 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 646 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 397 GLN Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 646 ILE Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain L residue 695 GLU Chi-restraints excluded: chain M residue 574 ILE Chi-restraints excluded: chain M residue 613 ARG Chi-restraints excluded: chain M residue 630 MET Chi-restraints excluded: chain M residue 642 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 397 GLN Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 646 ILE Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 695 GLU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 107 SER Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 107 SER Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain T residue 107 SER Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 107 SER Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 106 THR Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 107 SER Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 107 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 404 optimal weight: 1.9990 chunk 343 optimal weight: 7.9990 chunk 455 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 355 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 492 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 GLN A 643 ASN B 546 GLN B 643 ASN C 643 ASN D 643 ASN E 643 ASN G 628 GLN H 546 GLN H 628 GLN H 643 ASN I 546 GLN I 643 ASN J 546 GLN J 643 ASN K 643 ASN L 643 ASN N 628 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.093987 restraints weight = 41556.843| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.26 r_work: 0.2890 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 42126 Z= 0.211 Angle : 0.641 14.468 56952 Z= 0.327 Chirality : 0.049 0.238 6580 Planarity : 0.005 0.040 7322 Dihedral : 10.118 94.171 6335 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.92 % Allowed : 16.85 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.11), residues: 5278 helix: 2.16 (0.15), residues: 1148 sheet: 0.86 (0.10), residues: 2100 loop : -1.02 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 432 TYR 0.012 0.002 TYR R 37 PHE 0.012 0.002 PHE B 684 TRP 0.007 0.001 TRP G 471 HIS 0.002 0.001 HIS N 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (42098) covalent geometry : angle 0.63015 / 0.32 (56896) SS BOND : bond 0.00900 / 0.60 ( 28) SS BOND : angle 3.72021 / 2.60 ( 56) hydrogen bonds : bond 0.04104 / 2.75 ( 1520) hydrogen bonds : angle 5.28279 / 3.64 ( 4017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 594 time to evaluate : 1.797 Fit side-chains REVERT: A 397 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7744 (tp40) REVERT: A 574 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.8927 (tp) REVERT: A 630 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8319 (tpp) REVERT: A 695 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: B 397 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7695 (tp40) REVERT: B 695 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: C 388 LYS cc_start: 0.8451 (mtpt) cc_final: 0.7935 (mttp) REVERT: C 394 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8478 (mtmm) REVERT: C 397 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7657 (tp40) REVERT: C 613 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8414 (mtp180) REVERT: C 695 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: D 378 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7320 (mtt-85) REVERT: D 397 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7678 (tp40) REVERT: D 453 GLU cc_start: 0.8472 (tt0) cc_final: 0.8105 (tm-30) REVERT: D 532 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8848 (tp) REVERT: D 574 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9118 (tp) REVERT: D 630 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8385 (tpp) REVERT: E 397 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7783 (tp40) REVERT: E 492 LYS cc_start: 0.8076 (tttm) cc_final: 0.7814 (tttm) REVERT: E 574 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8792 (tp) REVERT: F 613 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8357 (mtt180) REVERT: F 695 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: F 705 MET cc_start: 0.8576 (mtm) cc_final: 0.8133 (mtp) REVERT: G 574 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8883 (tp) REVERT: G 695 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: H 397 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7753 (tp40) REVERT: H 574 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8874 (tp) REVERT: H 630 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8321 (tpp) REVERT: H 695 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: I 397 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7680 (tp40) REVERT: I 532 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8945 (tp) REVERT: I 695 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: J 388 LYS cc_start: 0.8439 (mtpt) cc_final: 0.7926 (mttp) REVERT: J 394 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8476 (mtmm) REVERT: J 397 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7657 (tp40) REVERT: J 613 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8415 (mtp180) REVERT: J 695 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: K 378 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7307 (mtt-85) REVERT: K 397 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7681 (tp40) REVERT: K 453 GLU cc_start: 0.8471 (tt0) cc_final: 0.8104 (tm-30) REVERT: K 532 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8845 (tp) REVERT: L 397 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7774 (tp40) REVERT: L 492 LYS cc_start: 0.8073 (tttm) cc_final: 0.7813 (tttm) REVERT: L 574 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8792 (tp) REVERT: M 394 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8252 (mttp) REVERT: M 613 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8352 (mtt180) REVERT: M 705 MET cc_start: 0.8583 (mtm) cc_final: 0.8143 (mtp) REVERT: N 574 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8886 (tp) REVERT: N 695 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: N 703 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8280 (mtt-85) REVERT: S 95 LYS cc_start: 0.8356 (tttt) cc_final: 0.7250 (mptt) REVERT: P 38 THR cc_start: 0.8797 (t) cc_final: 0.8514 (m) REVERT: P 95 LYS cc_start: 0.8297 (tttt) cc_final: 0.7141 (mptt) REVERT: R 95 LYS cc_start: 0.8242 (tttt) cc_final: 0.7061 (mptt) REVERT: T 95 LYS cc_start: 0.8326 (tttt) cc_final: 0.7153 (mptt) REVERT: U 95 LYS cc_start: 0.8234 (tttt) cc_final: 0.7145 (mptt) REVERT: V 95 LYS cc_start: 0.8395 (tttt) cc_final: 0.7106 (mptt) REVERT: W 38 THR cc_start: 0.8806 (t) cc_final: 0.8523 (m) REVERT: W 95 LYS cc_start: 0.8292 (tttt) cc_final: 0.7127 (mptt) REVERT: Y 95 LYS cc_start: 0.8254 (tttt) cc_final: 0.7037 (mptt) REVERT: Z 95 LYS cc_start: 0.8368 (tttt) cc_final: 0.7225 (mptt) REVERT: b 95 LYS cc_start: 0.8278 (tttt) cc_final: 0.7168 (mptt) outliers start: 219 outliers final: 102 residues processed: 714 average time/residue: 0.8637 time to fit residues: 734.8951 Evaluate side-chains 722 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 582 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 539 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 613 ARG Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 492 LYS Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 397 GLN Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 613 ARG Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain F residue 695 GLU Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 695 GLU Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 397 GLN Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 646 ILE Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain H residue 695 GLU Chi-restraints excluded: chain I residue 397 GLN Chi-restraints excluded: chain I residue 532 ILE Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 630 MET Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain I residue 695 GLU Chi-restraints excluded: chain J residue 397 GLN Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 575 LEU Chi-restraints excluded: chain J residue 613 ARG Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 646 ILE Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain J residue 695 GLU Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 397 GLN Chi-restraints excluded: chain K residue 532 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 646 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 397 GLN Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 646 ILE Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 574 ILE Chi-restraints excluded: chain M residue 613 ARG Chi-restraints excluded: chain M residue 630 MET Chi-restraints excluded: chain M residue 642 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 646 ILE Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 695 GLU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 107 SER Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 107 SER Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 107 SER Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 107 SER Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 106 THR Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 107 SER Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 107 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 111 optimal weight: 4.9990 chunk 435 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 chunk 473 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 495 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 ASN A 628 GLN A 643 ASN B 643 ASN C 643 ASN D 643 ASN E 643 ASN G 628 GLN H 612 ASN H 628 GLN H 643 ASN I 643 ASN J 643 ASN K 643 ASN L 643 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.095447 restraints weight = 41643.557| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.27 r_work: 0.2912 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 42126 Z= 0.151 Angle : 0.584 12.095 56952 Z= 0.299 Chirality : 0.047 0.208 6580 Planarity : 0.005 0.042 7322 Dihedral : 9.873 91.483 6335 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.34 % Allowed : 17.88 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.11), residues: 5278 helix: 2.38 (0.15), residues: 1148 sheet: 0.82 (0.10), residues: 2226 loop : -0.85 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 432 TYR 0.009 0.001 TYR C 463 PHE 0.008 0.001 PHE A 520 TRP 0.005 0.001 TRP N 471 HIS 0.001 0.001 HIS L 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (42098) covalent geometry : angle 0.57568 / 0.30 (56896) SS BOND : bond 0.00696 / 0.46 ( 28) SS BOND : angle 3.14358 / 2.11 ( 56) hydrogen bonds : bond 0.03729 / 2.51 ( 1520) hydrogen bonds : angle 5.17414 / 3.57 ( 4017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 599 time to evaluate : 1.749 Fit side-chains REVERT: A 397 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7734 (tp40) REVERT: A 574 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8759 (tp) REVERT: A 612 ASN cc_start: 0.9148 (m-40) cc_final: 0.8838 (m110) REVERT: A 630 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8342 (tpp) REVERT: A 695 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: B 397 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7696 (tp40) REVERT: B 695 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: C 388 LYS cc_start: 0.8433 (mtpt) cc_final: 0.7913 (mttp) REVERT: C 394 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8474 (mtmm) REVERT: C 397 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7658 (tp40) REVERT: C 453 GLU cc_start: 0.8490 (tt0) cc_final: 0.8206 (tm-30) REVERT: C 613 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8340 (mtp180) REVERT: C 695 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: D 378 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7353 (mtt180) REVERT: D 397 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7682 (tp40) REVERT: D 453 GLU cc_start: 0.8477 (tt0) cc_final: 0.8116 (tm-30) REVERT: D 532 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8890 (tp) REVERT: D 574 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9083 (tp) REVERT: D 630 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8400 (tpp) REVERT: E 492 LYS cc_start: 0.8062 (tttm) cc_final: 0.7798 (tttm) REVERT: E 574 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8692 (tp) REVERT: F 613 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8303 (mtt180) REVERT: F 695 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: F 705 MET cc_start: 0.8582 (mtm) cc_final: 0.8150 (mtp) REVERT: G 574 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8801 (tp) REVERT: G 695 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: H 397 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7731 (tp40) REVERT: H 574 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8723 (tp) REVERT: H 630 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8341 (tpp) REVERT: H 695 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: I 397 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7695 (tp40) REVERT: I 532 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8911 (tp) REVERT: I 613 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8248 (mtt180) REVERT: I 695 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: J 388 LYS cc_start: 0.8388 (mtpt) cc_final: 0.7864 (mttp) REVERT: J 394 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8466 (mtmm) REVERT: J 397 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7658 (tp40) REVERT: J 453 GLU cc_start: 0.8498 (tt0) cc_final: 0.8216 (tm-30) REVERT: J 613 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8335 (mtp180) REVERT: J 695 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: K 378 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7337 (mtt180) REVERT: K 397 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7685 (tp40) REVERT: K 453 GLU cc_start: 0.8478 (tt0) cc_final: 0.8116 (tm-30) REVERT: K 532 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8891 (tp) REVERT: L 492 LYS cc_start: 0.8054 (tttm) cc_final: 0.7790 (tttm) REVERT: L 574 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8689 (tp) REVERT: M 394 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8245 (mttp) REVERT: M 613 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8305 (mtt180) REVERT: M 695 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: M 705 MET cc_start: 0.8575 (mtm) cc_final: 0.8142 (mtp) REVERT: N 574 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8799 (tp) REVERT: N 695 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: S 95 LYS cc_start: 0.8363 (tttt) cc_final: 0.7208 (mptt) REVERT: P 38 THR cc_start: 0.8776 (t) cc_final: 0.8499 (m) REVERT: P 95 LYS cc_start: 0.8286 (tttt) cc_final: 0.7121 (mptt) REVERT: R 95 LYS cc_start: 0.8263 (tttt) cc_final: 0.7086 (mptt) REVERT: U 95 LYS cc_start: 0.8250 (tttt) cc_final: 0.7158 (mptt) REVERT: V 95 LYS cc_start: 0.8387 (tttt) cc_final: 0.7086 (mptt) REVERT: W 38 THR cc_start: 0.8774 (t) cc_final: 0.8515 (m) REVERT: W 95 LYS cc_start: 0.8286 (tttt) cc_final: 0.7109 (mptt) REVERT: Y 95 LYS cc_start: 0.8241 (tttt) cc_final: 0.7028 (mptt) REVERT: Z 95 LYS cc_start: 0.8370 (tttt) cc_final: 0.7197 (mptt) REVERT: b 95 LYS cc_start: 0.8259 (tttt) cc_final: 0.7149 (mptt) outliers start: 193 outliers final: 88 residues processed: 708 average time/residue: 0.8636 time to fit residues: 728.5736 Evaluate side-chains 704 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 578 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 539 ASP Chi-restraints excluded: chain C residue 613 ARG Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 492 LYS Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 613 ARG Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain F residue 695 GLU Chi-restraints excluded: chain G residue 388 LYS Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 695 GLU Chi-restraints excluded: chain H residue 397 GLN Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 646 ILE Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain H residue 695 GLU Chi-restraints excluded: chain I residue 397 GLN Chi-restraints excluded: chain I residue 532 ILE Chi-restraints excluded: chain I residue 613 ARG Chi-restraints excluded: chain I residue 630 MET Chi-restraints excluded: chain I residue 695 GLU Chi-restraints excluded: chain J residue 397 GLN Chi-restraints excluded: chain J residue 613 ARG Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 646 ILE Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain J residue 695 GLU Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 397 GLN Chi-restraints excluded: chain K residue 532 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 646 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 539 ASP Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 646 ILE Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 574 ILE Chi-restraints excluded: chain M residue 613 ARG Chi-restraints excluded: chain M residue 630 MET Chi-restraints excluded: chain M residue 642 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain M residue 695 GLU Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 646 ILE Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 695 GLU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 107 SER Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 107 SER Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 106 THR Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 107 SER Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 107 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 273 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 223 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 334 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 337 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 447 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 GLN A 643 ASN B 643 ASN C 643 ASN D 643 ASN E 643 ASN H 628 GLN H 643 ASN I 643 ASN J 643 ASN K 643 ASN L 643 ASN N 628 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.094589 restraints weight = 41503.726| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.27 r_work: 0.2898 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 42126 Z= 0.189 Angle : 0.623 14.516 56952 Z= 0.317 Chirality : 0.048 0.229 6580 Planarity : 0.005 0.041 7322 Dihedral : 10.123 92.966 6334 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.38 % Allowed : 17.79 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.11), residues: 5278 helix: 2.34 (0.15), residues: 1148 sheet: 0.87 (0.10), residues: 2226 loop : -0.84 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 432 TYR 0.011 0.001 TYR R 37 PHE 0.010 0.002 PHE I 684 TRP 0.006 0.001 TRP G 471 HIS 0.002 0.001 HIS G 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (42098) covalent geometry : angle 0.61341 / 0.31 (56896) SS BOND : bond 0.00772 / 0.55 ( 28) SS BOND : angle 3.53972 / 2.23 ( 56) hydrogen bonds : bond 0.03952 / 2.65 ( 1520) hydrogen bonds : angle 5.22534 / 3.60 ( 4017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 587 time to evaluate : 1.711 Fit side-chains REVERT: A 397 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7750 (tp40) REVERT: A 574 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8852 (tp) REVERT: A 630 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8338 (tpp) REVERT: A 695 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: B 397 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7692 (tp40) REVERT: B 613 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8268 (mtt180) REVERT: C 388 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7896 (mttp) REVERT: C 394 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8479 (mtmm) REVERT: C 397 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7654 (tp40) REVERT: C 574 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9088 (tp) REVERT: C 613 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8406 (mtp180) REVERT: C 695 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: D 378 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7295 (mtt-85) REVERT: D 397 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7679 (tp40) REVERT: D 453 GLU cc_start: 0.8468 (tt0) cc_final: 0.8109 (tm-30) REVERT: D 532 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8850 (tp) REVERT: D 574 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9098 (tp) REVERT: D 612 ASN cc_start: 0.9185 (m-40) cc_final: 0.8906 (m-40) REVERT: D 630 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8395 (tpp) REVERT: E 492 LYS cc_start: 0.8029 (tttm) cc_final: 0.7763 (tttm) REVERT: E 574 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8763 (tp) REVERT: F 613 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8346 (mtt180) REVERT: F 705 MET cc_start: 0.8586 (mtm) cc_final: 0.8137 (mtp) REVERT: G 574 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8837 (tp) REVERT: G 695 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: H 397 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7745 (tp40) REVERT: H 574 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8782 (tp) REVERT: H 630 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8337 (tpp) REVERT: H 695 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: I 397 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7680 (tp40) REVERT: I 613 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8287 (mtt180) REVERT: J 388 LYS cc_start: 0.8407 (mtpt) cc_final: 0.7882 (mttp) REVERT: J 394 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8476 (mtmm) REVERT: J 397 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7651 (tp40) REVERT: J 574 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9084 (tp) REVERT: J 613 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8405 (mtp180) REVERT: J 695 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: K 378 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7285 (mtt-85) REVERT: K 397 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7681 (tp40) REVERT: K 453 GLU cc_start: 0.8470 (tt0) cc_final: 0.8111 (tm-30) REVERT: K 532 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8848 (tp) REVERT: K 574 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9099 (tp) REVERT: K 612 ASN cc_start: 0.9192 (m-40) cc_final: 0.8912 (m-40) REVERT: L 492 LYS cc_start: 0.8036 (tttm) cc_final: 0.7755 (tttm) REVERT: L 574 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8759 (tp) REVERT: M 394 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8259 (mttp) REVERT: M 613 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8347 (mtt180) REVERT: M 705 MET cc_start: 0.8582 (mtm) cc_final: 0.8133 (mtp) REVERT: N 574 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8840 (tp) REVERT: N 695 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: S 95 LYS cc_start: 0.8388 (tttt) cc_final: 0.7225 (mptt) REVERT: P 38 THR cc_start: 0.8775 (t) cc_final: 0.8497 (m) REVERT: P 95 LYS cc_start: 0.8288 (tttt) cc_final: 0.7122 (mptt) REVERT: U 95 LYS cc_start: 0.8276 (tttt) cc_final: 0.7170 (mptt) REVERT: W 38 THR cc_start: 0.8785 (t) cc_final: 0.8506 (m) REVERT: W 95 LYS cc_start: 0.8272 (tttt) cc_final: 0.7103 (mptt) REVERT: Z 95 LYS cc_start: 0.8406 (tttt) cc_final: 0.7218 (mptt) REVERT: b 95 LYS cc_start: 0.8280 (tttt) cc_final: 0.7130 (mptt) outliers start: 195 outliers final: 96 residues processed: 691 average time/residue: 0.8718 time to fit residues: 717.3007 Evaluate side-chains 715 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 582 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 539 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 613 ARG Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 629 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 613 ARG Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 388 LYS Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 661 SER Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 695 GLU Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 397 GLN Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 646 ILE Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain H residue 695 GLU Chi-restraints excluded: chain I residue 397 GLN Chi-restraints excluded: chain I residue 613 ARG Chi-restraints excluded: chain I residue 630 MET Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain J residue 397 GLN Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 613 ARG Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 629 ASN Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 646 ILE Chi-restraints excluded: chain J residue 661 SER Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain J residue 695 GLU Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 397 GLN Chi-restraints excluded: chain K residue 532 ILE Chi-restraints excluded: chain K residue 574 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 646 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 539 ASP Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 646 ILE Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 574 ILE Chi-restraints excluded: chain M residue 613 ARG Chi-restraints excluded: chain M residue 630 MET Chi-restraints excluded: chain M residue 642 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 646 ILE Chi-restraints excluded: chain N residue 661 SER Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 695 GLU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 107 SER Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 107 SER Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 106 THR Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 106 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 107 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 259 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 430 optimal weight: 0.0980 chunk 486 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 449 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 522 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 445 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 GLN A 643 ASN B 643 ASN C 643 ASN D 643 ASN E 643 ASN G 628 GLN H 643 ASN I 643 ASN J 643 ASN K 643 ASN L 643 ASN N 628 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.095750 restraints weight = 41764.802| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.18 r_work: 0.2921 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 42126 Z= 0.165 Angle : 0.625 16.353 56952 Z= 0.317 Chirality : 0.047 0.209 6580 Planarity : 0.005 0.042 7322 Dihedral : 10.128 92.063 6334 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.18 % Allowed : 18.01 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.11), residues: 5278 helix: 2.42 (0.15), residues: 1148 sheet: 0.84 (0.10), residues: 2226 loop : -0.82 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 432 TYR 0.009 0.001 TYR R 37 PHE 0.009 0.001 PHE A 520 TRP 0.006 0.001 TRP H 471 HIS 0.002 0.001 HIS E 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (42098) covalent geometry : angle 0.60959 / 0.31 (56896) SS BOND : bond 0.00573 / 0.37 ( 28) SS BOND : angle 4.41553 / 3.24 ( 56) hydrogen bonds : bond 0.03794 / 2.55 ( 1520) hydrogen bonds : angle 5.17830 / 3.57 ( 4017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 581 time to evaluate : 1.799 Fit side-chains REVERT: A 397 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7702 (tp40) REVERT: A 574 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8745 (tp) REVERT: A 630 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8318 (tpp) REVERT: A 695 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: B 397 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7625 (tp40) REVERT: B 613 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8204 (mtt180) REVERT: B 695 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: C 394 LYS cc_start: 0.8788 (mtpt) cc_final: 0.8419 (mtmm) REVERT: C 397 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7592 (tp40) REVERT: C 453 GLU cc_start: 0.8474 (tt0) cc_final: 0.8177 (tm-30) REVERT: C 574 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9038 (tp) REVERT: C 613 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8297 (mtp180) REVERT: C 695 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: D 378 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7281 (mtt-85) REVERT: D 397 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7624 (tp40) REVERT: D 453 GLU cc_start: 0.8411 (tt0) cc_final: 0.8045 (tm-30) REVERT: D 532 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8875 (tp) REVERT: D 574 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9028 (tp) REVERT: D 612 ASN cc_start: 0.9160 (m-40) cc_final: 0.8819 (m-40) REVERT: D 630 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8391 (tpp) REVERT: E 574 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8700 (tp) REVERT: F 613 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8289 (mtt180) REVERT: F 652 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8023 (pt0) REVERT: F 705 MET cc_start: 0.8558 (mtm) cc_final: 0.8102 (mtp) REVERT: G 574 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8787 (tp) REVERT: G 695 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: H 397 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7699 (tp40) REVERT: H 574 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8720 (tp) REVERT: H 630 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8318 (tpp) REVERT: H 695 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: I 397 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7620 (tp40) REVERT: I 613 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8218 (mtt180) REVERT: I 695 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: J 388 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7821 (mttp) REVERT: J 394 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8420 (mtmm) REVERT: J 397 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7601 (tp40) REVERT: J 453 GLU cc_start: 0.8477 (tt0) cc_final: 0.8184 (tm-30) REVERT: J 574 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9035 (tp) REVERT: J 613 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8301 (mtp180) REVERT: J 695 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: K 378 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7261 (mtt-85) REVERT: K 397 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7625 (tp40) REVERT: K 453 GLU cc_start: 0.8412 (tt0) cc_final: 0.8047 (tm-30) REVERT: K 532 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8875 (tp) REVERT: K 612 ASN cc_start: 0.9166 (m-40) cc_final: 0.8826 (m-40) REVERT: L 492 LYS cc_start: 0.7997 (tttm) cc_final: 0.7714 (tttm) REVERT: L 574 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8697 (tp) REVERT: M 394 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8207 (mttp) REVERT: M 613 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8288 (mtt180) REVERT: M 705 MET cc_start: 0.8549 (mtm) cc_final: 0.8091 (mtp) REVERT: N 574 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8788 (tp) REVERT: N 695 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: S 95 LYS cc_start: 0.8325 (tttt) cc_final: 0.7131 (mptt) REVERT: P 38 THR cc_start: 0.8759 (t) cc_final: 0.8480 (m) REVERT: P 95 LYS cc_start: 0.8223 (tttt) cc_final: 0.7025 (mptt) REVERT: T 104 CYS cc_start: 0.7540 (t) cc_final: 0.7270 (m) REVERT: U 95 LYS cc_start: 0.8224 (tttt) cc_final: 0.7111 (mptt) REVERT: W 38 THR cc_start: 0.8752 (t) cc_final: 0.8492 (m) REVERT: W 95 LYS cc_start: 0.8226 (tttt) cc_final: 0.7030 (mptt) REVERT: Z 95 LYS cc_start: 0.8326 (tttt) cc_final: 0.7129 (mptt) REVERT: a 104 CYS cc_start: 0.7577 (t) cc_final: 0.7289 (m) REVERT: b 95 LYS cc_start: 0.8280 (tttt) cc_final: 0.7088 (mptt) outliers start: 186 outliers final: 97 residues processed: 689 average time/residue: 0.8623 time to fit residues: 708.6176 Evaluate side-chains 707 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 572 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 539 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 613 ARG Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 613 ARG Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 661 SER Chi-restraints excluded: chain F residue 690 THR Chi-restraints excluded: chain G residue 388 LYS Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 695 GLU Chi-restraints excluded: chain H residue 397 GLN Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 646 ILE Chi-restraints excluded: chain H residue 661 SER Chi-restraints excluded: chain H residue 690 THR Chi-restraints excluded: chain H residue 695 GLU Chi-restraints excluded: chain I residue 397 GLN Chi-restraints excluded: chain I residue 613 ARG Chi-restraints excluded: chain I residue 630 MET Chi-restraints excluded: chain I residue 661 SER Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain I residue 695 GLU Chi-restraints excluded: chain J residue 397 GLN Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 613 ARG Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 646 ILE Chi-restraints excluded: chain J residue 661 SER Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain J residue 695 GLU Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 397 GLN Chi-restraints excluded: chain K residue 532 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 646 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 539 ASP Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 646 ILE Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain L residue 690 THR Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 574 ILE Chi-restraints excluded: chain M residue 613 ARG Chi-restraints excluded: chain M residue 630 MET Chi-restraints excluded: chain M residue 642 VAL Chi-restraints excluded: chain M residue 661 SER Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 646 ILE Chi-restraints excluded: chain N residue 661 SER Chi-restraints excluded: chain N residue 690 THR Chi-restraints excluded: chain N residue 695 GLU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 107 SER Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 106 THR Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 107 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 188 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 426 optimal weight: 0.6980 chunk 328 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 402 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 GLN A 643 ASN B 643 ASN C 643 ASN D 643 ASN E 643 ASN G 628 GLN H 628 GLN H 643 ASN I 643 ASN J 643 ASN K 643 ASN L 643 ASN N 628 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.095508 restraints weight = 42477.723| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.36 r_work: 0.2920 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 42126 Z= 0.131 Angle : 0.591 14.404 56952 Z= 0.300 Chirality : 0.047 0.174 6580 Planarity : 0.005 0.041 7322 Dihedral : 9.853 88.571 6334 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.44 % Allowed : 19.00 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.11), residues: 5278 helix: 2.57 (0.15), residues: 1148 sheet: 0.79 (0.10), residues: 2226 loop : -0.79 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 432 TYR 0.007 0.001 TYR C 463 PHE 0.008 0.001 PHE A 520 TRP 0.005 0.001 TRP I 471 HIS 0.001 0.000 HIS F 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (42098) covalent geometry : angle 0.57749 / 0.29 (56896) SS BOND : bond 0.00423 / 0.26 ( 28) SS BOND : angle 4.10419 / 3.04 ( 56) hydrogen bonds : bond 0.03557 / 2.39 ( 1520) hydrogen bonds : angle 5.11223 / 3.52 ( 4017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 597 time to evaluate : 1.839 Fit side-chains REVERT: A 397 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7763 (tp40) REVERT: A 574 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 630 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8300 (tpp) REVERT: A 695 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: B 397 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7604 (tp40) REVERT: B 613 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8197 (mtt180) REVERT: B 695 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: C 394 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8441 (mtmm) REVERT: C 397 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7610 (tp40) REVERT: C 453 GLU cc_start: 0.8523 (tt0) cc_final: 0.8238 (tm-30) REVERT: C 574 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9017 (tp) REVERT: C 613 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8330 (mtp180) REVERT: C 630 MET cc_start: 0.8749 (mmm) cc_final: 0.8510 (tpp) REVERT: C 695 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: D 378 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7299 (mtt-85) REVERT: D 453 GLU cc_start: 0.8465 (tt0) cc_final: 0.8083 (tm-30) REVERT: D 532 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8830 (tp) REVERT: D 574 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8975 (tp) REVERT: D 612 ASN cc_start: 0.9148 (m-40) cc_final: 0.8801 (m-40) REVERT: D 630 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8399 (tpp) REVERT: E 574 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8712 (tp) REVERT: F 613 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8290 (mtt180) REVERT: F 652 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8052 (pt0) REVERT: G 574 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8774 (tp) REVERT: G 695 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: H 397 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7764 (tp40) REVERT: H 574 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8601 (tp) REVERT: H 630 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8300 (tpp) REVERT: H 695 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: I 397 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7598 (tp40) REVERT: I 613 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8213 (mtt180) REVERT: I 695 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8324 (tp30) REVERT: J 394 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8448 (mtmm) REVERT: J 397 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7603 (tp40) REVERT: J 453 GLU cc_start: 0.8533 (tt0) cc_final: 0.8252 (tm-30) REVERT: J 574 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9017 (tp) REVERT: J 613 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8329 (mtp180) REVERT: J 630 MET cc_start: 0.8747 (mmm) cc_final: 0.8512 (tpp) REVERT: J 695 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: K 378 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7290 (mtt-85) REVERT: K 453 GLU cc_start: 0.8471 (tt0) cc_final: 0.8088 (tm-30) REVERT: K 532 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8833 (tp) REVERT: K 612 ASN cc_start: 0.9158 (m-40) cc_final: 0.8813 (m-40) REVERT: L 574 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8713 (tp) REVERT: M 394 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8217 (mttp) REVERT: M 613 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8265 (mtt180) REVERT: N 574 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8771 (tp) REVERT: N 695 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: S 95 LYS cc_start: 0.8387 (tttt) cc_final: 0.7150 (mptt) REVERT: P 38 THR cc_start: 0.8738 (t) cc_final: 0.8459 (m) REVERT: P 95 LYS cc_start: 0.8252 (tttt) cc_final: 0.7035 (mptt) REVERT: U 95 LYS cc_start: 0.8241 (tttt) cc_final: 0.7128 (mptt) REVERT: W 38 THR cc_start: 0.8739 (t) cc_final: 0.8472 (m) REVERT: W 95 LYS cc_start: 0.8256 (tttt) cc_final: 0.7040 (mptt) REVERT: Z 95 LYS cc_start: 0.8389 (tttt) cc_final: 0.7156 (mptt) REVERT: b 95 LYS cc_start: 0.8318 (tttt) cc_final: 0.7089 (mptt) outliers start: 153 outliers final: 80 residues processed: 682 average time/residue: 0.8319 time to fit residues: 676.0453 Evaluate side-chains 709 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 593 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 539 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 613 ARG Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 539 ASP Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 613 ARG Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 661 SER Chi-restraints excluded: chain G residue 388 LYS Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 661 SER Chi-restraints excluded: chain G residue 695 GLU Chi-restraints excluded: chain H residue 397 GLN Chi-restraints excluded: chain H residue 539 ASP Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 646 ILE Chi-restraints excluded: chain H residue 661 SER Chi-restraints excluded: chain H residue 695 GLU Chi-restraints excluded: chain I residue 397 GLN Chi-restraints excluded: chain I residue 613 ARG Chi-restraints excluded: chain I residue 661 SER Chi-restraints excluded: chain I residue 695 GLU Chi-restraints excluded: chain J residue 397 GLN Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 613 ARG Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 646 ILE Chi-restraints excluded: chain J residue 695 GLU Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 532 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain L residue 539 ASP Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 646 ILE Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 613 ARG Chi-restraints excluded: chain M residue 630 MET Chi-restraints excluded: chain M residue 642 VAL Chi-restraints excluded: chain M residue 661 SER Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 646 ILE Chi-restraints excluded: chain N residue 695 GLU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 107 SER Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain T residue 107 SER Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 107 SER Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 104 CYS Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 104 CYS Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 104 CYS Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 107 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 348 optimal weight: 2.9990 chunk 459 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 526 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 330 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 389 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 448 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 GLN A 643 ASN B 643 ASN C 643 ASN D 643 ASN E 643 ASN G 628 GLN H 643 ASN I 643 ASN J 643 ASN K 643 ASN L 643 ASN N 628 GLN b 87 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.093248 restraints weight = 41704.200| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.37 r_work: 0.2880 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 42126 Z= 0.238 Angle : 0.671 11.557 56952 Z= 0.339 Chirality : 0.049 0.190 6580 Planarity : 0.005 0.043 7322 Dihedral : 10.429 94.882 6334 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.39 % Allowed : 19.16 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.11), residues: 5278 helix: 2.37 (0.15), residues: 1148 sheet: 0.89 (0.10), residues: 2226 loop : -0.85 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 432 TYR 0.012 0.002 TYR R 37 PHE 0.012 0.002 PHE B 684 TRP 0.007 0.002 TRP N 471 HIS 0.002 0.001 HIS H 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (42098) covalent geometry : angle 0.65734 / 0.33 (56896) SS BOND : bond 0.00384 / 0.29 ( 28) SS BOND : angle 4.34801 / 3.17 ( 56) hydrogen bonds : bond 0.04154 / 2.78 ( 1520) hydrogen bonds : angle 5.23998 / 3.60 ( 4017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 592 time to evaluate : 1.694 Fit side-chains REVERT: A 397 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7733 (tp40) REVERT: A 574 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8978 (tp) REVERT: A 630 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8294 (tpp) REVERT: A 695 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: B 397 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7628 (tp40) REVERT: B 613 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8300 (mtt180) REVERT: B 695 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: C 388 LYS cc_start: 0.8492 (mtpt) cc_final: 0.7907 (mttp) REVERT: C 394 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8459 (mtmm) REVERT: C 397 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7579 (tp40) REVERT: C 574 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9080 (tp) REVERT: C 695 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: D 378 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7287 (mtt-85) REVERT: D 397 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7661 (tp40) REVERT: D 453 GLU cc_start: 0.8499 (tt0) cc_final: 0.8133 (tm-30) REVERT: D 532 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8826 (tp) REVERT: D 612 ASN cc_start: 0.9200 (m-40) cc_final: 0.8925 (m-40) REVERT: E 397 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7734 (tp40) REVERT: E 492 LYS cc_start: 0.7987 (tttm) cc_final: 0.7682 (tttm) REVERT: E 574 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8848 (tp) REVERT: E 630 MET cc_start: 0.8732 (mmm) cc_final: 0.8347 (tpp) REVERT: F 613 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8329 (mtt180) REVERT: F 652 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8044 (pt0) REVERT: F 705 MET cc_start: 0.8700 (mtm) cc_final: 0.8438 (mtp) REVERT: G 574 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8856 (tp) REVERT: H 397 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7742 (tp40) REVERT: H 574 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8871 (tp) REVERT: H 630 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8305 (tpp) REVERT: H 695 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: I 397 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7628 (tp40) REVERT: I 613 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8313 (mtt180) REVERT: I 695 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: I 696 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8634 (tp) REVERT: J 388 LYS cc_start: 0.8496 (mtpt) cc_final: 0.7904 (mttp) REVERT: J 394 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8464 (mtmm) REVERT: J 397 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7572 (tp40) REVERT: J 574 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9078 (tp) REVERT: J 695 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: K 378 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7289 (mtt-85) REVERT: K 397 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7667 (tp40) REVERT: K 453 GLU cc_start: 0.8504 (tt0) cc_final: 0.8140 (tm-30) REVERT: K 532 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8832 (tp) REVERT: K 612 ASN cc_start: 0.9206 (m-40) cc_final: 0.8931 (m-40) REVERT: K 652 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8156 (pt0) REVERT: L 492 LYS cc_start: 0.7989 (tttm) cc_final: 0.7681 (tttm) REVERT: L 574 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8830 (tp) REVERT: L 630 MET cc_start: 0.8733 (mmm) cc_final: 0.8345 (tpp) REVERT: M 613 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8323 (mtt180) REVERT: M 705 MET cc_start: 0.8625 (mtm) cc_final: 0.8371 (mtp) REVERT: N 574 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8858 (tp) REVERT: O 38 THR cc_start: 0.8801 (t) cc_final: 0.8541 (m) REVERT: S 95 LYS cc_start: 0.8358 (tttt) cc_final: 0.7149 (mptt) REVERT: P 95 LYS cc_start: 0.8249 (tttt) cc_final: 0.7030 (mptt) REVERT: R 52 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8632 (mp) REVERT: W 38 THR cc_start: 0.8774 (t) cc_final: 0.8496 (m) REVERT: W 95 LYS cc_start: 0.8259 (tttt) cc_final: 0.7046 (mptt) REVERT: Z 95 LYS cc_start: 0.8357 (tttt) cc_final: 0.7147 (mptt) REVERT: b 95 LYS cc_start: 0.8301 (tttt) cc_final: 0.7128 (mptt) outliers start: 151 outliers final: 81 residues processed: 672 average time/residue: 0.8727 time to fit residues: 697.8936 Evaluate side-chains 701 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 585 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain E residue 397 GLN Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain F residue 613 ARG Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain F residue 661 SER Chi-restraints excluded: chain G residue 388 LYS Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 661 SER Chi-restraints excluded: chain H residue 397 GLN Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 646 ILE Chi-restraints excluded: chain H residue 661 SER Chi-restraints excluded: chain H residue 695 GLU Chi-restraints excluded: chain I residue 397 GLN Chi-restraints excluded: chain I residue 613 ARG Chi-restraints excluded: chain I residue 661 SER Chi-restraints excluded: chain I residue 690 THR Chi-restraints excluded: chain I residue 695 GLU Chi-restraints excluded: chain I residue 696 LEU Chi-restraints excluded: chain J residue 397 GLN Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 616 VAL Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 646 ILE Chi-restraints excluded: chain J residue 661 SER Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain J residue 695 GLU Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 397 GLN Chi-restraints excluded: chain K residue 532 ILE Chi-restraints excluded: chain K residue 575 LEU Chi-restraints excluded: chain K residue 616 VAL Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain L residue 388 LYS Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 646 ILE Chi-restraints excluded: chain L residue 648 VAL Chi-restraints excluded: chain M residue 565 VAL Chi-restraints excluded: chain M residue 613 ARG Chi-restraints excluded: chain M residue 630 MET Chi-restraints excluded: chain M residue 642 VAL Chi-restraints excluded: chain M residue 661 SER Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain N residue 574 ILE Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 646 ILE Chi-restraints excluded: chain N residue 661 SER Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 107 SER Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 104 CYS Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 104 CYS Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 104 CYS Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 104 CYS Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Z residue 51 LEU Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 107 SER Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 52 optimal weight: 0.9980 chunk 325 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 311 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 523 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 GLN A 643 ASN B 643 ASN C 643 ASN D 643 ASN E 643 ASN G 628 GLN H 643 ASN I 643 ASN J 643 ASN K 643 ASN L 643 ASN N 628 GLN U 87 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.095450 restraints weight = 42642.318| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.37 r_work: 0.2920 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 42126 Z= 0.129 Angle : 0.581 9.128 56952 Z= 0.296 Chirality : 0.047 0.146 6580 Planarity : 0.005 0.041 7322 Dihedral : 9.913 89.433 6334 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.92 % Allowed : 19.74 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.11), residues: 5278 helix: 2.60 (0.15), residues: 1148 sheet: 0.80 (0.10), residues: 2226 loop : -0.82 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 432 TYR 0.007 0.001 TYR J 463 PHE 0.007 0.001 PHE B 520 TRP 0.005 0.001 TRP C 471 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (42098) covalent geometry : angle 0.56945 / 0.29 (56896) SS BOND : bond 0.00221 / 0.17 ( 28) SS BOND : angle 3.70503 / 2.64 ( 56) hydrogen bonds : bond 0.03536 / 2.38 ( 1520) hydrogen bonds : angle 5.09987 / 3.52 ( 4017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17582.38 seconds wall clock time: 299 minutes 35.88 seconds (17975.88 seconds total)